Genera of phytopathogenic fungi: GOPHY 3

Abstract

This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.

Introduction

Genera of Phytopathogenic Fungi (GOPHY) is a series of papers with the main focus to provide a stable platform for the taxonomy of phytopathogenic fungi. All genera included here are associated with plant disease, but note that many species treated are not well-known plant pathogens, or Koch’s postulates remain to be completed for them. This series links to a larger initiative known as the “The Genera of Fungi project” (www.GeneraOfFungi.org, Crous et al., 2014a, Crous et al., 2015a, Giraldo et al., 2017), which aims to revise the generic names of all currently accepted fungi (Kirk et al. 2013). Specific aims were detailed by Marin-Felix et al. (2017), when this series was launched. One of the most important aims is to resolve generic and species concepts of the fungi studied, since many taxa have been shown to represent species complexes, or to comprise poly- or paraphyletic genera (Crous et al. 2015b). Other issues to resolve include the fact that type material for many genera and species has not been designated or is missing, and that the vast majority of these taxa were described before the DNA era (Hibbett et al. 2011) and thus lack DNA barcodes (Schoch et al. 2012). Therefore, another important aim is to generate DNA barcodes of type species and type specimens in order to fix the application of these names. Moreover, in cases where no type material has been preserved, taxa need to be recollected, epi- or neotypes designated, and registered in MycoBank to ensure traceability of the nomenclatural act (Robert et al. 2013). Finally, it is necessary to designate a single scientific name for fungi (Crous et al. 2015b) for which sexual-asexual links have been resolved.

Two issues of GOPHY have already been published, in which 41 genera were treated, including a total of two new genera, 46 new species, 15 new combinations and 10 typifications of older names (Marin-Felix et al., 2017, Marin-Felix et al., 2019). In this third contribution, a further 21 genera are treated, resulting in the clarification of their taxonomy and classification, and the introduction of three new genera, 42 new species, 23 new combinations, four new names and the typification of three older names.

For submissions to future issues in the GOPHY series, mycologists are encouraged to contact Pedro Crous (p.crous@wi.knaw.nl) to ensure there is no overlap with activities arising from other research groups. Preference will be given to genera that include novel species, combinations or typifications. Generic contributions published in each issue will also be placed in the database displayed on www.plantpathogen.org.

Material and methods

Isolates and morphological analysis

Descriptions of the new taxa and typifications are based on cultures obtained from the collection at the American Type Culture Collection, Manassas, Virginia, USA (ATCC), the Queensland Plant Pathology Herbarium, Brisbane, Australia (BRIP), the Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands (CBS), the working collection of P.W. Crous (CPC), housed at the Westerdijk Fungal Biodiversity Institute (WI), the Chinese General Microbiological Culture Collection Center, Beijing, China (CGMCC), the Facultat de Medicina i Ciències de la Salut, University Rovira i Virgili, Reus, Spain (FMR), and the Victorian Plant Pathogen Herbarium, Bundoora, Australia (VPRI). For fresh collections, we followed the procedures previously described in Waksman, 1922, Crous et al., 1991 and Calduch et al. (2004). Colonies were transferred to different media, i.e. cornmeal agar (CMA), 2 % malt extract agar (MEA), potato carrot agar (PCA), 2 % potato dextrose agar (PDA), synthetic nutrient-poor agar (SNA), oatmeal agar (OA), water agar (WA) (Crous et al. 2019b), pine needle agar (PNA; Smith et al. 1996), and incubated under different conditions to induce sporulation. Requirements of media and conditions of incubation are specified for each genus. Reference strains and specimens are maintained at ATCC, BRIP, CBS, CPC, CGMCC, FMR and VPRI.

Vegetative and reproductive structures were mounted in 100 % lactic acid or Shear’s solution either directly from specimens or from colonies sporulating on CMA, MEA, OA, PCA, PDA, PNA, SNA or WA. For cultural characterisation, isolates were grown and incubated on different culture media and temperatures as indicated for each genus. Colour notations were rated according to the colour charts of Kornerup & Wanscher (1978) for Alternaria, and Rayner (1970) for all other genera. Taxonomic novelties were deposited in MycoBank (www.MycoBank.org; Crous et al. 2004).

DNA isolation, amplification and analyses

Fungal DNA was extracted and purified directly from the colonies or host material as specified for each genus. Primers and protocols for the amplification and sequencing of gene loci, and software used for phylogenetic analyses can be found in the bibliographies provided for each genus. Phylogenetic analyses consisted of Maximum-Likelihood (ML) and Bayesian Inference (BI). ML was inferred as described in Hernández-Restrepo et al. (2016b), or by using MEGA v. 6.0 (Tamura et al. 2013). BI was carried out as described by Hernández-Restrepo et al. (2016b), or by using MrBayes on XSEDE v. 3.2.6 on the CIPRES portal (www.phylo.org). Sequence data generated in this study were deposited in GenBank and the alignments and trees in TreeBASE (http://www.treebase.org).

Results

Allophoma Q. Chen & L. Cai, Stud. Mycol. 82: 162. 2015. Fig. 1.



Fig. 1.

Allophoma spp. A, B. Disease symptoms. A. Symptoms caused by Allophoma hayatii (ex-type CBS 142859) on Lantana camara. B. Symptoms caused by Allophoma pterospermicola (ex-type CGMCC 3.19245) on Pterospermum xylocarpum. C–O. Asexual morph. C. Conidiomata of Allophoma pterospermicola (LC12181) sporulating on Maesa montana. D. Conidiomata of Allophoma oligotrophica (ex-type CGMCC 3.18114) sporulating on OA. E. Conidiomata of Allophoma minor (ex-type CBS 325.82). F. Section of the conidiomatal wall of Allophoma minor (ex-type CBS 325.82). G, H. Conidiogenous cells. G.Allophoma piperis (ex-epitype CBS 268.93). H.Allophoma oligotrophica (ex-type CGMCC 3.18114). I–M. Conidia. I.Allophoma minor (ex-type CBS 325.82). J.Allophoma piperis (ex-epitype CBS 268.93). K.Allophoma oligotrophica (ex-type CGMCC 3.18114). L.Allophoma cylindrispora (ex-type CBS 142453). M.Allophoma nicaraguensis (ex-type CBS 506.91). N. Swollen cells of Allophoma hayatii (ex-type CBS 142859). O. Chlamydospores of Allophoma hayatii (ex-type CBS 142859). Scale bars: D, E = 100 μm; O = 50 μm; N = 20 μm; F, I–M = 10 μm; G, H = 5 μm. Pictures A, N–O taken from Babaahmadi et al. (2018); D, H, K, from Chen et al. (2017); E, F, I from Aveskamp et al. (2010); G, J, M from Chen et al. (2015); L from Valenzuela-Lopez et al. (2018).

Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Didymellaceae.



Type species: Allophoma tropica (R. Schneid. & Boerema) Q. Chen & L. Cai, basionym: Phoma tropica R. Schneid. & Boerema, Phytopathol. Z. 83: 361. 1975. Isotype and ex-isotype strain: CBS H-7629, CBS 436.75 = DSM 63365.



DNA barcodes (genus): LSU, ITS.



DNA barcodes (species): rpb2, tub2. Table 1. Fig. 2.



Table 1.

DNA barcodes of accepted Allophoma spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	LSU	rpb2	tub2
Allophoma cylindrispora	CBS 142453T	LT592920	LN907376	LT593058	LT592989	Valenzuela-Lopez et al. (2018)
Al. hayatii	CBS 142859T	KY684812	KY684814	MF095108	KY684816	Babaahmadi et al. (2018)
	CBS 142860	KY684813	KY684815	MF095109	KY684817	Babaahmadi et al. (2018)
Al. labilis	CBS 124.93	GU237765	GU238091	KT389552	GU237619	Aveskamp et al., 2010, Chen et al., 2015
Al. minor	CBS 325.82T	GU237831	GU238107	KT389553	GU237632	Aveskamp et al. (2010), Chen et al. (2015)
Al. nicaraguensis	CBS 506.91T	GU237876	GU238058	KT389551	GU237596	Aveskamp et al., 2010, Chen et al., 2015
Al. oligotrophica	CGMCC 3.18114T	KY742040	KY742194	KY742128	KY742282	Chen et al. (2017)
	CGMCC 3.18115	KY742041	KY742195	KY742129	KY742283	Chen et al. (2017)
Al. piperis	CBS 268.93ET	GU237816	GU238129	KT389554	GU237644	Aveskamp et al., 2010, Chen et al., 2015
	CBS 108.93	GU237921	GU238130	KT389555	GU237645	Aveskamp et al., 2010, Chen et al., 2015
Al. pterospermicola	CGMCC 3.19245T	MK088573	MK088580	MK088587	MK088594	Present study
	LC12181	MK088569	MK088576	MK088583	MK088590	Present study
	LC12182	MK088570	MK088577	MK088584	MK088591	Present study
	LC12183	MK088571	MK088578	MK088585	MK088592	Present study
	LC12184	MK088572	MK088579	MK088586	MK088593	Present study
Al. tropica	CBS 436.75IsoT	GU237864	GU238149	KT389556	GU237663	Aveskamp et al., 2010, Chen et al., 2015
Al. zantedeschiae	CBS 131.93	FJ427084	GU238159	KT389557	FJ427188	Aveskamp et al., 2010, Chen et al., 2015
	CBS 229.32	KT389473	KT389690	KT389558	KT389767	Aveskamp et al., 2010, Chen et al., 2015

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; CGMCC: Chinese General Microbiological Culture Collection Center, Beijing, China; LC: Dr Lei Cai's personal culture collection, housed at CAS, China. ^T,ET and ^IsoT indicate ex-type,ex-epitype and ex-isotype strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; LSU: partial large subunit (28S) nrRNA gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tub2: partial β-tubulin gene.

Fig. 2.

Phylogenetic tree generated from a maximum parsimony analysis based on the combined LSU (860 bp), ITS (480 bp), tub2 (333 bp) and rpb2 (803 bp) sequences of all accepted species of Allophoma. The tree was rooted to Phoma herbarum CBS 615.75. Values above the branches represent parsimony bootstrap support values (> 50 %). Novel sequences and novel taxon are printed in bold. GenBank accession numbers are indicated in Table 1. ^{T, ET} and ^IsoT indicate ex-type, ex-epitype and ex-isotype strains, respectively. TreeBASE: S23493.

Conidiomata pycnidial, globose to flask-shaped, ovoid, superficial or (semi-)immersed, solitary or confluent, ostiolate, sometimes with an elongated neck; conidiomatal wall pseudoparenchymatous, multi-layered. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform to doliiform, sometimes flask-shaped or isodiametric. Conidia hyaline, smooth- and thin-walled, aseptate or 1-septate, variable in shape and size, i.e. ovoid, oblong, ellipsoidal to cylindrical, or slightly allantoid, mostly guttulate. Chlamydospores uni- or multicellular (pseudosclerotioid and dictyosporous), solitary or in chains, intercalary or terminal, smooth-walled, brown, where multicellular variable in shape and size. Swollen cells (pseudo-chlamydospores) pale brown, terminal or intercalary, solitary or in clusters, variable in size and shape, commonly in aerial mycelia. Sexual morph unknown (adapted from Chen et al., 2015, Babaahmadi et al., 2018).



Culture characteristics: Colonies on OA white when young, grey to olivaceous or dull green, brown, floccose to woolly, sometimes with rosy-buff tinges near the colony margins or yellow pigment in the sterile sectors, margins regular.



Optimal media and cultivation conditions: OA or sterile pine needles placed on OA under near-ultraviolet light (12 h light, 12 h dark) to promote sporulation at 25 °C.



Distribution: Worldwide.



Hosts: Wide host range, occurring as pathogens or saprobes, on Araceae, Fabaceae, Gesneriaceae, Myrtaceae, Papaveraceae, Piperaceae, Primulaceae, Rosaceae, Rubiaceae, Solanaceae, Sterculiaceae, Verbenaceae and other hosts, including humans.



Disease symptoms: Dieback, tissue necrosis, leaf spots, stem rot, leaf blotch, but also saprobic or isolated from other substrates and environments, e.g. air from karst caves and human infections.



Notes: The genus Allophoma was introduced by Chen et al. (2015) to accommodate five previously described Phoma species, namely Al. labilis (syn. Pho. labilis), Al. minor (syn. Pho. minor), Al. piperis (syn. Pho. piperis), Al. tropica (syn. Pho. tropica) and Al. zantedeschiae (syn. Pho. zantedeschiae), and a new species Al. nicaraguensis. Another four species have been described in the subsequent years, i.e. Al. cylindrispora (Valenzuela-Lopez et al. 2018), Al. hayatii (Babaahmadi et al. 2018), Al. oligotrophica (Chen et al. 2017) and Al. pterospermicola sp. nov. in the present study. Differentiating Allophoma from related phoma-like genera based on morphology alone is sometimes complicated. Furthermore, Allophoma species are morphologically similar and hard to differentiate from one another. Therefore, molecular data are essential for accurate identification of species within this genus, with ITS, LSU, tub2 and rpb2 being the loci selected for this purpose (Chen et al., 2015, Chen et al., 2017, Valenzuela-Lopez et al., 2018). No sexual morph of this genus has been observed to date.

 These fungi are generally found in soil, air and regarded as saprobes or as the causal organisms of various diseases of different herbaceous and woody plants, such as some ornamental plants, coffee, etc., and even human eye lesions (Boerema et al., 2004, Aveskamp et al., 2010, Chen et al., 2015, Chen et al., 2017, Babaahmadi et al., 2018, Valenzuela-Lopez et al., 2018).



References: Boerema et al. 2004 (morphology and pathogenicity), Aveskamp et al., 2010, Chen et al., 2015, Chen et al., 2017, Babaahmadi et al., 2018, Valenzuela-Lopez et al., 2018 (morphology, phylogeny and pathogenicity).



Allophoma pterospermicola Q. Chen & L. Cai, sp. nov. MycoBank MB828313. Fig. 3.



Fig. 3.

Allophoma pterospermicola (ex-type CGMCC 3.19245). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E, F. Colony on PDA (front and reverse). G. Conidiomata sporulating on OA. H, I. Conidiomata. J. Section of conidioma. K. Section of conidiomatal wall. L, M. Conidiogenous cells. N. Conidia. Scale bars: H, J = 20 μm; I = 40 μm; K, N = 10 μm; L, M = 5 μm.

Etymology: Name reflects Pterospermum, the host genus from which it was collected.



Conidiomata pycnidial, solitary or aggregated, globose to subglobose, brown, glabrous or with a few hyphal outgrowths, superficial, 60–330 × 67–280 μm, with 1–5 ostioles, sometimes elongated as a long neck, up to 150 μm long, papillate; conidiomatal wall pseudoparenchymatous, 3–5-layered, 12–20 μm thick, composed of isodiametric cells. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform to doliiform, 6–10 × 3–6 μm. Conidia oval to oblong, occasionally bacilliform, smooth- and thin-walled, hyaline, aseptate, 3–5.5 × 1.5–2 μm, with 1–2 minute guttules. Conidial matrix cream.



Culture characteristics: Colonies on OA, 33–40 mm diam after 1 wk, margins regular, floccose to woolly, white, pale brownish grey, with a pale salmon concentric ring, pale salmon near the margins, black pycnidia visible; reverse concolourous. Colonies on MEA, 20–25 mm diam after 1 wk, margins regular, aerial mycelium sparse, olivaceous; reverse concolourous. Colonies on PDA, 20–30 mm diam after 1 wk, margins regular, floccose to woolly, olivaceous, white near the margins; reverse dull green, white near the margins. Application of NaOH results in a pale brownish olivaceous discolouration of the agar.



Typus: China, Guangxi, Nonggang National Nature Reserve, on diseased leaves of Pterospermum xylocarpum (Sterculiaceae), Jun. 2017, Z.Y. Ma (holotype HMAS 247983, culture ex-type CGMCC 3.19245 = LC 12185).



Additional materials examined: China, Guangxi, Nonggang National Nature Reserve, on diseased leaves of Pterospermum xylocarpum (Sterculiaceae), Jun. 2017, Z.Y. Ma, LC 12183; ibid., LC 12184; Guangxi, Jingxi, Gulongshan, on diseased leaves of Maesa montana (Primulaceae), Jun. 2017, Z.Y. Ma, LC 12181; ibid., LC 12182.



Notes: Allophoma pterospermicola represents the first report of a species in the family Didymellaceae on the two host genera Pterospermum (Sterculiaceae) and Maesa (Primulaceae). This species is closely related to Al. minor, but differs in producing longer conidiogenous cells [6–10 × 3–6 μm in Al. pterospermicola vs. 4–5.5(–6.2) × 3–4.5(–4.7) in Al. minor] and slightly narrower conidia [3–5.5 × 1.5–2 μm in Al. pterospermicola vs. (3–)3.5–4.5(–5) × 1.8–2.5(–3) μm in Al. minor]. In addition, Al. pterospermicola grows much slower on OA, MEA and PDA than Al. minor, and the latter species has only been recorded on Syzygium aromaticum (Myrtaceae) (Aveskamp et al. 2010).



Authors: Q. Chen & L. Cai



Alternaria Nees, Das System der Pilze und Schwämme: 72. 1816 (1816–1817). Fig. 4.

Fig. 4.

Alternaria spp. A–D. Disease symptoms. A.Alternaria dauci on Daucus carota. B.Alternaria linariae on Solanum lycopersicum. C.Alternaria neoipomoeae on Ipomoeae batatas (Photo A.H. Thompson, ARC, South Africa). D.Alternaria solani on Solanum tuberosum (Photo J.E. van der Waals, University of Pretoria, South Africa). E–V. Asexual morph. E–O. Conidiophores. E.Alternaria caricis. F.Alternaria chartarum. G.Alternaria cinerariae. H.Alternaria conjuncta. I.Alternaria elegans. J.Alternaria embellisia. K.Alternaria indefessa. L.Alternaria japonica. M.Alternaria penicillata. N.Alternaria proteae. O.Alternaria tenuissima. P–T. Conidia. P.Alternaria blumeae. Q.Alternaria calendulae. R.Alternaria perpunctulata. S.Alternaria carotiincultae. T.Alternaria triglochinicola. U, V. Conidia producing secondary conidia. U.Alternaria mimicola. V.Alternaria molesta. Scale bars: 10 μm. Pictures A–D, P, Q taken from Woudenberg et al. (2014); E–O, R–V from Woudenberg et al. (2013).

For synonyms see Woudenberg et al. (2013).



Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Pleosporaceae.



Type species: Alternaria alternata (Fries) Keissler, basionym: Torula alternata Fr., Syst. Mycol. (Lundae) 3: 500. 1832 (nom. sanct.); additional synonyms listed in Woudenberg et al. (2015). Neotype designated by Simmons (1967): E.G.S. 11.050. Ex-epitype strain designated by de Hoog & Horré (2002): CBS 916.96 = E.G.S. 34.016.



DNA barcodes (genus): LSU, ITS.



DNA barcodes (species): ITS, ATPase, gapdh, rpb2, tef1. Table 2. Fig. 5, Fig. 6, Fig. 7.



Table 2.

DNA barcodes of accepted Alternaria spp.

Species	Section	Isolates1	GenBank accession numbers2					References
			ITS	gapdh	rpb2	tef1	ATPase
Alternaria abundans	Chalastospora	CBS 534.83T	JN383485	KC584154	KC584448	KC584707	JQ671802	Woudenberg et al., 2013, Deng et al., 2018
A. acalyphicola	Porri	CBS 541.94T	KJ718097	KJ717952	KJ718271	KJ718446	–	Woudenberg et al. (2014)
A. aconidiophora	Infectoriae	FMR 17111T	LR133931	LR133965	LR133967	LR133968	LR133969	Present study
A. agerati	Porri	CBS 117221	KJ718098	KJ717953	KJ718272	KJ718447	–	Woudenberg et al. (2014)
A. agripestis	Porri	CBS 577.94T	KJ718099	JQ646356	KJ718273	KJ718448	–	Woudenberg et al. (2014)
A. allii	Porri	CBS 107.28T	KJ718100	KJ717954	KJ718274	KJ718449	–	Woudenberg et al. (2014)
A. alstroemeriae	Alternaria	CBS 118809T	KP124297	KP124154	KP124765	KP125072	–	Woudenberg et al. (2015)
A. altcampina	Pseudoalternaria	FMR 16476T	LR133895	LR133900	–	–	LR133906	Present study
A. alternantherae	Althernantherae	CBS 124392	KC584179	KC584096	KC584374	KC584633	–	Woudenberg et al. (2013)
A. alternariacida	Porri	CBS 105.51T	KJ718105	KJ717959	KJ718279	KJ718454	–	Woudenberg et al. (2014)
A. alternariae	Ulocladium	CBS 126989T	AF229485	AY278815	KC584470	KC584730	–	Woudenberg et al. (2013)
A. alternarina	Infectoriae	CBS 119396T	JQ693648	JQ646289	JQ905199	LR134367	JQ671817	Poursafar et al. (2018), Geng et al. (unpubl. data), present study
A. alternata	Alternaria	CBS 916.96T	AF347031	AY278808	KC584375	KC584634	–	Woudenberg et al. (2013)
A. anagallidis	Porri	CBS 117128	KJ718106	JQ646338	KJ718280	EU130544	–	Woudenberg et al. (2014)
A. anigozanthi	Eureka	CBS 121920T	KC584180	KC584097	KC584376	KC584635	–	Woudenberg et al. (2013)
A. anodae	Porri	PPRI 12376	KJ718110	KJ717963	KJ718284	KJ718458	–	Woudenberg et al. (2014)
A. aragakii	Porri	CBS 594.93T	KJ718111	KJ717964	KJ718285	KJ718459	–	Woudenberg et al. (2014)
A. arborescens	Alternaria	CBS 102605T	AF347033	AY278810	KC584377	KC584636	–	Woudenberg et al. (2013)
A. arbusti	Infectoriae	CBS 596.93T	JQ693644	JQ646365	LR134184	–	JQ671940	Poursafar et al. (2018), present study
A. argyranthemi		CBS 116530T	KC584181	KC584098	KC584378	KC584637	–	Woudenberg et al. (2013)
A. argyroxiphii	Porri	CBS 117222T	KJ718112	JQ646350	KJ718286	KJ718460	–	Woudenberg et al. (2014)
A. armoraciae	Chalastospora	CBS 118702T	KC584182	KC584099	KC584379	KC584638	LR134098	Woudenberg et al. (2013), present study
A. arrhenatheri	Pseudoalternaria	LEP 140372T	JQ693677	JQ693635	–	–	JQ693603	Poursafar et al. (2018)
A. aspera	Pseudoulocladium	CBS 115269T	KC584242	KC584166	KC584474	KC584734	–	Woudenberg et al. (2013)
A. atra	Ulocladioides	CBS 195.67T	AF229486	KC584167	KC584475	KC584735	–	Woudenberg et al. (2013)
A. avenicola	Panax	CBS 121459T	KC584183	KC584100	KC584380	KC584639	–	Woudenberg et al. (2013)
A. axiaeriisporifera	Gypsophilae	CBS 118715T	KC584184	KC584101	KC584381	KC584640	–	Woudenberg et al. (2013)
A. azadirachtae	Porri	CBS 116444T	KJ718115	KJ717967	KJ718289	KJ718463	–	Woudenberg et al. (2014)
A. bataticola	Porri	CBS 531.63T	KJ718117	JQ646349	KJ718291	KJ718465	–	Woudenberg et al. (2014)
A. betae-kenyensis	Alternaria	CBS 118810T	KP124419	KP124270	KP124888	KP125197	–	Woudenberg et al. (2015)
A. blumeae	Porri	CBS 117364T	KJ718126	AY562405	KJ718300	KJ718474	–	Woudenberg et al. (2014)
A. bornmuelleri	Undifilum	DAOM 231361T	FJ357317	FJ357305	KC584491	KC584751	–	Woudenberg et al. (2013)
A. botryospora	Embellisioides	CBS 478.90T	AY278844	AY278831	KC584461	KC584720	–	Woudenberg et al. (2013)
A. botrytis	Ulocladium	CBS 197.67T	KC584243	KC584168	KC584476	KC584736	–	Woudenberg et al. (2013)
A. brassicae		CBS 116528	KC584185	KC584102	KC584382	KC584641	–	Woudenberg et al. (2013)
A. brassicaepekinensis	Ulocladioides	CBS 121493T	KC584244	KC584170	KC584478	KC584738	–	Woudenberg et al. (2013)
A. brassicicola	Brassicicola	CBS 118699	JX499031	KC584103	KC584383	KC584642	–	Woudenberg et al. (2013)
A. brassicifolii	Pseudoalternaria	CNU 111118T	JQ317188	KM821537	–	–	KY412558	Deng et al. (2018)
A. breviramosa	Chalastospora	CBS 121331T	FJ839608	KC584148	KC584442	KC584700	LR134099	Woudenberg et al. (2013), present study
A. broccoli-italicae	Infectoriae	CBS 118485T	KM821536	KM821538	LR134194	LR134262	KY412557	Deng et al. (2018), present study
A. burnsii	Alternaria	CBS 107.38T	KP124420	JQ646305	KP124889	KP125198	–	Woudenberg et al. (2015)
A. caespitosa	Infectoriae	CBS 177.80T	KC584250	KC584178	KC584492	KC584752	LR134114	Woudenberg et al. (2013), present study
A. calendulae	Porri	CBS 224.76T	KJ718127	KJ717977	KJ718301	KJ718475	–	Woudenberg et al. (2014)
A. californica	Infectoriae	CBS 119409T	JQ693645	JQ646285	LR134181	LR134245	JQ671813	Poursafar et al. (2018), present study
A. calycipyricola	Panax	CBS 121545T	KC584186	KC584104	KC584384	KC584643	–	Woudenberg et al. (2013)
A. cantlous	Ulocladioides	CBS 123007T	KC584245	KC584171	KC584479	KC584739	–	Woudenberg et al. (2013)
A. capsici-annui	Ulocladium	CBS 504.74	KC584187	KC584105	KC584385	KC584644	–	Woudenberg et al. (2013)
A. caricis	Nimbya	CBS 480.90T	AY278839	AY278826	KC584467	KC584726	JQ671780	Woudenberg et al., 2013, Deng et al., 2018
A. carotiincultae	Radicina	CBS 109381T	KC584188	KC584106	KC584386	KC584645	–	Woudenberg et al. (2013)
A. carthami	Porri	CBS 635.80	KJ718131	KJ717981	KJ718305	KJ718479	–	Woudenberg et al. (2014)
A. carthamicola	Porri	CBS 117092T	KJ718134	KJ717984	KJ718308	KJ718482	–	Woudenberg et al. (2014)
A. cassiae	Porri	CBS 478.81	KJ718135	KJ717985	KJ718309	KJ718483	–	Woudenberg et al. (2014)
A. catananches	Porri	CBS 137456T	KJ718139	KJ717989	KJ718313	KJ718487	–	Woudenberg et al. (2014)
A. centaureae	Porri	CBS 116446T	KJ718140	KJ717990	KJ718314	KJ718488	–	Woudenberg et al. (2014)
A. cerasidanica	Infectoriae	CBS 121923T	LR135744	LR135747	LR135746	LR135745	LR135748	Present study
A. cesenica	Infectoriae	MFLUCC 13-0450T	KP711383	–	–	KP711386	–	Liu et al. (2015)
A. cetera	Chalastospora	CBS 121340T	JN383482	AY562398	KC584441	KC584699	LR134101	Woudenberg et al., 2013, Deng et al., 2018
A. chartarum	Pseudoulocladium	CBS 200.67T	AF229488	KC584172	KC584481	KC584741	–	Woudenberg et al. (2013)
A. cheiranthi	Cheiranthus	CBS 109384	AF229457	KC584107	KC584387	KC584646	–	Woudenberg et al. (2013)
A. chlamydospora	Phragmosporae	CBS 491.72T	KC584189	KC584108	KC584388	KC584647	–	Woudenberg et al. (2013)
A. chlamydosporigena	Embellisia	CBS 341.71	KC584231	KC584156	KC584451	KC584710	–	Woudenberg et al. (2013)
A. chlamydosporifera	Radicina	FMR 17360T	LR133924	LR133927	LR133926	LR133929	–	Present study
A. cichorii	Porri	CBS 102.33T	KJ718141	KJ717991	KJ718315	KJ718489	–	Woudenberg et al. (2014)
A. cinerariae	Sonchi	CBS 116495	KC584190	KC584109	KC584389	KC584648	–	Woudenberg et al. (2013)
A. cirsinoxia	Porri	CBS 113261T	KJ718143	KJ717993	KJ718317	KJ718491	–	Woudenberg et al. (2014)
A. citrullicola	Porri	CBS 103.32T	KJ718144	KJ717994	KJ718318	KJ718492	–	Woudenberg et al. (2014)
A. concatenata	Pseudoulocladium	CBS 120006T	KC584246	AY762950	KC584480	KC584740	–	Woudenberg et al. (2013)
A. conidiophora	Porri	CBS 137457T	KJ718145	KJ717995	-	KJ718493	–	Woudenberg et al. (2014)
A. conjuncta	Infectoriae	CBS 196.86T	FJ266475	AY562401	KC584390	KC584649	JQ671824	Woudenberg et al., 2013, Poursafar et al., 2018
A. conoidea	Brassicicola	CBS 132.89	AF348226	FJ348227	KC584452	KC584711	–	Woudenberg et al. (2013)
A. consortialis	Ulocladioides	CBS 104.31T	KC584247	KC584173	KC584482	KC584742	–	Woudenberg et al. (2013)
A. crassa	Porri	CBS 110.38T	KJ718147	KJ717997	KJ718320	KJ718495	–	Woudenberg et al. (2014)
A. cyamopsidis	Porri	CBS 364.67	KJ718156	KJ718003	KJ718329	KJ718504	–	Woudenberg et al. (2014)
A. cumini	Eureka	CBS 121329T	KC584191	KC584110	KC584391	KC584650	–	Woudenberg et al. (2013)
A. cucumerina	Porri	CBS 116114T	KJ718153	KJ718000	KJ718326	KJ718501	–	Woudenberg et al. (2014)
A. cucurbitae	Ulocladioides	CBS 483.81	FJ266483	AY562418	KC584483	KC584743	–	Woudenberg et al. (2013)
A. curvata	Infectoriae	FMR 16901T	LR133898	LR133899	LR133901	LR133902	LR133905	Present study
A. dactylidicola	Infectoriae	MFLUCC 15-0466T	KY703616	–	KY750720	–	–	Thambugala et al. (2017)
A. dauci	Porri	CBS 111.38T	KJ718158	KJ718005	KJ718331	KJ718506	–	Woudenberg et al. (2014)
A. daucicaulis	Infectoriae	CBS 119398T	JQ693653	JQ646294	LR134177	LR134241	JQ671822	Poursafar et al. (2018), present study
A. dennisii		CBS 476.90T	JN383488	JN383469	KC584454	KC584713	–	Woudenberg et al. (2013)
A. deserticola	Porri	CBS 110799T	KJ718249	KJ718077	KJ718424	KJ718595	–	Woudenberg et al. (2014)
A. dianthicola	Dianthicola	CBS 116491	KC584194	KC584113	KC584394	KC584653	–	Woudenberg et al. (2013)
A. dichondrae	Porri	CBS 200.74T	KJ718167	KJ718012	KJ718340	KJ718515	–	Woudenberg et al. (2014)
A. didymospora	Phragmosporae	CBS 766.79	FJ357312	FJ357300	KC584455	KC584714	JQ671796	Woudenberg et al., 2013, Deng et al., 2018
A. doliconidium	Alternaria	KUMCC 17-0263T	MG828864	–	–	–	–	Wanasinghe et al. (2018)
A. echinaceae	Porri	CBS 116117T	KJ718170	KJ718015	KJ718343	KJ718518	–	Woudenberg et al. (2014)
A. eichhorniae	Alternaria	CBS 489.92T	KC146356	KP124276	KP124895	KP125204	–	Woudenberg et al. (2015)
A. elegans	Dianthicola	CBS 109159T	KC584195	KC584114	KC584395	KC584654	–	Woudenberg et al. (2013)
A. ellipsoidea	Gypsophilae	CBS 119674T	KC584196	KC584115	KC584396	KC584655	–	Woudenberg et al. (2013)
A. embellisia	Embellisia	CBS 339.71	KC584230	KC584155	KC584449	KC584708	–	Woudenberg et al. (2013)
A. eryngii	Panax	CBS 121339	JQ693661	AY562416	KC584397	KC584656	–	Woudenberg et al. (2013)
A. ethzedia	Infectoriae	CBS 197.86T	AY278833	AY278795	KC584398	KC584657	JQ671805	Woudenberg et al., 2013, Poursafar et al., 2018
A. euphorbiicola	Euphorbiicola	CBS 119410	KJ718173	KJ718018	KJ718346	KJ718521	–	Woudenberg et al. (2014)
A. eureka	Eureka	CBS 193.86T	JN383490	JN383471	KC584456	KC584715	–	Woudenberg et al. (2013)
A. fimeti	Infectoriae	FMR 17110T	LR133920	LR133921	LR133923	LR133922	LR133925	Present study
A. forlicesenensis	Infectoriae	MFLUCC 13-0456T	KY769657	–	–	–	–	Thambugala et al. (2017)
A. frumenti	Infectoriae	CBS 119401T	JQ693654	JQ646295	LR134172	LR134370	JQ671823	Poursafar et al. (2018), present study
A. gaisen	Alternaria	CBS 632.93	KC584197	KC584116	KC584399	KC584658	–	Woudenberg et al. (2013)
A. geniostomatis	Eureka	CBS 118701T	KC584198	KC584117	KC584400	KC584659	–	Woudenberg et al. (2013)
A. gossypina	Alternaria	CBS 104.32T	KP124430	JQ646312	KP124900	KP125209	–	Woudenberg et al. (2015)
A. graminicola	Infectoriae	CBS 119400T	JQ693650	JQ646291	LR134180	LR134249	JQ671819	Poursafar et al. (2018), present study
A. grandis	Porri	CBS 109158T	KJ718239	JQ646341	KJ718414	EU130547	–	Woudenberg et al. (2014)
A. gypsophilae	Gypsophilae	CBS 107.41T	KC584199	KC584118	KC584401	KC584660	–	Woudenberg et al. (2013)
A. hampshirensis	Infectoriae	MFLUCC 17-0783T	MG828866	–	MG829247	–	–	Wanasinghe et al. (2018)
A. helianthiinficiens		CBS 208.86T	JX101649	KC584120	KC584403	EU130548	–	Woudenberg et al. (2013)
A. heterospora	Ulocladioides	CBS 123376T	KC584248	KC584176	KC584488	KC584748	–	Woudenberg et al. (2013)
A. hordeiaustralica	Infectoriae	CBS 119402T	JQ693641	JQ646283	LR134179	LR134243	JQ671811	Poursafar et al. (2018), present study
A. hordeicola	Infectoriae	CBS 121458T	JQ693642	JQ646284	LR134175	LR134371	JQ671812	Poursafar et al. (2018), present study
A. humuli	Infectoriae	CBS 119404T	JQ693652	JQ646293	LR134174	LR134199	JQ671821	Poursafar et al. (2018), present study
A. hyacinthi	Embellisioides	CBS 416.71T	KC584233	KC584158	KC584457	KC584716	–	Woudenberg et al. (2013)
A. incomplexa	Infectoriae	CBS 121330T	JQ693658	JQ646287	LR134185	LR134250	JQ671815	Poursafar et al. (2018), present study
A. indefessa	Cheiranthus	CBS 536.83T	KC584234	KC584159	KC584458	KC584717	–	Woudenberg et al. (2013)
A. infectoria	Infectoriae	CBS 210.86T	AF347034	AY278793	KC584404	KC584662	JQ671804	Woudenberg et al., 2013, Poursafar et al., 2018
A. inflata	Pseudoalternaria	FMR 16477 T	LR133930	LR133938	–	–	LR133966	Present study
A. intercepta	Infectoriae	CBS 119406T	JQ693656	JQ646297	LR134170	–	JQ671826	Poursafar et al. (2018), present study
A. ipomoeae	Porri	CBS 219.79T	KJ718175	KJ718020	KJ718348	KJ718523	–	Woudenberg et al. (2014)
A. iridiaustralis	Alternaria	CBS 118486T	KP124435	KP124284	KP124905	KP125214	–	Woudenberg et al. (2015)
A. japonica	Japonicae	CBS 118390	KC584201	KC584121	KC584405	KC584663	–	Woudenberg et al. (2013)
A. jacinthicola	Alternaria	CBS 133751T	KP124438	KP124287	KP124908	KP125217	–	Woudenberg et al. (2015)
A. jesenskae	Porri	CBS 133855T	KJ718177	KJ718022	KJ718350	KJ718525	–	Woudenberg et al. (2014)
A. juxtiseptata	Gypsophilae	CBS 119673T	KC584202	KC584122	KC584406	KC584664	–	Woudenberg et al. (2013)
A. kordkuyana	Pseudoalternaria	IRAN 16888FT	MF033843	MF033826	–	–	MF033860	Poursafar et al. (2018)
		FMR 17061	LR133970	LR133998	–	–	LR134001	Present study
		FMR 17372	LR133995	LR133997	–	–	LR133999	Present study
A. kulundii	Soda	CBS 137525T	KJ443262	KJ649618	KJ443176	KJ443219	–	Grum-Grzhimaylo et al. (2016)
A. lawrencei	Infectoriae	FMR 17004T	LR133907	LR133908	LR133911	LR133912	LR133914	Present study
A. leptinellae	Eureka	CBS 477.90T	KC584235	KC584160	KC584459	KC584718	–	Woudenberg et al. (2013)
A. leucanthemi	Teretispora	CBS 421.65T	KC584240	KC584164	KC584472	KC584732	–	Woudenberg et al. (2013)
A. limaciformis	Phragmosporae	CBS 481.81T	KC584203	KC584123	KC584407	KC584665	JQ671798	Woudenberg et al. (2013), Deng et al. (2018)
A. limicola	Euphorbiicola	CBS 483.90T	KJ718178	JQ646329	KJ718351	KJ718526	–	Woudenberg et al. (2014)
A. linariae	Porri	CBS 105.41T	KJ718180	KJ718024	KJ718353	KJ718528	–	Woudenberg et al. (2014)
A. longipes	Alternaria	CBS 540.94	AY278835	AY278811	KC584409	KC584667	–	Woudenberg et al. (2013)
A. lolii	Embellisioides	CBS 115266T	JN383492	JN383473	KC584460	KC584719	–	Woudenberg et al. (2013)
A. macrospora	Porri	CBS 117228T	KC584204	KC584124	KC584410	KC584668	–	Woudenberg et al. (2013)
A. malorum	Chalastospora	CBS 135.31	JQ693638	JQ646278	–	–	JQ671800	Poursafar et al. (2018)
		FMR 17369	LR134074	LR134077	–	–	LR134029	Present study
A. merytae	Infectoriae	CBS 119403T	JQ693651	JQ646292	LR134119	LR134198	JQ671820	Poursafar et al. (2018), present study
A. metachromatica	Infectoriae	CBS 553.94T	JQ693660	AY562404	JQ905189	FJ214931	JQ671809	Andersen et al., 2009, Poursafar et al., 2018, Geng et al. (unpubl. data)
A. mimicula	Brassicicola	CBS 118696T	FJ266477	AY562415	KC584411	KC584669	–	Woudenberg et al. (2013)
A. molesta	Phragmosporae	CBS 548.81T	KC584205	KC584125	KC584412	KC584670	–	Woudenberg et al. (2013)
A. montanica	Porri	CBS 121343T	KJ718194	KJ718033	KJ718367	KJ718541	–	Woudenberg et al. (2014)
A. montsantina	Infectoriae	FMR 17060T	LR133913	LR133915	LR133918	LR133919	LR133916	Present study
A. mouchaccae	Phragmosporae	CBS 119671T	KC584206	AY562399	KC584413	KC584671	–	Woudenberg et al. (2013)
A. multiformis	Ulocladioides	CBS 102060T	FJ266486	KC584174	KC584484	KC584744	–	Woudenberg et al. (2013)
A. multirostrata	Porri	CBS 712.68T	KJ718195	JQ646362	KJ718368	EU130546	–	Woudenberg et al. (2014)
A. murispora	Infectoriae	MFLU 14-0758T	NR_137964	–	–	–	–	Ariyawansa and Hyde (unpubl. data)
A. neoipomoeae	Porri	PPRI 11845T	KJ718198	KJ718036	KJ718371	KJ718544	–	Woudenberg et al. (2014)
A. nepalensis	Japonicae	CBS 118700T	KC584207	KC584126	KC584414	KC584672	–	Woudenberg et al. (2013)
A. nitrimali	Porri	CBS 109163T	KJ718201	JQ646358	KJ718374	KJ718547	–	Woudenberg et al. (2014)
A. nobilis	Gypsophilae	CBS 116490	KC584208	KC584127	KC584415	KC584673	–	Woudenberg et al. (2013)
A. novae-guineensis	Porri	CBS 116120T	KJ718202	KJ718039	KJ718375	KJ718548	–	Woudenberg et al. (2014)
A. novae-zelandiae	Infectoriae	CBS 119405T	JQ693655	JQ646296	LR134120	LR134197	JQ671825	Poursafar et al. (2018), present study
A. obclavata	Chalastospora	CBS 124120T	KC584225	KC584149	KC584443	KC584701	LR134100	Woudenberg et al. (2013), present study
A. obovoidea	Ulocladioides	CBS 101229	FJ266487	FJ266498	KC584485	KC584745	–	Woudenberg et al. (2013)
A. obtecta	Porri	CBS 117367	KJ718204	KJ718041	KJ718377	KJ718550	–	Woudenberg et al. (2014)
A. oregonensis	Infectoriae	CBS 542.94T	FJ266478	FJ266491	KC584416	KC584674	JQ671827	Woudenberg et al., 2013, Poursafar et al., 2018
A. oudemansii	Ulocladium	CBS 114.07T	FJ266488	KC584175	KC584486	KC584746	–	Woudenberg et al. (2013)
A. panax	Panax	CBS 482.81	KC584209	KC584128	KC584417	KC584675	–	Woudenberg et al. (2013)
A. papavericola	Crivellia	CBS 116606T	FJ357310	FJ357298	KC584446	KC584705	–	Woudenberg et al. (2013)
A. paralinicola	Porri	CBS 116652T	KJ718206	KJ718043	KJ718379	KJ718552	–	Woudenberg et al. (2014)
A. passiflorae	Porri	CBS 113.38	KJ718207	JQ646353	KJ718380	KJ718553	–	Woudenberg et al. (2014)
A. parvicaespitosa	Pseudoalternaria	LEP 014858T	MF033859	MF033842	–	–	KJ908217	Poursafar et al. (2018)
A. penicillata	Crivellia	CBS 116608T	FJ357311	FJ357299	KC584440	KC584698	–	Woudenberg et al. (2013)
A. perpunctulata	Althernantherae	CBS 115267T	KC584210	KC584129	KC584418	KC584676	–	Woudenberg et al. (2013)
A. petroselini	Radicina	CBS 112.41T	KC584211	KC584130	KC584419	KC584677	–	Woudenberg et al. (2013)
A. petuchovskii	Soda	CBS 137517T	KJ443254	KJ649616	KJ443170	KJ443211	–	Grum-Grzhimaylo et al. (2016)
A. peucedani		CNU 111485T	KF728231	KF889361	–	–	–	Deng et al. (2014)
A. photistica	Panax	CBS 212.86T	KC584212	KC584131	KC584420	KC584678	JQ671807	Woudenberg et al., 2013, Deng et al., 2018
A. phragmospora	Phragmosporae	CBS 274.70T	JN383493	JN383474	KC584462	KC584721	–	Woudenberg et al. (2013)
A. pipionipisi	Porri	CBS 116115T	KJ718214	KJ718049	KJ718387	KJ718560	–	Woudenberg et al. (2014)
A. planifunda	Embellisioides	CBS 537.83T	FJ357315	FJ357303	KC584463	KC584722	–	Woudenberg et al. (2013)
A. poaceicola	Infectoriae	MFLUCC 13-0346T	KY026587	–	KY460971	–	–	Thambugala et al. (2017)
A. pobletensis	Chalastospora	FMR 16448T	LR133896	LR133897	–	–	LR133903	Present study
A. porri	Porri	CBS 116699T	KJ718218	KJ718053	KJ718391	KJ718564	–	Woudenberg et al. (2014)
A. proteae	Embellisioides	CBS 475.90T	AY278842	KC584161	KC584464	KC584723	–	Woudenberg et al. (2013)
A. protenta	Porri	CBS 116696	KJ718221	JQ646335	KJ718394	KJ718567	–	Woudenberg et al. (2014)
A. pseudorostrata	Porri	CBS 119411T	JN383483	AY562406	KC584422	KC584680	–	Woudenberg et al. (2013)
A. pseudoventricosa	Infectoriae	FMR 16900T	LR133928	LR133935	LR133934	LR133936	LR133937	Present study
A. radicina	Radicina	CBS 245.67T	KC584213	KC584133	KC584423	KC584681	–	Woudenberg et al. (2013)
A. ranunculi	Porri	CBS 116330T	KJ718225	KJ718058	KJ718398	KJ718571	–	Woudenberg et al. (2014)
A. ricini	Porri	CBS 215.31T	KJ718226	KJ718059	KJ718399	KJ718572	–	Woudenberg et al. (2014)
A. rosae	Pseudoalternaria	CBS 121341T	JQ646279	JQ646279	–	–	JQ671803	Poursafar et al. (2018)
		FMR 15720	LR134076	LR134070	–	–	LR134004	Present study
		FMR 17376	LR134071	LR13403	–	–	LR134003	Present study
		FMR 17377	LR134073	LR134072	–	–	LR134028	Present study
A. roseogrisea	Infectoriae	CBS 121921T	LR134102	LR134103	LR134192	LR134260	LR134104	Present study
A. rostellata	Porri	CBS 117366T	KJ718229	JQ646332	KJ718402	KJ718575	–	Woudenberg et al. (2014)
A. saponariae	Gypsophilae	CBS 116492	KC584215	KC584135	KC584425	KC584683	–	Woudenberg et al. (2013)
A. scirpicola	Nimbya	CBS 481.90	KC584237	KC584163	KC584469	KC584728	JQ671781	Woudenberg et al., 2013, Deng et al., 2018
A. scirpinfestans	Nimbya	EGS 49-185T	JN383499	JN383480	–	JQ672404	JQ671783	Lawrence et al. (2012), Lawrence et al. (unpubl. data)
A. scirpivora	Nimbya	EGS 50-021T	JN383500	JN383481	–	JQ672405	JQ671782	Lawrence et al. (2012), Lawrence et al. (unpubl. data)
A. scorzonerae	Porri	CBS 103.46	KJ718190	JQ646363	KJ718363	KJ718537	–	Woudenberg et al. (2014)
A. selini	Radicina	CBS 109382T	AF229455	AY278800	KC584426	KC584684	–	Woudenberg et al. (2013)
A. sennae	Porri	CBS 477.81T	KJ718230	JQ646344	KJ718403	EU130543	–	Woudenberg et al. (2014)
A. septospora	Pseudoulocladium	CBS 109.38	FJ266489	FJ266500	KC584487	KC584747	–	Woudenberg et al. (2013)
A. septorioides	Brassicicola	CBS 106.41T	KC584216	KC584136	KC584427	KC584685	–	Woudenberg et al. (2013)
A. sesami	Porri	CBS 115264	JF780939	KJ718061	KJ718405	KJ718577	–	Woudenberg et al. (2014)
A. shukurtuzii	Soda	CBS 137520T	KJ443257	KJ649620	KJ443172	KJ443214	–	Grum-Grzhimaylo et al. (2016)
A. sidae	Porri	CBS 117730T	KJ718232	KJ718062	KJ718406	KJ718578	–	Woudenberg et al. (2014)
A. simsimi	Dianthicola	CBS 115265T	JF780937	KC584137	KC584428	KC584686	–	Woudenberg et al. (2013)
A. silybi	Porri	CBS 134092T	KJ718233	KJ718063	KJ718407	KJ718579	–	Woudenberg et al. (2014)
A. slovaca	Infectoriae	CBS 567.66T	KC584226	KC584150	KC584444	KC584702	LR134368	Woudenberg et al. (2013), present study
A. smyrnii	Radicina	CBS 109380	AF229456	KC584138	KC584429	KC584687	–	Woudenberg et al. (2013)
A. solani	Porri	CBS 106.21	KJ718236	KJ718066	KJ718410	KJ718582	–	Woudenberg et al. (2014)
A. solani-nigri	Porri	CBS 113403	KJ718243	KJ718071	KJ718418	KJ718589	–	Woudenberg et al. (2014)
A. soliaridae		CBS 118387T	KC584218	KC584140	KC584431	KC584689	–	Woudenberg et al. (2013)
A. solidaccana	Brassicicola	CBS 118698T	KC584219	KC584141	KC584432	KC584690	–	Woudenberg et al. (2013)
A. sonchi	Sonchi	CBS 119675	KC584220	KC584142	KC584433	KC584691	–	Woudenberg et al. (2013)
A. steviae	Porri	CBS 117362T	KJ718252	KJ718079	KJ718427	KJ718598	–	Woudenberg et al. (2014)
A. subcucurbitae	Ulocladioides	CBS 121491T	KC584249	EU855803	KC584489	KC584749	–	Woudenberg et al. (2013)
A. tagetica	Porri	CBS 479.81	KC584221	KC584143	KC584434	KC584692	–	Woudenberg et al. (2013)
A. tellustris	Embellisia	CBS 538.83T	FJ357316	AY562419	KC584465	KC584724	JQ671794	Woudenberg et al., 2013, Deng et al., 2018
A. terricola	Ulocladioides	CBS 202.67T	FJ266490	KC584177	KC584490	KC584750	–	Woudenberg et al. (2013)
A. tillandsiae	Porri	CBS 116116T	KJ718260	KJ718087	KJ718435	KJ718606	–	Woudenberg et al. (2014)
A. thalictrigena		CBS 121712T	EU040211	KC584144	KC584436	KC584694	–	Woudenberg et al. (2013)
A. thunbergiae	Porri	CBS 116331T	KJ718257	KJ718084	KJ718432	KJ718603	–	Woudenberg et al. (2014)
A. tomato	Alternaria	CBS 103.30	KP124445	KP124294	KP124915	KP125224	–	Woudenberg et al. (2015)
A. triglochinicola	Eureka	CBS 119676T	KC584222	KC584145	KC584437	KC584695	–	Woudenberg et al. (2013)
A. triticimaculans	Infectoriae	CBS 578.94T	JQ693657	JQ646280	LR134183	–	JQ671806	Poursafar et al. (2018), present study
A. triticina	Infectoriae	CBS 763.84T	AY278834	JQ646281	LR134186	FJ214942	JQ671808	Andersen et al., 2009, Poursafar et al., 2018, Present study
A. tropica	Porri	CBS 631.93T	KJ718261	KJ718088	KJ718436	KJ718607	–	Woudenberg et al. (2014)
A. tumida	Embellisioides	CBS 539.83T	FJ266481	FJ266493	KC584466	KC584725	–	Woudenberg et al. (2013)
A. quercicola	Infectoriae	CBS 141466T	KX228295	KX228362	LR134188	LR134259	LR134115	Crous et al. (2013), present study
A. vaccariae	Gypsophilae	CBS 116533	KC584223	KC584146	KC584438	KC584696	–	Woudenberg et al. (2013)
A. vaccariicola	Gypsophilae	CBS 118714T	KC584224	KC584147	KC584439	KC584697	–	Woudenberg et al. (2013)
A. venezuelensis	Porri	CBS 116121T	KJ718263	KJ718090	KJ718438	KJ718609	–	Woudenberg et al. (2014)
A. ventricosa	Infectoriae	CBS 121546T	JQ693649	JQ646290	LR134134	KY352501	JQ671818	Poursafar et al. (2018), Fotedar et al. (unpubl. data), present study
A. viburni	Infectoriae	CBS 119407T	JQ693647	JQ646288	LR134166	LR134200	JQ671816	Poursafar et al. (2018), present study
A. zinniae	Porri	CBS 117223	KJ718270	KJ718096	KJ718445	KJ718616	–	Woudenberg et al. (2014)

¹CBS: Culture collection of the Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; CNU: Culture Collection Center of the Chungnam National University; DAOM: Canadian Collection of Fungal Cultures, Ottawa, Canada; EGS: Personal collection of Dr. E.G. Simmons; FMR: Facultat de Medicina, Universitat Rovira i Virgili, Reus, Spain; IRAN: Fungal Culture Collections of the Iranian Research Institute of Plant Protection; KUMCC, Culture collection of Kunming Institute of Botany, Kunming, China; LEP: Mycological Herbarium of All-Russian Institute of Plant Protection, Saint Petersburg, Russia; MFLU and MFLUCC: Herbarium and culture collection of Mae Fah Luang University, Chiang Rai, Thailand, respectively; PPRI: ARC-Plant Protection Research Institute, Roodeplaat, South Africa. ^T indicates ex-type strains.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; gapdh: partial glyceraldehyde-3-phosphate dehydrogenase gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; ATPase: partial plasma membrane ATPase gene.

Fig. 5.

Maximum Likelihood (ML) tree constructed with ITS (529 bp), ATPase (1180 bp), gapdh (489 bp), rpb2 (573 bp) and tef1 (239 bp) sequences of ex-type strains of the species in section Infectoriae. The phylogenetic tree was rooted to Alternaria abundans CBS 534.83 and Alternaria breviramosa CBS 121331 (section Chalastospora). Bootstrap support values above 70 % are shown at the nodes. GenBank accession numbers are indicated in Table 2. The novel species described in this study are indicated in bold. ^T indicates ex-type strain. TreeBASE: S23786.

Fig. 6.

Maximum Likelihood (ML) tree constructed with ITS (576 bp), ATPase (1198 bp) and gapdh (491 bp) sequences of ex-type strains of species in the sections Pseudoalternaria and Chalastospora. The phylogenetic tree was rooted to Alternaria caricis CBS 480.90 and A. scirpicola CBS 481.90 (section Nimbya). Bootstrap support values above 70 % are shown at the nodes. GenBank accession numbers are indicated in Table 2. The novel species described in this study are indicated in bold. ^T indicates ex-type strain. TreeBASE: S23787.

Fig. 7.

Maximum Likelihood (ML) tree constructed with ITS (523 bp), gapdh (503 bp), rpb2 (860 bp) and tef1 (247 bp) sequences of ex-type strains of species in section Radicina. The phylogenetic tree was rooted to Alternaria caricis CBS 480.90 and A. scirpicola CBS 481.90 (section Nimbya). Bootstrap support values above 70 % are shown at the nodes. GenBank accession numbers are indicated in Table 2. The novel species described in this study are indicated in bold. ^T indicates ex-type strain. TreeBASE: S23788.

Ascomata small, solitary to clustered, erumpent to almost superficial at maturity, dark brown, globose to ovoid, apically papillate, ostiolate, smooth or setose at maturity, with a thin ascomatal wall; centrum formed by a hamathecium with cellular pseudoparaphyses and asci in basal layer. Asci bitunicate, fissitunicate, uni- or biseriate, (4–6–)8-spored, cylindrical to cylindro-clavate, straight or somewhat curved, with a short furcate pedicel. Ascospores ellipsoid to fusoid, muriform, slightly constricted at septa, 3–7-transverse septa, 1–2 series of longitudinal septa through the two original central segments, end cells without septa, or with one longitudinal or oblique septum, or with a Y-shaped pair of septa, yellow-brown, smooth-walled, without guttules. Conidiophores macronematous or semi-macronematous, mononematous, simple or branched, pale brown or brown. Conidiogenous cells integrated, terminal becoming intercalary, mono- or polytretic and sympodial, cicatrised. Conidia solitary or in simple or branched chains, dry, ovoid, obovoid, cylindrical, narrowly ellipsoid or obclavate, beaked or non-beaked, pale or medium olivaceous brown to brown, smooth-walled or verrucose, with transverse and with or without oblique or longitudinal septa; septa can be thick, dark, an internal cell-like structure can be formed. Species with meristematic growth are known (adapted from Ellis, 1976, Woudenberg et al., 2013, Woudenberg et al., 2014, Grum-Grzhimaylo et al., 2016).



Culture characteristics: Colonies effuse, grey, olivaceous brown, dark blackish brown or black; mycelium immersed or partly superficial, composed of colourless, olivaceous brown or brown hyphae.



Optimal media and cultivation conditions: For morphological examinations the use of PCA and V-8 is recommended, incubated at moderate temperatures (ca. 22–25 ºC) under near-ultraviolet light (8 h light, 16 h dark), without humidity control, for 5–7 d or more if necessary (Simmons 2007). We also recommend microscopic examination of OA cultures due to the alterations observed on the conidial wall when grown on PCA.



Distribution: Worldwide.



Hosts: Mainly pathogens of a wide range of plant families, such as Apiaceae, Asteraceae, Brassicaceae, Cyperaceae, Poaceae, Rosaceae, Rutaceae, Solanaceae, among others (Thomma, 2003, Lawrence et al., 2016). Some are implicated as human pathogens (de Hoog et al. 2011).



Disease symptoms: Most species are foliar pathogens, causing necrotic lesions as brown/black spots or “target spot” with the fungus residing in the central area, but also inducing leaf blight; seed-borne species may attack seedlings, resulting in damping-off, stem lesions or collar rot; sunken and dark lesions are present in roots, tubers, stems and fruits infections; some rots and decay are typical symptoms of post-harvest diseases (Laemmlen, 2001, Thomma, 2003, Lawrence et al., 2008). Phytotoxins are also produced during the invasion process as virulence factors which affect a wide spectrum of plant species. Alternaria toxins diffuse into host tissues resulting in a chlorotic or yellow halo around lesions, exacerbating the severity of the symptoms (Singh et al. 2015).



Notes: Alternaria is characterised mainly by its asexual morph with darkly pigmented multi-celled conidia, which are typically dictyosporous, some phragmosporous, and arranged single or in chains on the conidiophore. Some of these morphological features can also be observed in other closely related genera such as Paradendryphiella (Woudenberg et al. 2013) or Stemphylium (Woudenberg et al. 2017). However, Paradendryphiella mainly differs by its denticulate conidiogenous cells with prominent conidial scars aggregated at the apex of simple or branched conidiophores, and Stemphylium by showing percurrent conidiophores with apically swollen conidiogenous cells.

 Extensive morphological investigations of the genus Alternaria were carried out by Emory G. Simmons, which culminated with his monograph on Alternaria species identification (Simmons 2007). Based on the sporulation patterns and conidial morphology, he described several Alternaria species-groups which were typified by representative species (Simmons 1992). In recent years, based on molecular phylogenetic approaches using DNA sequence data, it has been shown that the main morphological groups identified by Simmons represent monophyletic species groups. Lawrence et al. (2013) provided the first strongly supported phylogenetic hypothesis among Alternaria lineages and elevated several of those monophyletic species groups to the taxonomic status of sections, each with a type species. Successive phylogenetic investigations added additional sections within the genus by synonymising genera such as Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Nimbya, Pseudoalternaria, Sinomyces, Teretispora, Ulocladium, Undiphilum and Ybotromyces (Woudenberg et al., 2013, Woudenberg et al., 2014, Lawrence et al., 2016). Therefore, the genus Alternaria currently comprises close to 280 species, most of them classified in 27 sections. Taxonomic traits and species composition of all Alternaria sections are summarised in Lawrence et al. (2016).

 Considering, however, the overlap of morphological traits among Alternaria sections/species and that the culture conditions can greatly influence the morphology of these fungi, molecular identification is practically mandatory for the classification of Alternaria isolates. Although the ITS barcode is considered a good phylogenetic marker to define sections, it has limited discriminatory power to distinguish species, making multi-locus sequence analysis with several protein-coding loci essential for accurate species identification. While Woudenberg et al. (2013), in addition to the nrDNA regions, used the combination of gapdh, rpb2 and tef1 loci for redefining the genus, the combination of other phylogenetic markers has since been analysed to determine relationships and species delineation in studies on a particular section; i.e. ITS, Alt a-1, endoPG, gapdh, OPA10-2, rpb2 and tef1 for section Alternaria (Woudenberg et al. 2015); ITS, ATPase, tef1 and gapdh for sections Infectoriae and Pseudoalternaria (Andersen et al., 2009, Deng et al., 2018, Poursafar et al., 2018); ITS, Alt a-1, gapdh, rpb2 and tef1 for section Porri (Woudenberg et al. 2014); and ITS, Alt a-1 and gapdh for section Sonchi (Lawrence et al., 2012, Deng et al., 2014). Nevertheless, according to Lawrence et al. (2013) the plasma membrane ATPase, cmdA, and Alt a-1 loci are the most informative markers for Alternaria species delimitation. However, considering that the latter locus unreliably amplifies some species within sect. Infectoriae, they suggested that the most suitable genetic markers for molecular identification at the species level are ATPase and cmdA genes (Lawrence et al., 2013, Lawrence et al., 2016). Unfortunately, the latter marker has not been used for the phylogeny of any of the above-mentioned sections.

 Alternaria is a very successful pathogenic genus that causes disease on a great number of economically important plants, causing large economic losses due to the number of plant species affected and worldwide distributions of several Alternaria species (Meena et al. 2017). They are commonly described causing stem canker, leaf blight or leaf spot on a large variety of crops, including cereals, ornamentals, oil crops, vegetables such as broccoli, cauliflower, carrot, onion and potato, and fruits like apple, citrus, pear and strawberry, among others. Species in section Alternaria, such as A. alternata, A. arborescens or A. tenuissima, as well as others from sections Alternantherae, Brassiccicola, Crivellia, Gypsophilae, Nimbya, Radicina or Sonchi, are frequently reported causing such diseases, but the largest group of phytopathogens in the genus is concentrated in section Porri (Lawrence et al., 2016, Meena et al., 2017). The most relevant plant pathogens in this latter section are A. bataticola, A. porri, A. solani and A. tomatophila (Woudenberg et al. 2014). Alternaria species also produce diverse phytotoxins, which affect their host plants at different stages of pathogenesis (Thomma, 2003, Lawrence et al., 2008, Meena et al., 2017). Some of these phytotoxins have been evaluated by the European Food Safety Authority as potentially causing risks to human health (Meena et al. 2017).

 In humans, Alternaria species are commonly associated with hypersensitivity pneumonitis, bronchial asthma, allergic sinusitis and rhinitis. To a lesser extent, they have been also described as causing paranasal sinusitis, ocular infections, onychomycosis, cutaneous and subcutaneous infections, granulomatous pulmonary disease, soft palate perforation and disseminated disease (Pastor and Guarro, 2008, de Hoog et al., 2011).

 In several surveys of microfungi from Spanish regions with different climates and biodiversity, samples of plant litter (leaves, bark and twigs) and dung of wild and farm herbivore animals (rabbits, rodents, goats, cattle and horses) were collected. From these samples, we found 16 interesting Alternaria isolates, belonging to sections Infectoriae, Pseudoalternaria, Chalastospora and Radicina. The multi-locus phylogenetic analysis based on five above-mentioned gene markers showed that 10 of them were undescribed species for the genus, and the others were identified as A. kourtkuyana, A. rosae and A. malorum (Fig. 5, Fig. 6, Fig. 7). Most of these novel species have been isolated from herbivore dung, which appear to represent a reservoir of interesting Alternaria species which could represent potential plant pathogens.



References: Ellis, 1976, Simmons, 2007 (morphology); Laemmlen, 2001, Thomma, 2003, Lawrence et al., 2008, Meena et al., 2017 (plant infections); Pastor and Guarro, 2008, de Hoog et al., 2011 (human infections); Woudenberg et al., 2013, Woudenberg et al., 2014, Woudenberg et al., 2015, Grum-Grzhimaylo et al., 2016, Lawrence et al., 2016, Poursafar et al., 2018 (morphology and phylogeny).



Alternaria aconidiophora Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829626. Fig. 8.



Fig. 8.

Alternaria aconidiophora (ex-type FMR 17111). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D–F. Conidia. Scale bars = 10 μm.

Etymology: Name refers to the lack of conidiophores from vegetative hyphae.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae 1–4 μm wide, septate, branched, hyaline to greyish, smooth-walled. Conidiophores absent. Conidiogenous loci inconspicuous on vegetative hyphae, scarce. Conidia commonly solitary at centre of the colony, globose, ovoid, near ellipsoid or obclavate, 12–31 × 7–12 μm, with some darkened middle transverse septa, 1–5 transverse, 0–1(–2) longitudinal or oblique septa per transverse segment, brown, smooth-walled. Secondary conidiophores present, may be formed apically from the conidial body as a short extension often geniculate, with one or two, terminal or subterminal conidiogenous loci. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 64 mm diam after 1 wk at 25 °C, flat, cottony at centre, slightly radially folded towards the periphery, aerial mycelium abundant, margins regular; surface white (1A1); reverse yellowish white (4A2). On PCA attaining 54 mm diam, flat, aerial mycelium scarce, margins regular; surface greyish green to greenish grey (1D3/1B1); reverse greenish grey (1C2/1B1). On OA reaching 61 mm diam, flat, aerial mycelium scarce, margins regular; surface and reverse colourless.



Cardinal temperature for growth: Optimum 25 °C, maximum 37 °C, minimum 5 °C.



Typus: Spain, Catalonia, Alta Ribagorça, Vall de Boí, isolated from forest leaf litter, Dec. 2017, J. Gené (holotype CBS H-23891, culture ex-type CBS 145419 = FMR 17111).



Notes: Alternaria aconidiophora together with A. fimeti, both species introduced here from herbivore dung, are placed in an unsupported clade in Alternaria section Infectoriae (Fig. 5). Morphologically, the latter differs from A. aconidiophora in having conspicuous sporulation with well-differentiated conidiophores and verrucose conidia up to 44 μm long. The conidia of A. aconidiophora are smooth-walled and 12–31 μm long.



Alternaria altcampina Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829627. Fig. 9.



Fig. 9.

Alternaria altcampina (ex-type FMR 16476). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D–I. Conidiophores and conidia. Scale bars: D–E = 20 μm; F–I = 10 μm.

Etymology: Name refers to the region of Alt Camp (Catalonia), from where the fungus was collected.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae 2–4 μm wide, branched, pale yellowish brown to brown, septate, smooth-walled to verruculose. Conidiophores macronematous, arising laterally or terminally from aerial hyphae, erect to slightly flexuous, unbranched, occasionally branched, up to 10-septate, 12–88 × 3–4 μm, brown becoming pale towards apex, smooth-walled, with 1 terminal and up to 3 subterminal conidiogenous loci. Conidia in branched chains, occasionally solitary, ovoid, obclaviform, ellipsoidal or somewhat cylindrical, 9–43 × 6–8 μm, with darkened middle transverse septa, (1–)2–3(–6) transverse, 0–1 longitudinal or oblique septa in up to 4 of the transverse segments, usually inconspicuous, pale yellowish to yellowish brown, verrucose. Secondary conidiophores commonly formed apically as a beak from conidial body, or as a lateral conidiogenous loci from body cells bearing conidia in short chains. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 73 mm diam after 1 wk at 25 °C, flat, densely floccose, aerial mycelium abundant, margins fimbriate; surface olive brown to blond (4D3/4C4), white at the periphery; reverse yellowish brown to orange-grey (5E4/5B2). On PCA attaining 66 mm diam, flat, granular, aerial mycelium scarce, margins regular; surface dark green (30F8); reverse dull green (30E4). On OA reaching 70 mm diam, flat, loosely floccose at centre, aerial mycelium scarce, margins regular; surface dark green (28F4); reverse dull green (29E3).



Cardinal temperature for growth: Optimum 25 °C, maximum 37 °C, minimum 5 °C.



Typus: Spain, Catalonia, Alt Camp, isolated from goat dung, Mar. 2017, I. Iturrieta-González, M. Guevara-Suarez & J. Guarro (holotype CBS H-23892, culture ex-type CBS 145420 = FMR 16476).



Notes: Based on the phylogeny of ITS, ATPase and gapdh, A. altcampina is classified in Alternaria section Pseudoalternaria (Fig. 6). It is closely related to the recently described species A. parvicaespitosa, which was isolated from harvested blueberry fruit (California, USA), and A. kordkuyana, isolated from symptomatic wheat heads of Triticum aestivum (Kordkuy, Iran). Alternaria parvicaespitosa differs in having smaller conidia (10–25 × 7–12 μm) with smooth to slightly punctulate outer walls (Gannibal & Lawrence 2016), and A. kordkuyana by its larger conidia [30–50(−60) × 7–11 μm] and shorter conidiophores (10–40 × 3–4 μm) (Poursafar et al. 2018).



Alternaria chlamydosporifera Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829628. Fig. 10.



Fig. 10.

Alternaria chlamydosporifera (ex-type FMR 17360). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D–H. Conidiophores and conidia. I. Chlamydospores. Scale bars: D = 50 μm; E, I = 20 μm; F–H = 10 μm.

Etymology: Name refers to the production of abundant chlamydospores in culture.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae 3–6 μm wide, septate, branched, pale brown to brown, smooth-walled. Conidiophores macronematous, arising directly from aerial hyphae, erect to slightly flexuous, occasionally geniculate at apex, 1–4-septate, unbranched or scarcely branched, 14–140 × 3–5 μm, dark brown, verruculose, with 1–2 conidiogenous loci. Conidia mostly solitary, occasionally in short chains with up to two conidia, ellipsoidal or ovoid, occasionally subglobose, 12–41 × 7–20 μm, with darkened middle transverse septa, 1–3(–4) transverse, and 0–1(–2) longitudinal septa per transverse segments, brown to dark brown, verruculose. Secondary conidiophores can be formed apically from conidial body as a beak, geniculate, with 1–3 terminal or lateral conidiogenous loci, bearing solitary or short chains of conidia. Chlamydospores abundant, immersed, intercalary, irregular shape, rarely broadly ellipsoidal or clavate, muriform, sometimes showing central constriction, 60–91 × 32–57 μm, dark brown to black. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 82 mm diam after 1 wk at 25 °C, flat, densely floccose, aerial mycelium abundant, margins regular; surface greyish brown (5E3); reverse black to greyish brown (5E3). On PCA attaining 68 mm diam, flat, with granular appearance by the presence of abundant chlamydospores, aerial mycelium scarce, margins regular; surface dark green (29F5); reverse dark green (30F8). On OA reaching 71 mm diam, flat, loosely floccose at centre, slightly granular towards the periphery, aerial mycelium scarce, margins slightly lobate; surface dark green (29F4); reverse dark green (29F4).



Cardinal temperature for growth: Optimum 25 °C, maximum 37 °C, minimum 5 °C.



Typus: Spain, Huesca, Baells, isolated from rabbit dung, Apr. 2018, G. Sisó & D. García (holotype CBS H-23893, culture ex-type CBS 145421 = FMR 17360).



Notes: Alternaria chlamydosporifera belongs to Alternaria section Radicina (Fig. 7). It is included in a well-supported clade (95 % BS) with A. petroselini, A. selini and A. smyrnii, which are pathogens of Apiaceae (Lawrence et al. 2016). Alternaria petroselini and A. selini can be easily differentiated by the lack of chlamydospores in culture and their larger (50–66 μm in A. petroselini vs. 48–65 μm in A. selini) and usually ellipsoidal conidia (Simmons 1995). Although A. smyrnii, the closest relative to A. chlamydosporifera, has been described as producing sclerotial knots in culture that are able to form fertile conidiophores, its conidia are considerably longer (67–96 μm) (Simmons 1995) than those of A. chlamydosporifera (12–41 μm long). In addition, we have never observed conidiophores associated with the chlamydospores of the latter species.



Alternaria curvata Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829628. Fig. 11.



Fig. 11.

Alternaria curvata (ex-type FMR 16901). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D–F. Conidiophore and conidia. Scale bars = 10 μm.

Etymology: Name refers to the presence of curved conidia.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae 2–6 μm wide, septate, branched, hyaline to yellowish brown to brown, smooth-walled to verruculose. Conidiophores macronematous, arising laterally or terminally from aerial hyphae, erect to slightly flexuous, usually unbranched, up to 14-septate, 23–80 × 3–5 μm, brown to dark brown, smooth-walled, with a terminal or occasionally a sub-terminal conidiogenous loci. Conidia forming branched chains, with up to 5 conidia in unbranched part, ovoid or nearly ellipsoidal, often slightly curved, 13–47(–70) × 4–16 μm, with darkened middle transverse septa, (0–)1–5(–7) transverse, and 0–2(–3) longitudinal or oblique septa per transverse segment, brown to dark brown, verrucose to tuberculate. Secondary conidiophores can be formed apically or laterally from the conidial body as a short extension bearing conidia in short chains. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 63 mm diam after 1 wk at 25 °C, flat, densely floccose, aerial mycelium abundant, margins regular; surface white to dull green (1A1/30D4); reverse dark green to olive yellow (30F8/2D6), white at the periphery. On PCA attaining 62 mm diam, flat, loosely floccose, aerial mycelium scarce, margins regular; surface olive (3F4); reverse dark green to grey (29F4/29B1). On OA reaching 61 mm diam, scarce aerial mycelium towards the periphery, margins regular; surface greyish green (30E5), with greyish mycelium tufts at centre; reverse dull green (29E4).



Cardinal temperature for growth: Optimum 25 °C, maximum 37 °C, minimum 5 °C.



Typus: Spain, Catalonia, Tarragona, Els Ports Natural Park, isolated from goat dung, Oct. 2017, G. Sisó & C. González-García (holotype CBS H-23894, culture ex-type CBS 145422 = FMR 16901).



Notes: Alternaria curvata was included in the section Infectoriae, forming an unsupported basal clade together with A. montsantina and A. pseudoventricosa, both introduced here, and A. ventricosa (Fig. 5). Morphologically, the former two species differ from A. curvata in lacking curved conidia. Alternaria ventricosa has asymmetrical conidia, due to the hyperplasia and hypertrophy of cells, especially on one side of the conidia (Roberts 2007). Other morphologically similar species are A. fimeti and A. triticina, which also have curved conidia. However, A. triticina is phylogenetically more distant and its conidia are strongly inequilateral and wider (up to 22 μm) (Simmons 2007) than those of A. curvata (4–16 μm wide). Alternaria fimeti can be differentiated from A. curvata by the production of longer conidiophores (22–182 μm in A. fimeti vs. 23–80 μm in A. curvata) and the absence or scarce development of secondary conidiophores.



Alternaria fimeti Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829630. Fig. 12.



Fig. 12.

Alternaria fimeti (ex-type FMR 17110). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D–G. Conidiophores and conidia. Scale bars: D = 20 μm; E–G = 10 μm.

Etymology: Name refers to the substrate where the species was isolated, herbivore dung.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae 2–5 μm wide, septate, branched, hyaline to subhyaline to pale yellowish, verruculose. Conidiophores semi- to macronematous, arising laterally or terminally from aerial hyphae, erect to slightly flexuous, unbranched (can be slightly branched on OA), up to 9-septate, 22–182 × 1–5 μm, pale brown, smooth-walled, with 1 terminal conidiogenous locus. Conidia solitary or in short chains of up to six conidia, ovoid, obpyriform or obclavate, some slightly curved, 9–44 × 5–14(–23) μm, with darkened middle transverse septa, 0–5 transverse (up to 7 in OA), and 0–1(–2) longitudinal or oblique septa per segment, brown, verrucose. Secondary conidiophores only scarcely produced on OA as apical or lateral extension from conidial body, up to 25 μm long. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 66 mm diam after 1 wk at 25 °C, flat, densely floccose, aerial mycelium abundant, margins fimbriate; surface yellowish grey to yellowish white (3C2/3A2); reverse yellowish brown to light yellow (5E8/4A5). On PCA attaining 65 mm diam, flat, slightly floccose at centre, aerial mycelium scarce, margins regular; surface olive-brown (4F5); reverse olive-brown (4F8/4E4). On OA reaching 64 mm diam, flat, slightly floccose, scarce aerial mycelium, margins regular; surface dull green (30E5) with grey floccose area; reverse dull green (30E4).



Cardinal temperature for growth: Optimum 25 °C, maximum 37 °C, minimum 5 °C.



Typus: Spain, Catalonia, Priorat, Montsant Natural Park, Arbolí, isolated from small rodent dung, Feb. 2018, I. Iturrieta-González, E. Carvalho & J. Gené (holotype CBS H-23895, culture ex-type CBS 145423 = FMR 17110).



Note: Alternaria fimeti is placed in a clade of section Infectoriae together with A. aconidiophora (see notes of this latter species).



Alternaria inflata Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829631. Fig. 13.



Fig. 13.

Alternaria inflata (ex-type FMR 16477). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D, F–G. Conidiophores and conidia. E. Chlamydospores. Scale bars = 10 μm.

Etymology: Name refers to the presence of swollen cells in the conidial body.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae of 1–3 μm wide, septate, branched, hyaline to pale brown, smooth-walled to verruculose. Conidiophores arising laterally or terminally from aerial hyphae, erect to slightly flexuous, semi- to macronematous, up to 10-septate, commonly unbranched, 9–73(–105) × 2–5 μm, pale brown to brown, smooth-walled, with one terminal conidiogenous loci or up to three subterminal conidiogenous loci. Conidia solitary or in short chains with up to four conidia, broadly ellipsoidal or ovoid, 13–41 × 5–14 μm, often with some swollen cells protruding the conidium outline, some with darkened middle transverse septa, (1–)2–3(–5) transverse septa, and 0–2 longitudinal or oblique septa per transverse segment, brown, verruculose. Secondary conidiophores scarcely produced, as an apical extension up to 15 μm long, bearing conidia in short chains. Chlamydospores present, consisting of intercalary, thick-walled, brown swollen cells, up to 8 × 6 μm, arranged in chains or in clusters. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 62 mm diam after 1 wk at 25 °C, flat, aerial mycelium abundant, floccose, margins fimbriate; surface white (1A1); reverse greyish yellow to yellowish white (4C6/4A2). On PCA attaining 67 mm diam, flat, scarce aerial mycelium, margins regular; surface dull green to grey (30E4/30B1); reverse dark green to grey (30E4/30B1). On OA reaching 61 mm diam, flat, loosely floccose, margins regular; surface pale grey (1B1); reverse pale grey (1B1).



Cardinal temperature for growth: Optimum 25 °C, maximum 37 °C, minimum 5 °C.



Typus: Spain, Catalonia, Conca de Barberà, Poblet, isolated from rabbit dung, Mar. 2017, J. Guarro & I. Iturrieta-González (holotype CBS H-23896, culture ex-type CBS 145424 = FMR 16477).



Notes: Our phylogeny shows that A. inflata belongs to section Pseudoalternaria (Fig. 6). It clustered in a well-supported clade (86 % BS) with A. altcampina, A. kordkuyana and A. parvicaespitosa, but formed a single basal lineage representative of a distinct species. Alternaria inflata can be differentiated from all the species in the section by the production of chlamydospores and by the formation of broadly ellipsoidal conidia, usually with swollen cells protruding from the conidial body. In addition, A. altcampina also differs in the production of secondary conidiophores, A. parvicaespitosa in its shorter conidiophores (up to 70 μm) and conidia (10–25 μm) (Gannibal & Lawrence 2016), and A. kordkuyana in the production of longer conidial chains [up 5–8(–10) conidia] and conidia measuring 30–50(–60) × 7–11 μm with up to seven transverse septa (Poursafar et al. 2018).

 With the additions of A. altcampina and A. inflata section Pseudoalternaria now comprises seven species. It is of note, however, that most of these taxa are only known from a single collection. In our survey of asexual fungi from herbivore dung, we identified several Spanish isolates belonging to other species in the section, namely A. kordkuyana and A. rosae (Fig. 6). Considering that most of the species in section Pseudoalternaria are mainly associated with herbaceous plants of the families Brassicaceae, Ericaceae, Poacea or Rosaceae, it is not surprising to find these fungi in faeces of herbivorous animals.



Alternaria lawrencei Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829632. Fig. 14.



Fig. 14.

Alternaria lawrencei (ex-type FMR 17004). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D–K. Conidiophores and conidia. Scale bars: D = 20 μm; E–K = 10 μm.

Etymology: Name in honour of Daniel P. Lawrence for his contribution to the taxonomy of the genus Alternaria.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae 1–3 μm wide, septate, branched, pale brown, smooth-walled. Conidiophores macronematous, solitary, arising directly from aerial hyphae, erect to slightly flexuous, occasionally geniculate at apex, usually unbranched, up to 10-septate, 9–125 × 3–4(–5) μm, brown, smooth-walled, with 1–2 lateral or terminal conidiogenous loci; micronematous conidiophores also present, reduced to intercalary conidiogenous cells with a single conidiogenous locus on hyphae. Conidia solitary or in short chains, up to six conidia in the unbranched part, ovoid, obpyriform or obclavate, 6–71 × 7–15 μm, with darkened middle transverse septa, (1–)2–7(–9) transverse, and 0–2(–3) longitudinal or oblique septa, pale brown to brown, verrucose to tuberculate. Secondary conidiophores commonly formed apically on conidia as a geniculate extension with several conidiogenous loci, or as lateral extensions from cells of conidial body, up to 35 μm long, producing conidia solitary or in short chains. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 68 mm diam after 1 wk at 25 °C, low convex, cottony, aerial mycelium abundant, margins regular; surface white (1A1); reverse yellowish brown to greyish yellow (5E7/4B6). On PCA attaining 69 mm diam, low convex, slightly floccose, aerial mycelium relatively abundant at centre, margins regular; surface yellowish grey to olive (2D2/1E3); reverse dark green to olive (30F8/1E3). On OA reaching 63 mm diam, loosely floccose at centre, flat and scarce aerial mycelium towards the periphery, margins regular and diffuse; surface olive (2F4) to olive-grey (2B1); reverse olive to yellowish grey (2F8/2D2).



Cardinal temperature for growth: Optimum 25 °C, maximum 37 °C, minimum 5 °C.



Typus: Spain, Catalonia, Tarragona, Els Ports Natural Park, isolated from goat dung, Oct. 2017, G. Sisó & C. González-García (holotype CBS H-23897, culture ex-type CBS 145425 = FMR 17004).



Notes: Although A. lawrencei is clearly placed in section Infectoriae, the multi-locus analysis did not reveal any phylogenetic relationship with any species included in the analysis (Fig. 4). It is of note, however, that eight species of the section (i.e. A. cerasi, A. cesenica, A. dactylidicola, A. forlicesenensis, A. hampshirensis, A. litorea, A. murispora and A. poaceicola) could not be included in our analysis due to their limited molecular data. Nevertheless, A. cesenica, A. dactylidicola, A. forlicesenensis, A. hampshirensis, A. murispora and A. poaceicola can be distinguished from A. lawrencei by the production of a sexual morph (Ariyawansa et al., 2015b, Liu et al., 2015, Thambugala et al., 2017, Wanasinghe et al., 2018), A. cerasi by its inequilateral conidia (Potebnia, 1907, Simmons, 2007), and A. litorea by the production of shorter primary conidiophores (40–50 μm long) and smooth-walled conidia that are 22–32 μm long (Simmons 2007).



Alternaria montsantina Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829633. Fig. 15.



Fig. 15.

Alternaria montsantina (ex-type FMR 17060). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D–H. Conidiophores and conidia. Scale bars: D = 50 μm; E–H = 10 μm.

Etymology: Name refers to the place, Montsant Natural Park (Catalonia), where the fungus was collected.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae 1–7 μm wide, septate, branched, usually forming hyphal coils, subhyaline to pale brown, smooth-walled to verruculose. Conidiophores macronematous, arising laterally or terminally from aerial hyphae, erect to slightly flexuous, unbranched, up to 15-septate, 12–137 × 3–6 μm, often with geniculate apical portion containing intercalary and terminal conidiogenous loci, brown, smooth-walled to verruculose. Conidia solitary or in short chains with up to five conidia, subglobose, ovoid or obpyriform, 8–65 × 6–12 μm, with 1–3(–11) transverse septa, and 0–2 longitudinal or oblique septa, brown, verrucose to tuberculate. Secondary conidiophores commonly produced apically as a long, often geniculate extension, up to 105 μm long and 10-septate, bearing terminal conidial chains. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 76 mm diam after 1 wk at 25 °C, flat, densely floccose, aerial mycelium abundant, margins regular; surface pastel grey to greyish yellow (1C1/2C4) and with a white edge; reverse blond to white (4C4/1A1). On PCA attaining 70 mm diam, flat, loosely floccose at centre, aerial mycelium moderate, margins regular; surface olive brown to white (4D4/1A1); reverse olive to white (3D4/1A1). On OA reaching 75 mm diam, flat, cottony, margins regular; surface yellowish grey to olive (3D2/2F4) and white edge; reverse olive to white (2F4/1A1).



Cardinal temperature for growth: Optimum 25 °C, maximum 37 °C, minimum 5 °C.



Typus: Spain, Catalonia, Priorat, Montsant Natural Park, Swamp of Siurana, isolated from an unidentified twig, Feb. 2018, I. Iturrieta-González, E. Carvalho & J. Gené (holotype CBS H-23898, culture ex-type CBS 145426 = FMR 17060).



Notes: Alternaria montsantina is placed in a weakly supported basal clade of the section Infectoriae, together with A. curvata, A. pseudoventricosa and A. ventricosa (Fig. 5). Morphologically, this new species can be distinguished from A. curvata and A. ventricosa by the absence of curved or inequilateral inflated conidia. Alternaria montsantina differs from A. pseudoventricosa in the production of longer (12–137 μm) and often geniculate primary and secondary conidiophores, bearing solitary conidia or arranged in short chains (up to five conidia). Conidiophores in A. pseudoventricosa are 30–44 μm long, and the conidial chains include up to 19 conidia.



Alternaria pobletensis Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829634. Fig. 16.



Fig. 16.

Alternaria pobletensis (ex-type FMR 16448). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D–I. Conidiophores and conidia. Scale bars: D = 20 μm; E–I = 10 μm.

Etymology: Name refers to the place, Poblet (Catalonia), from where the species was collected.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae 2–5 μm wide, branched, pale brown, septate, smooth-walled. Conidiophores semi- to macronematous, solitary, arising directly from aerial hyphae, erect to slightly flexuous, occasionally slightly geniculate at apex, unbranched or branched, up to 8-septate, 14–82 × 4–5(–6) μm, brown, smooth-walled, with 1–2 lateral or terminal conidiogenous loci. Conidia commonly in short, scarcely branched chains, with up to seven conidia, obpyriform or obclavate, some ellipsoidal or subcylindrical, 8–50 × 5–20 μm, (1–)3–7(–9) transverse septa, often middle septa darker, and 0–1(–2) longitudinal or oblique septa per transverse segment, pale brown to brown, smooth-walled or verruculose. Secondary conidiophores commonly produced apically as a short beak up to 11 μm long, or laterally from cells of conidial body, bearing conidia in short chains. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 46 mm diam after 1 wk at 25 °C, flat, floccose at the centre, velvety towards the periphery, aerial mycelium moderate, margins regular; surface olive (3F8), whitish at the periphery; reverse black to yellowish brown (5D5). On PCA attaining 58 mm diam, flat, velvety, margins regular; surface dark green to dull green (30F8/28D3); reverse dark green to dull green (30F8/28D3). On OA reaching 55 mm diam, flat, loosely floccose, margins regular; surface greyish green to dull green (29C3/29E4); reverse dark green to dull green (30F8/30E3).



Cardinal temperature for growth: Optimum 25 °C, maximum 35 °C, minimum 5 °C.



Typus: Spain, Catalonia, Conca de Barberà, Poblet, isolated from unidentified herbivore dung, Mar. 2017, J. Guarro & I. Iturrieta-González (holotype CBS H-23899, culture ex-type CBS 145427 = FMR 16448).



Notes: Alternaria pobletensis clustered in section Chalastospora in a single branch clearly separated from the other six species that currently comprise the section (Fig. 7). Other species of section Chalastospora rarely produce conidia with longitudinal septa (Woudenberg et al. 2013); however, the conidia in A. pobletensis usually have two or more longitudinal or oblique septa. Its closest relative is A. breviramosa. This was originally described as Chalastospora ellipsoidea, found on Triticum (Poaceae) in Australia (Crous et al. 2009a), but later its name was changed to avoid confusion with Alternaria ellipsoidea, an already described species from section Gypsophilae (Woudenberg et al. 2013). Section Gypsophilae contains all Alternaria species that occur on Caryophyllaceae (Lawrence et al. 2016). Alternaria breviramosa differs from A. pobletensis by having shorter conidiophores (up to 25 μm), often reduced to conidiogenous cells, and ellipsoidal, subcylindrical to fusoid conidia with only transverse septa (Crous et al. 2009a).



Alternaria pseudoventricosa Iturrieta-González, Dania García & Gené, sp. nov. MycoBank MB829635. Fig. 17.



Fig. 17.

Alternaria pseudoventricosa (ex-type FMR 16900). A. Colonies on PDA. B. Colonies on PCA. C. Colonies on OA. D–F. Conidiophores and conidia. Scale bars: D = 20 μm; E, F = 10 μm.

Etymology: Name refers to the apparent phylogenetic relationship to A. ventricosa.



Asexual morph on PCA: Mycelium superficial and immersed. Hyphae 1–7 μm wide, septate, branched, hyaline to pale brown, smooth-walled. Conidiophores macronematous, arising laterally from aerial hyphae, erect to slightly flexuous, up to 4-septate, unbranched, 30–45 × 4–6 μm, brown, smooth-walled, with one terminal conidiogenous locus. Conidia commonly in unbranched chains, with up to 19 conidia, obpyriform or obclavate, 10–48(–66) × 5–14 μm, with darkened middle transverse septa, 1–7 transverse, 0–1 longitudinal or oblique septa, brown to dark brown, verrucose to tuberculate. Secondary conidiophores scarce, as a beak arising from the conidial body. Sexual morph not observed.



Culture characteristics: Colonies on PDA reaching 64 mm diam after 1 wk at 25 °C, flat, cottony at the centre, floccose towards the periphery, margins regular; surface white (1A1); reverse yellowish white (4A2). On PCA attaining 62 mm diam, flat towards the periphery, margins regular; surface dark green (29F4), with tuft of white aerial mycelium at centre; reverse dark green to grey (29F8/29B1). On OA reaching 67 mm diam, flat, loosely floccose, margins regular; surface dull green (29E4); reverse dull green (29E4).



Cardinal temperature for growth: Optimum 25 °C, maximum 37 °C, minimum 5 °C.



Typus: Spain, Catalonia, Tarragona, Els Ports Natural Park, isolated from horse dung, Oct. 2017, G. Sisó & C. González-García (holotype CBS H-23900, culture ex-type CBS 145428 = FMR 16900).



Notes: Alternaria pseudoventricosa and A. ventricosa clustered in an unsupported monophyletic basal clade in section Infectoriae (Fig. 5). They can be differentiated by their conidial morphology. Conidia in A. ventricosa are usually asymmetric, laterally swollen, and pale cinnamon brown (Roberts 2007). In contrast, those of A. pseudoventricosa are obpyriform or obclavate and brown to dark brown.



Authors: I. Iturrieta-González, D. García, M. Hernández-Restrepo & J. Gené



Brunneosphaerella Crous, Stud. Mycol. 64: 31. 2009. Fig. 18.



Fig. 18.

Brunneosphaerella spp. A–E. Disease symptoms. A, B.Brunneosphaerella protearum (epitype CBS H-20335). C.Brunneosphaerella nitidae (holotype CBS H-20334). D, E. Ascomata visible on lesion surface. D.Brunneosphaerella protearum (CBS H-20335). E.Brunneosphaerella nitidae (holotype CBS H-20334). F–H. Vertical sections through ascomata showing wall structure. F.Brunneosphaerella jonkershoekensis (holotype PREM 59447). G, H.Brunneosphaerella protearum (CBS H-20335). I–M. Asci. I.Brunneosphaerella jonkershoekensis (holotype PREM 59447). J, K.Brunneosphaerella nitidae (holotype CBS H-20334). L, M.Brunneosphaerella protearum (CBS H-20335). N–Q. Ascospores. N, O.Brunneosphaerella jonkershoekensis (holotype PREM 59447). P.Brunneosphaerella nitidae (holotype CBS H-20334). Q.Brunneosphaerella protearum (CBS H-20335). R, S. Germinating ascospores. R.Brunneosphaerella nitidae (holotype CBS H-20334). S.Brunneosphaerella protearum (CBS H-20335). Scale bars: G = 75 μm; F, I = 50 μm; H, J–M, P–S = 10 μm; N, O = 5 μm. Pictures A, B, D, F–I, L–O, Q, S taken from Crous et al. (2009b); C, E, J, K, P, R from Crous et al. (2011).

Classification: Dothideomycetes, Dothideomycetidae, Capnodiales, Mycosphaerellaceae.



Type species: Brunneosphaerella protearum (Syd. & P. Syd.) Crous, basionym: Leptosphaeria protearum Syd. & P. Syd. Epitype and ex-epitype strain designated by Crous et al. (2011): CBS H-20335, CBS 130597 = CPC 16338.



DNA barcodes (genus): LSU, ITS.



DNA barcodes (species): chs, rpb2, tef1. Table 3.



Table 3.

DNA barcodes of accepted Brunneosphaerella spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	chs	rpb2	tef1
Brunneosphaerella jonkershoekensis	CPC 13902ET	JN712439	JN712609	MF951441	JN712571	Crous et al., 2011, Videira et al., 2017
B. nitidae	CBS 130595T	GU214625	JN712619	MF951442	JN712581	Crous et al., 2009b, Crous et al., 2011, Videira et al., 2017
B. protearum	CBS 130597ET	GU214626	JN712620	MF951443	JN712582	Crous et al., 2009b, Crous et al., 2011, Videira et al., 2017
B. roupeliae	CBS 144602T	MK539950	–	MK540080	–	Present study

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; CPC: Culture collection of Pedro Crous, housed at the Westerdijk Fungal Biodiversity Institute. ^T and ^ET indicate ex-type and ex-epitype strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; chs: partial chitin synthase-1 gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene.

Ascomata amphigenous, immersed to semi-immersed, black, single, gregarious, substomatal, pyriform or globose with a papillate, periphysate ostiole; ascomatal wall consisting of three strata of slightly compressed textura angularis, an outer stratum of dark brown, thick-walled cells, becoming paler in the central stratum, and hyaline, thin-walled in the inner stratum. Pseudoparaphyses absent. Asci clavate to cylindro-clavate, often curved, tapering to a pedicel, narrowing slightly to a rounded apex with an indistinct ocular chamber, 8-spored, bitunicate with fissitunicate dehiscence. Ascospores biseriate, fusiform, broader at the apical end, initially hyaline and 1-septate, becoming yellow-brown and 3-septate at maturity, slightly constricted at median to supra-median septum (adapted from Crous et al. 2009b).



Culture characteristics: Colonies on OA spreading, flat, with sparse to moderate aerial mycelium, lobate and smooth, rarely feathery, margins. On OA surface pale luteous, smoke grey with submerged iron-grey margins, or olivaceous grey with iron-grey, pale olivaceous grey and smoke grey patches. On PDA surface olivaceous grey, sometimes with pale olivaceous grey to smoke grey patches, or smoke grey with iron-grey margins; reverse iron-grey. On MEA surface pale olivaceous grey, smoke grey, dirty white with patches of smoke grey, or smoke grey with dirty white and olivaceous grey patches and submerged iron-grey margins; reverse iron-grey or olivaceous grey.



Optimal media and cultivation conditions: MEA, OA, PDA and SNA at 25 °C under near-ultraviolet light to promote sporulation.



Distribution: Africa, mainly reported from South Africa. Also reported from Pacific Islands (Hawaii) and Europe (Portugal and Spain).



Hosts: Protea spp. (Proteaceae).



Disease symptoms: Leaf spots and Brunneosphaerella leaf blight.



Notes: Brunneosphaerella was introduced by Crous et al. (2009b) to accommodate Leptosphaeria protearum, which is a major leaf spot and blight pathogen of Protea spp. causing severe losses in plantations of South African Protea spp. wherever they are cultivated. Morphologically, Brunneosphaerella is distinct from Leptosphaeria in that ascospores are always brown at maturity, and asexual morphs have brown, percurrently proliferating conidiogenous cells. A new species isolated from leaves of Protea repens in South Africa, B. jonkershoekensis, was included in the genus when it was introduced (Crous et al. 2009b). This species appears to be a serious pathogen of Pr. repens in the Western Cape Province of South Africa. Subsequently, Crous et al. (2011) described the third species known from the genus, B. nitidae. This was isolated from the same area as B. jonkershoekensis, but B. nitidae was isolated from leaves of Pr. nitida, causing leaf spots on this host. Thus, the genus comprises four species, all of which were isolated from species of Protea in South Africa. The ITS sequences of the four species are highly similar. However, these can be easily delimited based on the chs, rpb2 and tef1 sequences.



References: Crous et al., 2009b, Crous et al., 2011, Videira et al., 2017 (morphology and phylogeny).



Brunneosphaerella roupeliae Crous, sp. nov. MycoBank MB829609. Fig. 19.



Fig. 19.

Brunneosphaerella roupeliae (ex-type CBS 144602). A. Close-up of leaf spot with ascomata. B, C. Asci with ascospores. D. Germinating ascospores. Scale bars = 10 μm.

Etymology: Name refers to Protea roupeliae, the host species from which it was collected.



Leaf spots amphigenous, sub-circular, 5–20 mm diam, medium brown, with raised, dark brown border. Ascomata pseudothecial, amphigenous, black, immersed to erumpent, globose, to 250 μm diam, with apical ostiole; ascomatal wall of 2–3 layers of brown cells of textura angularis. Asci aparaphysate, fasciculate, bitunicate, subsessile, ellipsoid-fusoid, straight to slightly curved, 8-spored, 65–110 × 11–15 μm. Ascospores bi- to triseriate, overlapping, guttulate, thick-walled, straight to slightly curved, obovoid with obtuse ends, widest in middle of apical cell, 3-septate, constricted at median septum, tapering towards both ends, but more prominently towards lower end, (19–)22–23(–25) × 5(–6) μm. Ascospores germinating from both ends, becoming brown and verruculose, constricted at primary septum, with germ tubes parallel to the long axis, ascospore becoming 7–9 μm diam.



Culture characteristics: Colonies erumpent, spreading, with moderate aerial mycelium, and even, lobate margins, reaching 10 mm diam after 2 wk at 25 °C. On MEA surface pale olivaceous grey, reverse olivaceous grey; on PDA surface and reverse olivaceous grey, and on OA surface pale luteous.



Typus: South Africa, KwaZulu-Natal Province, Drakensberg, Monks Cowl, on leaves of Protea roupeliae (Proteaceae), 18 Jan. 2010, A. Wood, HPC 1522 (holotype CBS H-23847, culture ex-type CPC 32914 = CBS 144602).



Notes: Brunneosphaerella roupeliae was isolated from the same host genus in South Africa as the other three species of the genus, Protea. The ITS and LSU sequences located this species in the genus Brunneosphaerella since both sequences showed more than 99 % of nucleotide similarity with the ex-type strains of the other three species. The rpb2 sequence showed a nucleotide similarity of 95.86 % with the ex-epitype strain of B. protearum, 95.45 % with the ex-epitype strain of B. jonkershoekensis, and 94.5 % with the ex-type strain of B. nitidae. The tef1 sequence showed a nucleotide similarity of 95.66 % with the ex-epitype strain of B. protearum and the ex-type strain of B. nitidae, and 94.44 % with the epitype strain of B. jonkershoekensis. Brunneosphaerella roupeliae produces the shortest ascospores of the genus [(19–)22–23(–25) μm in B. roupeliae vs. (25–)27–34(–37) μm in B. jonkershoekensis vs. (20–)24–28(–30) μm in B. nitidae vs. (20–)23–26(–30) μm in B. protearum].



Authors: P.W. Crous, J.Z. Groenewald & Y. Marin-Felix



Elsinoe Racib., Parasit. Alg. Pilze Java's (Jakarta) 1: 14. 1900. Fig. 20, Fig. 21.

Fig. 20.

Disease symptoms of Elsinoe spp. A.Elsinoe ampelina on Vitis vinifera. B.Elsinoe asclepiadea on Asclepias mellodora. C.Elsinoe bidentis on Bidens segetum. D.Elsinoe erythrinae on Erythrina sp. E.Elsinoe eucalypticola on Eucalyptus sp. F.Elsinoe fawcettii on Citrus sp. G.Elsinoe freyliniae on Freylinia lanceolata. H.Elsinoe perseae on Persea americana. I.Elsinoe othonnae on Othonna quinquedentata. J.Elsinoe poinsettiae on Euphorbia sp. K.Elsinoe punicae on Punica granatum. L.Elsinoe terminaliae on Terminalia catappa. Pictures taken from Fan et al. (2017).

Fig. 21.

Elsinoe spp. A–J. Sexual morph. A. Subcutilar ascoma of Elsinoe fecunda. B–D. Asci. B.Elsinoe eucalypticola (ex-type CBS 124765). C, D.Elsinoe fecunda (holotype, PREM 56503). E–J. Ascospores. E–H.Elsinoe eucalypticola (ex-type CBS 124765). I, J.Elsinoe fecunda. K–P. Asexual morph. K, L. Conidiophores. K.Elsinoe asclepiadea (ex-type CPC 18544). L.Elsinoe othonnae (ex-type CBS 139910). M–P. Conidia. M.Elsinoe asclepiadea (ex-type CPC 18544). N.Elsinoe erythrinae (ex-epitype CPC 18542). O.Elsinoe tectificae (ex-type CBS 124777). P.Elsinoe othonnae (ex-type CBS 139910). Scale bars: A = 100 μm; B–D, K–U = 10 μm; E–J = 5 μm; C applies to C and B; J applies I and J. Pictures taken from Fan et al. (2017).

Synonyms: Sphaceloma de Bary, Ann. Oenol. 4: 165. 1874.

Manginia Viala & Pacottet, C. r. hebd. Séanc. Acad. Sci., Paris 139: 88. 1904.

Melanobasidium Maubl., Bull. Soc. mycol. Fr. 22: 69. 1906.

Plectodiscella Woron., Mykol. Zentbl. 4: 232. 1914.

Isotexis Syd., in Sydow & Petrak, Annls mycol. 29: 261. 1931.

Melanobasis Clem. & Shear, Gen. fung., Edn 2 (Minneapolis): 224. 1931.

Melanodochium Syd., Annls mycol. 36: 310. 1938.

Bitancourtia Thirum. & Jenkins, Mycologia 45: 781. 1953.

Kurosawaia Hara, List of Japanese Fungi, 4^th Edn: 172. 1954.

Uleomycina Petr., Sydowia 8: 74. 1954.

Melanophora Arx, Verh. K. ned. Akad. Wet., tweede sect. 51: 43. 1957.



Classification: Dothideomycetes, Dothideomycetidae, Myriangiales, Elsinoaceae.



Type species: Elsinoe canavaliae Racib. Type or reference material not available.



DNA barcode (genus): LSU.



DNA barcodes (species): ITS, rpb2, tef1. Table 4. Fig. 22.



Table 4.

DNA barcodes of accepted Elsinoe spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	LSU	rpb2	tef1
Elsinoe abutilonis	CBS 510.50T	KX887185	KX886949	KX887068	KX886831	Fan et al. (2017)
E. ampelina	CBS 208.25	KX887186	KX886950	KX887069	KX886832	Fan et al. (2017)
E. anacardii	CBS 470.62T	KX887189	KX886953	KX887072	KX886835	Fan et al. (2017)
E. annonae	CBS 228.64	KX887190	KX886954	KX887073	KX886836	Fan et al. (2017)
E. arachidis	CBS 511.50T	KX887191	KX886955	KX887074	KX886837	Fan et al. (2017)
E. arrudai	CBS 220.50T	KX887194	KX886958	KX887077	KX886840	Fan et al. (2017)
E. asclepiadea	CBS 141937T	KX887195	KX886959	KX887078	KX886841	Fan et al. (2017)
E. australis	CBS 314.32ET	KX887198	KX886962	KX887081	KX886844	Fan et al. (2017)
E. banksiae	STE-U 2678T	AF227197	–	–	–	Swart et al. (2001)
E. banksiicola	CBS 113734T	KX887199	KX886963	KX887082	KX886845	Fan et al. (2017)
E. barleriicola	CBS 471.62T	KX887200	KX886964	KX887083	KX886846	Fan et al. (2017)
E. bidentis	CBS 512.50T	KX887201	KX886965	KX887084	KX886847	Fan et al. (2017)
E. brasiliensis	CPC 18528ET	KX887204	–	KX887087	KX886850	Fan et al. (2017)
E. caleae	CBS 221.50T	KX887205	KX886968	KX887088	KX886851	Fan et al. (2017)
E. centrolobii	CBS 222.50T	KX887206	KX886969	KX887089	KX886852	Fan et al. (2017)
E. citricola	CPC 18535T	KX887207	KX886970	KX887090	KX886853	Fan et al. (2017)
E. coryli	CBS 275.76T	KX887209	KX886972	KX887092	KX886855	Fan et al. (2017)
E. diospyri	CBS 223.50T	KX887210	KX886973	KX887093	KX886856	Fan et al. (2017)
E. eelemani	DAR 83016T	KX372292	–	KX398204	KX398203	Crous et al. (2016a)
E. embeliae	CBS 472.62T	KX887211	KX886974	–	KX886857	Fan et al. (2017)
E. erythrinae	CPC 18542ET	KX887214	KX886977	KX887096	KX886860	Fan et al. (2017)
E. eucalypticola	CBS 124765T	KX887215	KX886978	KX887097	KX886861	Fan et al. (2017)
E. eucalyptorum	CBS 120084T	KX887216	KX886979	KX887098	KX886862	Fan et al. (2017)
E. euphorbiae	CBS 401.63T	KX887217	KX886980	KX887099	KX886863	Fan et al. (2017)
E. fagarae	CBS 514.50T	KX887218	KX886981	KX887100	KX886864	Fan et al. (2017)
E. fawcettii	CBS 139.25T	KX887219	KX886982	KX887101	KX886865	Fan et al. (2017)
E. fici	CBS 515.50	KX887223	KX886986	KX887105	KX886869	Fan et al. (2017)
E. fici-caricae	CBS 473.62T	KX887224	KX886987	KX887106	KX886870	Fan et al. (2017)
E. flacourtiae	CBS 474.62T	KX887225	KX886988	KX887107	KX886871	Fan et al. (2017)
E. freyliniae	CBS 128204T	KX887226	KX886989	KX887108	KX886872	Fan et al. (2017)
E. genipae	CBS 342.39T	KX887227	KX886990	KX887109	KX886873	Fan et al. (2017)
E. genipae-americanae	CBS 516.50T	KX887228	KX886991	KX887110	KX886874	Fan et al. (2017)
E. glycines	CBS 389.64ET	KX887229	KX886992	KX887111	KX886875	Fan et al. (2017)
E. hederae	CBS 517.50T	KX887231	KX886994	KX887113	KX886877	Fan et al. (2017)
E. ichnocarpi	CBS 475.62T	KX887232	KX886995	KX887114	KX886878	Fan et al. (2017)
E. jasminae	CBS 224.50T	KX887233	KX886996	KX887115	KX886879	Fan et al. (2017)
E. jasminicola	CBS 212.63T	KX887234	KX886997	–	KX886880	Fan et al. (2017)
E. krugii	CPC 18531ET	KX887235	KX886998	KX887116	KX886881	Fan et al. (2017)
E. lagoa-santensis	CBS 518.50T	KX887239	KX887002	KX887120	KX886885	Fan et al. (2017)
E. ledi	CBS 167.33ET	KX887240	KX887003	KX887121	KX886886	Fan et al. (2017)
E. lepagei	CBS 225.50T	KX887241	KX887004	KX887122	–	Fan et al. (2017)
E. leucopogonis	CBS 144439T	MH327822	MH327858	MH327885	MH327897	Crous et al. (2018)
E. leucospermi	CBS 111207T	KX887242	KX887005	KX887123	KX886887	Fan et al. (2017)
E. lippiae	CBS 166.40T	KX887248	KX887011	KX887129	KX886893	Fan et al. (2017)
E. mangiferae	CBS 226.50T	KX887249	KX887012	KX887130	KX886894	Fan et al. (2017)
E. mattiroloanum	CBS 287.64	KX887250	KX887013	KX887131	KX886895	Fan et al. (2017)
E. menthae	CBS 322.37ET	KX887253	KX887016	KX887134	KX886898	Fan et al. (2017)
E. mimosae	CPC 19478ET	KX887255	KX887018	KX887136	KX886900	Fan et al. (2017)
E. oleae	CBS 227.59T	KX887256	KX887019	KX887137	KX886901	Fan et al. (2017)
E. othonnae	CBS 139910T	KR476726	–	MK540083	–	Crous et al. (2015c), present study
E. perseae	CBS 406.34T	KX887258	KX887021	KX887139	KX886903	Fan et al. (2017)
E. phaseoli	CBS 165.31T	KX887263	KX887026	KX887144	KX886908	Fan et al. (2017)
E. picconiae	CBS 145026T	MK539951	MK540022	MK540081	MK540164	Present study
E. piri	CBS 163.29	KX887267	KX887030	KX887148	KX886912	Fan et al. (2017)
E. pitangae	CBS 227.50T	KX887269	KX887032	KX887150	KX886914	Fan et al. (2017)
E. poinsettiae	CBS 109333	KX887270	KX887033	KX887151	KX886915	Fan et al. (2017)
E. pongamiae	CBS 402.63ET	KX887272	KX887035	KX887153	KX886917	Fan et al. (2017)
E. populi	CBS 289.64	KX887273	KX887036	KX887154	KX886918	Fan et al. (2017)
E. preissianae	CBS 142129T	KY173406	KY173498	–	–	Crous et al. (2016a)
E. proteae	STE-U 1349T	AF097578	–	–	–	Swart et al. (2001)
E. protearum	CBS 113618T	KX887275	KX887038	KX887156	KX886920	Fan et al. (2017)
E. punicae	CPC 19968	KX887276	KX887039	KX887157	KX886921	Fan et al. (2017)
E. quercus-ilicis	CBS 232.61T	KX887277	KX887040	–	KX886922	Fan et al. (2017)
E. randii	CBS 170.38IsoT	KX887278	KX887041	KX887158	KX886923	Fan et al. (2017)
E. rhois	CBS 519.50T	KX887280	KX887043	KX887160	KX886925	Fan et al. (2017)
E. ricini	CBS 403.63	KX887281	KX887044	KX887161	KX886926	Fan et al. (2017)
E. rosarum	CBS 212.33ET	KX887283	KX887046	KX887163	KX886928	Fan et al. (2017)
E. salicina	CPC 17824T	KX887286	KX887049	KX887166	KX886931	Fan et al. (2017)
E. semecarpi	CBS 477.62T	KX887287	KX887050	KX887167	KX886932	Fan et al. (2017)
E. sesseae	CPC 18549	KX887288	KX887051	KX887168	KX886933	Fan et al. (2017)
E. sicula	CBS 398.59T	KX887289	KX887052	KX887169	KX886934	Fan et al. (2017)
E. solidaginis	CBS 191.37ET	KX887290	KX887053	KX887170	KX886935	Fan et al. (2017)
E. tectificae	CBS 124777T	KX887292	KX887055	KX887172	KX886937	Fan et al. (2017)
E. terminaliae	CBS 343.39ET	KX887293	KX887056	KX887173	–	Fan et al. (2017)
E. theae	CBS 228.50T	KX887295	KX887058	KX887175	KX886939	Fan et al. (2017)
E. tiliae	CBS 350.73	KX887296	KX887059	KX887176	KX886940	Fan et al. (2017)
E. veneta	CBS 164.29ET	KX887297	KX887060	KX887177	KX886941	Fan et al. (2017)
E. verbenae	CPC 18561ET	KX887298	KX887061	KX887178	KX886942	Fan et al. (2017)
E. veronicae	CBS 145362T	MK539952	MK540023	MK540082	–	Present study
E. violae	CBS 336.35T	KX887302	KX887065	KX887182	KX886946	Fan et al. (2017)
E. zizyphi	CBS 378.62T	KX887303	KX887066	KX887183	KX886947	Fan et al. (2017)

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; CPC: Culture collection of Pedro Crous, housed at Westerdijk Fungal Biodiversity Institute; DAR: Plant Pathology Herbarium, New South Wales, Australia; STE-U: Department of Plant Pathology, Stellenbosch University, South Africa. ^{T, ET} and ^IsoT indicate ex-type, ex-epitype and ex-isotype strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; LSU: partial large subunit (28S) nrRNA gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene.

Fig. 22.

RAxML phylogram obtained from the combined ITS (609 bp), LSU (741 bp), rpb2 (747 bp) and tef1 (422 bp) sequence alignment of all accepted species of Elsinoe. The tree was rooted to Myriangium hispanicum CBS 247.33. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 % are shown at the nodes. GenBank accession numbers are listed in Table 4. ^{T, ET} and ^IsoT indicate ex-type, ex-epitype and ex-isotype strains, respectively. TreeBASE: S23834.

Ascostromata solitary, aggregated, or gregarious, wart-like, or as small distinctively coloured elevations, or pulvinate, immersed to semi-immersed, globose to subglobose, white, pale yellow or brown, soft, multi-loculate, locules scattered in upper part of ascostromata; ascostromatal wall composed of pseudoparenchymatous cells of textura globulosa to textura angularis; locules with few to numerous asci inside each locule, ostiolate; ostiole minute. Periphyses absent. Asci 8-spored, bitunicate, fissitunicate, saccate to globose, with a minute pedicel, and ocular chamber. Ascospores irregularly arranged, oblong or fusiform with slightly acutely rounded ends, with 2–3 transverse septa, hyaline, smooth-walled, lacking a sheath. Acervuli or sporodochia subepidermal, pseudoparenchymatous. Conidiophores hyaline to pale brown, polyphialidic. Conidiogenous cells formed directly from the upper cells of the pseudoparenchyma, mono- to polyphialidic, integrated or discrete, determinate, hyaline to pale brown, without visible periclinal thickening. Conidia hyaline, smooth-walled, aseptate, ellipsoidal, guttulate (adapted from Fan et al. 2017).



Culture characteristics: Colonies on MEA, slow growing, raised, irregular, erumpent, folded or cerebriform, smooth and irregular margins, with sparse to moderate white to grey aerial mycelium. On MEA, surface white to pale luteous, cinnamon, sepia, apricot, saffron with or without purplish grey in centre, brown with apricot margins, rosy buff in centre with cinnamon margins, livid red, scarlet red with diffuse red pigment in agar, or iron-grey; reverse umber, ochreous, iron-grey, dark vinaceous, or centre scarlet and orange with cinnamon margins.



Optimal media and cultivation conditions: MEA, OA, PDA, SNA and WA at 22 °C under near-ultraviolet light (12 h light, 12 h dark).



Distribution: Worldwide.



Hosts: Wide range of hosts, including some economically important crops such as avocado, cassava, citrus, grapevines, ornamentals such as poinsettias, field crops and woody hosts.



Disease symptoms: Scab, leaf and fruit spot and anthracnose disease.



Notes: Elsinoe comprises plant pathogenic species that cause scab and spot anthracnose on a wide range of hosts, including some economically important crops and ornamentals. The disease symptoms that these species produce are easily recognisable, being known as “signature-bearing diseases”, for the cork-like appearance of older infected tissues with scab-like appearance. Also, these can produce other disease symptoms often called anthracnose, as in the case of infected grapevines (Barrus and Horsfall, 1928, Jenkins, 1947, Farr et al., 1989, Pan, 1994, Phillips, 1994, Gottwald, 1995). However, the use of this name is confusing since it is used much broader to include diseases caused by Colletotrichum. Although many species of Elsinoe causing scab disease have been described, only few of them cause important diseases (Holliday 1980), having the main impact on the appearance of the harvested product and its market acceptability rather than on crop productivity (Swart et al. 2001). Species of Elsinoe seem to be host-specific since 77 of the 81 species accepted in the present study occur on only one host species or genus.

 Elsinoe and its asexual morph, Sphaceloma, were recently reviewed by Fan et al. (2017). In that study, 26 new combinations were proposed for the species originally placed in Sphaceloma. Moreover, eight new species were introduced and 13 epitypes were designated. Based on phylogenetic data, Fan et al. (2017) accepted 75 species in the genus. However, E. banksiae, which was described by Swart et al. (2001), and three species described by Crous et al. (2016a), i.e. E. eelemani, E. eucalyptigena and E. preissianae, were not included in that study. Our phylogenetic analysis corroborated the placement of these species in the main well-supported clade representing the genus Elsinoe, except for E. eucalyptigena, whose placement remains unknown and, therefore it is not considered an accepted species of Elsinoe in the present study. Moreover, another three new species have been subsequently described by Crous et al. (2018), i.e. E. banksiigena, E. elaeocarpi and E. leucopogonis. However, in our phylogenetic analysis, the two first species were not located in the Elsinoe s. str. clade, and are thus excluded from the genus at present. Therefore, hitherto a total of 79 species are accepted, plus the new species described in the present study. Unfortunately, there are no cultures and molecular data of the type species of the genus, E. canavaliae, which needs to be epitypified in order to clarify its phylogenetic position.



References: Fan et al. 2017 (morphology and phylogeny).



Elsinoe picconiae Crous, sp. nov. MycoBank MB829611. Fig. 23.



Fig. 23.

Elsinoe picconiae (ex-type CBS 145026). A. Colony on OA. B, C. Conidiogenous cells. D. Conidia. Scale bars = 10 μm.

Etymology: Name refers to Picconia, the host from which this fungus was collected.



Conidiomata sporodochial or acervular on leaves, medium brown, up to 250 μm diam; conidiomatal wall composed of textura angularis. Conidiophores subcylindrical to doliiform, hyaline to pale brown, smooth-walled, 0–1-septate, unbranched, 10–15 × 3–4 μm. Conidiogenous cells polyphialidic, hyaline, smooth-walled, subcylindrical to doliiform, 5–8 × 3–4 μm. Conidia hyaline, aseptate, ellipsoid, apex obtuse, base truncate, (4–)5–6(–7) × (2–)2.5 μm.



Culture characteristics: Colonies erumpent, spreading, with sparse aerial mycelium, folded surface, and smooth, lobate margins, reaching 7 mm diam after 2 wk at 25 °C. On MEA surface rust, reverse sienna; on PDA surface coral, reverse bay; on OA surface scarlet with diffuse scarlet pigment.



Typus: Spain, Tenerife, Los Silos, leaf of Picconia excelsa (Oleaceae), 12 Mar. 2017, A. van Iperen, HPC 2063 (holotype CBS H-23848, culture ex-type CBS 145026 = CPC 33648).



Notes: Elsinoe picconiae is related to E. freyliniae, E. oleae and E. salicina. However, E. picconiae can be easily distinguished by its narrower conidia [(2–)2.5 μm vs. (2.5–)3–4 μm in E. freyliniae, 3–6 μm in E. oleae, and (2.5–)3–4.5(–5) μm in E. salicina]. Moreover, E. picconiae is the first species of the genus isolated from Picconia excelsa.



Elsinoe veronicae Crous, Thangavel & Y. Marín, sp. nov. MycoBank MB829610. Fig. 24.



Fig. 24.

Elsinoe veronicae (ex-type CBS 145362). A. Colony on OA. B, C. Conidiogenous cells. D. Conidia. Scale bars = 10 μm.

Etymology: Name refers to Veronica, the host from which this fungus was collected.



Conidiomata sporodochial, erumpent, 80–200 μm diam, based on a pale brown stroma, giving rise to densely aggregated conidiophores. Conidiophores hyaline to pale brown, smooth-walled, subcylindrical, 1–2-septate, 15–30 × 2.5–3.5 μm, unbranched or branched above. Conidiogenous cells integrated, subcylindrical, hyaline, smooth-walled, 7–10 × 2.5–3.5 μm, polyphialidic. Conidia solitary, aggregating in mucoid mass, aseptate, hyaline, smooth-walled, guttulate, ellipsoid, apex subobtuse, tapering at base to truncate hilum, (4–)5–5.5(–6.5) × 2.5(–3) μm.



Culture characteristics: Colonies erumpent, spreading, surface folded with moderate aerial mycelium, and even, lobate margins, reaching 25 mm diam after 2 wk. On MEA surface brick, reverse cinnamon; on PDA surface brick to scarlet, reverse brick in centre, scarlet in outer region; on OA surface scarlet with diffuse scarlet pigment.



Typus: New Zealand, Auckland, St. John, Morrin Road, on Veronica sp. (Scrophulariaceae), 2013, R. Thangavel (holotype CBS H-23865, culture ex-type CBS 145362 = CPC 34137 = T17_00408D).



Notes: Elsinoe veronicae is closely related to E. othonnae. Although the ITS sequences of both species showed more than 99 % nucleotide similarity, the rpb2 sequences showed only 96.95 % similarity. Morphologically, these are also similar differing mainly in their conidial size [(4–)5–5.5(–6.5) × 2.5(–3) μm in E. veronicae vs. (5–)6–7 × (2.5–)3(–4) μm in E. othonnae]. Moreover, E. veronicae was found on Veronica (Scrophulariaceae) in New Zealand, while E. othonnae has only been reported on Othonna (Asteraceae) in South Africa (Crous et al. 2015c).



Authors: Y. Marin-Felix, R. Thangavel & P.W. Crous



Exserohilum K.J. Leonard & Suggs, Mycologia 66: 290. 1974. Fig. 25.

Fig. 25.

Exserohilum spp. A–E. Sexual morph. A. Ascomata of Exserohilum minor (ex-isotype IMI 294530). B, C. Asci of Exserohilum minor (ex-isotype IMI 294530). D, E. Ascospores. D.Exserohilum minor (ex-isotype IMI 294530). E.Exserohilum khartoumensis (ex-isotype CBS 132708). F–AA. Asexual morph. F–N. Conidiophores and conidia. F, L.Exserohilum oryzicola (ex-isotype CBS 502.90). G.Exserohilum turcicum (ex-epitype CBS 690.71). H, N.Exserohilum holmii (ex-isotype CBS 413.65 and BRIP 12679). I. Exserohilum pedicellatum (CBS 375.76). J, M.Exserohilum rostratum (CBS 120380, CBS 196.29). K.Exserohilum monoceras (CBS 198.29). O. Detail of the conidial hilum of Exserohilum oryzicola (ex-isotype CBS 502.90). P–AA. Conidia. P, Q, Z, AA.Exserohilum rostratum (CBS 128054, CBS 120380, BRIP 11422). R.Exserohilum holmii (BRIP 12679). S.Exserohilum pedicellatum (BRIP 12040). T, U.Exserohilum turcicum (BPI 431157 holotype). V.Exserohilum oryzicola (BRIP 16229). W.Exserohilum protrudens (BRIP 14816). X.Exserohilum corniculatum (ex-type BRIP 11426). Y.Exserohilum neoregelia (CBS 132833). Scale bars A = 50 μm; others = 10 μm; C applies to B and C; E applies to D and E. Pictures taken from Hernández-Restrepo et al. (2018).

Synonyms: Setosphaeria K.J. Leonard & Suggs, Mycologia 66: 294. 1974.

Luttrellia Khokhr. & Gornostaĭ (as ‘Lutrellia’; non Luttrellia Shearer), Vodorosli, Griby i Mkhi Dal’nego Vostoka [Algae, Fungi and Mosses of the Soviet Far-East] (Vladivostok): 80. 1978.



Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Pleosporaceae.



Type species: Exserohilum turcicum (Pass.) K.J. Leonard & Suggs, basionym: Helminthosporium turcicum Pass. Ex-epitype and ex-epitype strain designated by Hernández-Restrepo et al. (2018): CBS H-23323, CBS 690.71.



DNA barcodes (genus): LSU, ITS.



DNA barcodes (species): ITS, gapdh, rpb2. Table 5. Fig. 26.



Table 5.

DNA barcodes of accepted Exserohilum spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	LSU	gapdh	rpb2
Exserohilum corniculatum	BRIP 11426T	LT837453	LT883391	LT883533	LT852480	Hernández-Restrepo et al. (2018)
Ex. holmii	CBS 413.65IsoT	LT837459	LT715621	LT715890	LT852489	Hernández-Restrepo et al. (2018)
Ex. khartoumensis	IMI 249194IsoT	LT837461	LT715619	LT715888	LT852490	Hernández-Restrepo et al. (2018)
Ex. minor	BRIP 14616T	LT837470	LT883403	LT883545	LT852502	Hernández-Restrepo et al. (2018)
Ex. monoceras	BRIP 12271A	LT837475	LT883406	LT883548	LT852507	Hernández-Restrepo et al. (2018)
Ex. neoregeliae	CBS 132832T	LT837476	LT715617	LT715886	LT852508	Hernández-Restrepo et al. (2018)
Ex. oryzicola	CBS 502.90IsoT	HF934949	HF934886	LT715878	HF934851	Amaradasa et al., 2014, Hernández-Restrepo et al., 2018
Ex. pedicellatum	CBS 322.64ET	KT265258	HF934889	LT715902	HF934854	Amaradasa et al., 2014, Chowdhary et al., 2015, Hernández-Restrepo et al., 2018
Ex. protrudens	BRIP 14814T	LT631308	LT715611	LT715880	LT715741	Hernández-Restrepo et al. (2018)
Ex. rostratum	CBS 325.87	KT265237	LT715629	LT715898	LT852492	Chowdhary et al., 2015, Hernández-Restrepo et al., 2018
Ex. turcicum	CBS 690.71ET	LT837487	LT883415	LT882581	–	Hernández-Restrepo et al. (2018)

¹BRIP: Queensland Plant Pathology Herbarium, Brisbane, Australia; CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; IMI: International Mycological Institute, CABI-Bioscience, Egham, Bakeham Lane, UK. ^{T, ET, IsoT} and ^A indicate ex-type, ex-epitype, ex-isotype and authentic strains.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; LSU: partial large subunit (28S) nrRNA gene; gapdh: partial glyceraldehyde-3-phosphate dehydrogenase gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene.

Fig. 26.

RAxML phylogram obtained from the combined ITS (793 bp), gapdh (578 bp) and rpb2 (860 bp) sequence alignment of all the accepted species of Exserohilum. The tree was rooted to Curvularia and Bipolaris. RAxML bootstrap support (BS) values above 70 % are shown in the nodes. GenBank accession numbers are indicated in Table 5. ^{T, ET, IsoT} and ^A indicate ex-type, ex-epitype, ex-isotype and authentic strains. TreeBASE: S23834.

Ascomata superficial, immersed or erumpent, globose to ellipsoid, unilocular, dark brown to black, with or without a neck, ostiolate, with simple rigid setae around the ostiolar apex and on the upper half of the ascoma where they are often mixed with hyaline, filiform, septate hyphae; ascomatal wall composed of pseudoparenchymatous cells, dark brown and thick-walled on the outside, but with more or less hyaline cells towards the inside, cells of textura angularis. Pseudoparaphyses filiform, hyaline, septate, branched, anastomosing. Asci arising from a basal cushion of thin-walled pseudoparenchymatous cells, bitunicate, 1–8-spored, cylindrical to cylindrical-clavate, short or moderately long-stalked, thick-walled, with an apical nasse and fissitunicate dehiscence. Ascospores fusoid, hyaline to pale brown, smooth-walled, 2–6 or rarely more transversely septate, constricted at the septa, surrounded by a hyaline mucilaginous sheath which often extends some distance beyond the ends of the spore. Conidiophores macronematous, mononematous, septate, cylindrical, olivaceous brown to brown, smooth-walled to verruculose, often geniculate above. Conidiogenous cells integrated, terminal and intercalary, sympodial, mono- or polytretic, cicatrised; conidiogenous nodes smooth to rough. Conidia fusiform, cylindrical or obclavate, straight to curved, multi-distoseptate, with a protruding hilum (adapted from Hernández-Restrepo et al. 2018).



Culture characteristics: Colonies on PDA brown or grey olivaceous to olivaceous black, sometimes white, pale grey, hairy, cottony to powdery, margins fimbriate.



Optimal media and cultivation conditions: Sterilised Zea mays leaves placed on 1.5 % WA or PDA at 25 °C under near-ultraviolet light (12 h light, 12 h dark) to induce sporulation.



Distribution: Worldwide.



Host: Mainly pathogens of grasses, but some also on non-grass hosts. Other substrates where they can be found include river sediments, soil, grains, plant debris, and humans. Exserohilum rostratum has been reported as a human pathogen.



Disease symptoms: In plants: leaf blight, leaf spots, melting out, root rot, and foot rot, among others. In humans: skin infections, keratitis, non-invasive allergies, invasive sinusitis, and disseminated infections.



Notes: Exserohilum is differentiated from the closely related Bipolaris, Curvularia and Pyrenophora by producing conidia with a protruding hilum (Leonard & Suggs 1974). Recently the taxonomy and phylogeny of Exserohilum has been revisited by Hernández-Restrepo et al. (2018). Based on morphological and molecular data 11 phylogenetic species are accepted (Fig. 26, Table 5). Three species were excluded from the genus, namely Ex. novae-zelandiae relocated to Sporidesmiella, and Ex. paspali and Ex. sorghicola to Curvularia, while another 15 species were retained in Exserohilum, although some were doubtful. Species in Exserohilum are morphologically very variable and a molecular analysis is required for a correct species identification.

 The type species of the genus, Ex. turcicum (= Helminthosporium turcicum), was described from Italy causing northern leaf blight of corn (Passerini, 1876, Saccardo, 1886). Other species attacking economically significant crops include Ex. pedicellatum, causing root rot on maize and brown lesions on wheat roots (Henry, 1924, Sivanesan, 1987), and Ex. rostratum, producing leaf spot on banana, maize and wheat, foot rot in wheat, damping off of sugarcane seedlings, blackening and seed germination failure in cereals (Drechsler, 1923, Leonard, 1976, Sivanesan, 1987, Lin et al., 2011).

 Previously, three different species, Ex. longirostratum, Ex. macginnisii and Ex. rostratum, were recognised as human pathogens (McGinnis et al., 1986, Padhye et al., 1986, de Hoog et al., 2000, da Cunha et al., 2012). However, a multi-locus phylogenetic analysis (Hernández-Restrepo et al. 2018) demonstrated that they are actually the same phylogenetic species. Exserohilum rostratum has been reported as an agent of phaeohyphomycosis and sometimes causing life-threatening infections in humans (McGinnis et al., 1986, Padhye et al., 1986, Aquino et al., 1995, Adler et al., 2006). This species was recently implicated in an outbreak of fungal meningitis associated with contaminated methylprednisolone in the USA (Kainer et al. 2012).



References: Drechsler, 1923, Drechsler, 1934, Luttrell, 1963, Leonard and Suggs, 1974, Sivanesan, 1987 (taxonomy, morphology and pathogenicity), Leonard 1976 (sexual/asexual connection), de Hoog et al., 2000, da Cunha et al., 2012 (human pathogens), Hernández-Restrepo et al. 2018 (morphology, phylogeny, review).



Author: M. Hernández-Restrepo



Neosetophoma Gruyter et al., Mycologia 102: 1075. 2010. Fig. 27.



Fig. 27.

Neosetophoma lunariae (ex-type CBS 141409). A. Conidiomata on OA. B. Conidiomata showing ostiolar region. C, D. Conidiogenous cells. E. Conidia. Scale bars = 10 μm; C applies to C and D. Pictures taken from Hernández-Restrepo et al. (2016a).

Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Phaeosphaeriaceae.



Type species: Neosetophoma samarorum (Desm.) Gruyter et al., basionym: Phoma samarorum Desm. Epitype and ex-epitype strain designated by Gruyter et al. (2010): CBS H-20319, CBS 138.96.



DNA barcode (genus): LSU. Fig. 28.



Fig. 28.

RAxML phylogram obtained from the combined ITS (626 bp) and LSU (852 bp) sequence alignment of members of the family Phaeosphaeriaceae. The tree was rooted to Coniothyrium glycines CBS 124141 and Coniothyrium sidae CBS 135108. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 %and Bayesian posterior probability scores above 0.95 are shown at the nodes. Numbers between parentheses correspond to GenBank accession numbers for ITS and LSU sequences, respectively. ^{T, ET, HT, IsoT, LT} and ^NT indicate ex-type, ex-epitype, holotype, ex-isotype, ex-lectotype and ex-neotype strains, respectively. TreeBASE: S23834.

DNA barcodes (species): ITS, rpb2, tef1, tub2. Table 6. Fig. 29.



Table 6.

DNA barcodes of accepted Neosetophoma spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	rpb2	tef1	tub2
Neosetophoma aseptata	CBS 145363T	MK539953	MK540084	–	–	Present study
Nph. clematidis	MFLUCC 13-0734T	KP744450	–	–	–	Liu et al. (2015)
Nph. garethjonesii	MFLUCC 14-0528T	KY496758	–	KY514402a	–	Tibpromma et al. (2017)
Nph. guiyangensis	GZCC 18-0111T	MH018134	–	–	–	Hyde et al. (2018)
Nph. iranianum	IBRC-M 30176T	MF684861	–	–	–	Karunarathna et al. (2017)
Nph. italica	MFLUCC 13-0388T	KP711356	–	–	–	Liu et al. (2015)
Nph. lunariae	CBS 141409T	KX306763	–	–	–	Hernández-Restrepo et al. (2016a)
Nph. phragmitis	CBS 145364T	MK539954	MK540085	MK540148b	–	Present study
Nph. poaceicola	MFLUCC 16-0886T	KY568986	–	–	–	Thambugala et al. (2017)
Nph. rosae	MFLUCC 15-1073T	MG828925	–	MG829218a	–	Wanasinghe et al. (2018)
Nph. rosarum	MFLUCC 17-0308T	MG828927	–	–	–	Wanasinghe et al. (2018)
Nph. rosigena	MFLUCC 17-0768T	MG828928	–	–	–	Wanasinghe et al. (2018)
Nph. samarorum	CBS 138.96ET	KF251160	KF252168	KF253119b	KF252655	Quaedvlieg et al. (2013)
Nph. sambuci	CBS 145365T	MK539955	MK540086	MK540149b	–	Present study
Nph. shoemakeri	MFLUCC 17-0780	MG844346	–	MG844352a	–	Hyde et al. (2018)
Nph. xingrensis	GZCC 18-0110T	MH018135	–	–	–	Hyde et al. (2018)

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; GZCC: Guizhou Academy of Agricultural Sciences Culture Collection, Guiyang, China; IBRC: Herbarium of the Plant bank, Iranian Biological Resource Center, Karaj, Iran; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Ria, Thailand. ^T and ^ET indicate ex-type and ex-epitype strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene. ^a and ^b in tef1 column indicate the primers used for sequencing: ^a: EF1-983F / EF1-2218R; ^b: EF1-728F / EF-2.

Fig. 29.

RAxML phylogram obtained from the combined ITS (585 bp), LSU (848 bp) and rpb2 (744 bp) sequence alignment of all accepted species of Neosetophoma. The tree was rooted to Phaeosphaeriopsis glaucopunctata MFLUCC 13-0265 and Phaeosphaeriopsis agavacearum CPC 29122. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 % and Bayesian posterior probability scores above 0.95 are shown at the nodes. GenBank accession numbers of LSU are listed in Fig. 28, and of the other loci in Table 6, Table 10. ^T and ^ET indicate ex-type and ex-epitype strains, respectively. TreeBASE: S23834.

Ascomata ostiolate, globose to subglobose, solitary to gregarious, dark brown to black, immersed to slightly erumpent or superficial, smooth; ascomatal wall composed of 2–4 layers of brown to reddish-brown or dark brown to black cells of textura angularis to textura prismatica. Hamathecium comprising numerous, septate, cellular or filamentous pseudoparaphyses, embedded in a hyaline gelatinous matrix. Asci 8-spored, bitunicate, fissitunicate, cylindrical to clavate, short pedicellate, with a furcate pedicel, apically rounded, with a minute or indistinct ocular chamber. Ascospores overlapping, 1–3-seriate, hyaline or subhyaline when young, becoming pale yellow, pale brown or yellowish brown to brown at maturity, 1–5-septate, straight to slightly curved, fusoid or narrowly fusoid, with rounded or acute ends, constricted or not at the septum, enlarged at the second cell below apex, guttulate, smooth-walled, without any mucilaginous sheath and appendages. Conidiomata pycnidial, solitary to confluent, immersed or superficial, globose to subglobose or irregular, with mycelial outgrowths, or confluent, unilocular, occasionally multi-locular, with papillate ostioles, sometimes developing long necks, honey, olivaceous, olivaceous black, pale brown, brown, dark brown, or black, with up to 10 layers of pseudoparenchymatal cells of textura angularis. Conidiophores reduced to conidiogenous cells. Conidiogenous cells phialidic, extending percurrently at apex, hyaline, doliiform to ampulliform, determinate, hyaline, smooth-walled. Conidia hyaline, slightly yellowish or pale brown, 0–3(–4)-septate, ellipsoidal, cylindrical, subcylindrical, fusiform, or tear-drop shape, straight to curved, usually attenuate at one end, or apex and base obtuse, or sometimes with bluntly rounded to truncate base, continuous or constricted at the septa, smooth-walled, often guttulate (asexual morph description adapted from Gruyter et al. 2010).



Culture characteristics: Colonies flat, with a moderate amount of aerial mycelium. On PDA surface fluffy, circular or irregular, margins entire or filiform, white, pale grey, grey, greenish grey, or mouse grey; reverse yellowish, yellowish grey, greyish white, grey olivaceous, or dark brown. On MEA pale grey to almost white, buff, or brown to dark brown; reverse dark brown, or buff with patches of grey olivaceous.



Optimal media and cultivation conditions: CMA, PDA, PNA and OA at 25 °C under continuous near-ultraviolet light to promote sporulation.



Distribution: Asia, Europe and North America.



Hosts: Pathogens or saprophytes found on a wide range of host including Cirsium arvense (Asteraceae), Clematis vitalba (Ranunculaceae), Iris germanica (Iridaceae), Lunaria annuna (Brassicaceae), Malva sp. (Malvaceae), Phlox paniculata (Polemoniaceae), Phragmites australis (Poaceae), Rosa canina (Rosaceae), Sambucus spp., Viburnum opulus (Caprifoliaceae), and Urtica dioica (Urticaceae). Also isolated from soil.



Disease symptoms: Leaf spots.



Notes: Neosetophoma was introduced by de Gruyter et al. (2010) to accommodate Phoma samarorum, which is a pathogen causing leaf spots of grasses. Subsequently, 12 new species have been added to this genus, all of which appear to be saprobes, except for Nph. iranianum, which was isolated from soil (Karunarathna et al. 2017), and Nph. lunariae, which is endophytic (Hernández-Restrepo et al. 2016a).

 This genus is characterised by globose to irregular conidiomata with papillate ostioles, and yellowish to brownish conidia usually attenuated at one end, less frequent with apex and base obtuse or with a bluntly rounded to truncate base. The sexual morph was observed for the first time by Tibpromma et al. (2017), when Nph. garethjonesii was introduced. Subsequently, four new species producing a sexual morph have been described, of which only one also produces the asexual morph, namely Nph. shoemakeri (Hyde et al. 2018).



References: de Gruyter et al., 2010, Quaedvlieg et al., 2013, Tibpromma et al., 2017, Hyde et al., 2018, Wanasinghe et al., 2018 (morphology and phylogeny).



Neosetophoma aseptata Crous, R.K. Schumach. & Y. Marín, sp. nov. MycoBank MB829639. Fig. 30.



Fig. 30.

Neosetophoma aseptata (ex-type CBS 145363). A. Conidiomata sporulating on OA. B, C. Conidiogenous cells. D. Conidia. Scale bars: A = 300 μm; others = 10 μm.

Etymology: Name refers to its aseptate conidia, which have never been observed in the other species of the genus.



Conidiomata solitary, brown, erumpent, globose, 250–350 μm diam with 1–3 ostioles; conidiomatal wall of 3–4 layers of brown cells of textura angularis. Conidiophores reduced to conidiogenous cells lining inner cavity, hyaline, smooth-walled, subcylindrical to ellipsoid, phialidic with minute collarette, 4–8 × 4–5 μm. Conidia solitary, aseptate, hyaline, smooth-walled, subcylindrical to ellipsoid, apex obtuse, base truncate, (3.5–)4–5 × (1.5–)2 μm.



Culture characteristics: Colonies flat, spreading, surface folded, with moderate aerial mycelium and even, lobate margins, reaching 50 mm diam after 2 wk. On MEA surface pale olivaceous grey, reverse umber with diffuse umber pigment; on PDA surface olivaceous grey, reverse umber with diffuse umber pigment; on OA surface saffron with patches of grey olivaceous.



Typus: Germany, near Berlin, moist meadow, on Viburnum opulus (Caprifoliaceae), 7 Jun. 2017, R.K. Schumacher, HPC 2131, RKS 123 (holotype CBS H-23866, culture ex-type CBS 145363 = CPC 33919).



Notes: Neosetophoma aseptata was located in a large, well-supported clade (96 % BS / 1 PP) comprising Nph. clematidis, Nph. iranianum, Nph. lunariae, Nph. rosae and Nph. shoemakeri. Neosetophoma aseptata can be easily distinguished by its aseptate conidia, being 1-septate in Nph. shoemakeri, 1–3-septate in Nph. iranianum and Nph. rosae, 3-septate in Nph. clematidis, and (1–)3(–4)-septate in Nph. lunariae. Moreover, Nph. aseptata produces the smallest conidia in the complex [(3.5–)4–5 × (1.5–)2 μm in Nph. aseptata vs. 4–6 × 2–4 μm in Nph. iranianum vs. 7.5–10.5 × 2.5–3 μm in Nph. shoemakeri vs. 8–14 × 1.5–3 μm in Nph. rosae vs. 11–15 × 2–4 μm in Nph. clematidis vs. (10–)14–17(–22) × (2.5–)3 μm in Nph. lunariae]. Neosetophoma clematidis produces the largest conidiomata in this complex, being up to 475 μm diam (up to 300 μm in Nph. aseptata and Nph. lunaria, up to 180 μm in Nph. shoemakeri, up to 130 μm in Nph. rosae, up to 120 μm in Nph. iranianum).

 Neosetophoma aseptata is the first species isolated from Viburnum. Neosetophoma samarorum and Nph. sambuci are reported in Sambucus spp., which is a member of the same family, Caprifoliaceae.



Neosetophoma phragmitis Crous, R.K. Schumach. & Y. Marín, sp. nov. MycoBank MB829640. Fig. 31.



Fig. 31.

Neosetophoma phragmitis (ex-type CBS 145364). A. Conidiomata sporulating on SNA. B, C. Conidiogenous cells. D. Conidia. Scale bars: A = 200 μm; others = 10 μm.

Etymology: Name refers to Phragmites, the host from which this fungus was collected.



Conidiomata solitary, pycnidial, brown, globose, 180–200 μm diam, neck papillate with central ostiole; conidiomatal wall of 3–4 layers of brown cells of textura angularis. Conidiophores reduced to conidiogenous cells lining inner cavity, hyaline, smooth-walled, ampulliform, 5–8 × 2.5–3 μm, proliferating percurrently at apex. Conidia solitary, pale brown, smooth-walled, aseptate, straight, apex obtuse, base truncate, (3–)4–5(–6) × 2 μm.



Culture characteristics: Colonies flat, spreading, with moderate aerial mycelium and feathery margins, covering dish in 2 wk. On MEA surface and reverse ochreous; on PDA surface and reverse hazel; on OA surface hazel.



Typus: Germany, near Berlin, on leaf sheath of Phragmites australis (Poaceae), 16 Apr. 2016, R.K. Schumacher, HPC 1178 (holotype CBS H-23867, culture ex-type CBS 145364 = CPC 30680).



Notes: In the phylogenetic analysis based on ITS, LSU and rpb2 sequences, Nph. phragmitis was located in an independent branch removed from the other species of the genus. This is the first species isolated from Phragmitis australis (Poaceae). Neosetophoma poaceicola is the only species that was reported before on a member of the Poaceae, being isolated from a grass host. However, both species are not related, and Nph. phragmitis only produces the asexual morph, while only the sexual morph was observed in Nph. poaceicola.



Neosetophoma sambuci Crous, R.K. Schumach. & Y. Marín, sp. nov. MycoBank MB829641. Fig. 32.



Fig. 32.

Neosetophoma sambuci (ex-type CBS 145365). A. Conidiomata sporulating on PNA. B. Conidioma on SNA showing papillate neck. C. Conidiogenous cells. D. Conidia. Scale bars: A, B = 200 μm; others = 10 μm.

Etymology: Name refers to the genus Sambucus, the host from which this fungus was collected.



Conidiomata solitary, erumpent, brown, pycnidial, globose, 150–200 μm diam, with central ostiole; conidiomatal wall of 3–4 layers of brown textura angularis. Conidiophores reduced to conidiogenous cells lining the inner cavity, hyaline, smooth-walled, ampulliform, phialidic, 4–6 × 3–4 μm. Conidia solitary, pale brown, smooth-walled, guttulate, subcylindrical, apex obtuse, base truncate, aseptate, becoming 1-septate and swollen (ellipsoid) with age, (5–)7–8(–10) × (2–)2.5(–3) μm.



Culture characteristics: Colonies flat, spreading, covering dish in 2 wk, with sparse to moderate aerial mycelium. On MEA surface ochreous, reverse umber; on PDA surface and reverse olivaceous grey; on OA surface ochreous.



Typus: Germany, near Berlin, on twig of Sambucus nigra (Caprifoliaceae), 11 Mar. 2016, R.K. Schumacher, HPC 1072 (holotype CBS H-23868, culture ex-type CBS 145365 = CPC 30357).



Notes: In the phylogenetic analysis based on ITS, LSU and rpb2 sequences, Nph. sambuci was located in a well-supported clade (97 % BS / 0.98 PP) together with Nph. garethjonesii, Nph. samarorum and Nph. rosigena. Neosetophoma garethjonesii can be easily distinguished from the other species by only producing a sexual morph. The other three species produce an asexual morph, and can be differentiated by the size of their conidia [4–16 × 1.5–3 μm in Nph. samarorum vs. (5–)7–8(–10) × (2–)2.5(–3) μm in Nph. sambuci vs. 4–6 × 1.5–2.5 μm in Nph. rosigena]. Moreover, conidia in Nph. sambuci are pale brown while in Nph. samarorum they are slightly yellowish and in Nph. rosigena they are olivaceous brown. Neosetophoma sambuci was isolated from twigs of Sambucus nigra (Caprifoliaceae). The only species previously reported on this host was Nph. samarorum.



Authors: Y. Marin-Felix & P.W. Crous



Neostagonospora Quaedvl. et al., Stud. Mycol. 75: 364. 2013. Fig. 33.



Fig. 33.

Neostagonospora spp. A, B. Conidioma forming in culture. A.Neostagonospora caricis (ex-type CBS 135092). B.Neostagonospora elegiae (ex-type CBS 135101). C–G. Conidiogenous cells. C, D.Neostagonospora caricis (ex-type CBS 135092). E–G.Neostagonospora elegiae (ex-type CBS 135101). H, I. Conidia. H.Neostagonospora caricis (ex-type CBS 135092). I.Neostagonospora elegiae (ex-type CBS 135101). Scale bars: B = 150 μm; all others = 10 μm; C applies to C and D. Pictures taken from Quaedvlieg et al. (2013).

Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Phaeosphaeriaceae.



Type species: Neostagonospora caricis Quaedvlieg et al. Holotype and ex-type strain: CBS H-21306, CBS 135092.



DNA barcode (genus): LSU. Fig. 28.



DNA barcodes (species): ITS, rpb2, tef1, tub2. Table 7. Fig. 34.



Table 7.

DNA barcodes of accepted Neostagonospora spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	rpb2	tef1	tub2
Neostagonospora arrhenatheri	MFLUCC 15-0464T	KX926417	–	MG520901a	–	Phookamsak et al., 2017, Thambugala et al., 2017
Nst. caricis	CBS 135092T	KF251163	KF252171	–	KF252658	Quaedvlieg et al. (2013)
Nst. elegiae	CBS 135101T	KF251164	KF252172	KF253122b	KF252659	Quaedvlieg et al. (2013)
Nst. phragmitis	MFLUCC 16-0493T	KX926416	–	MG520902a	–	Phookamsak et al. (2017), Thambugala et al. (2017)
Nst. sorghi	CBS 145366T	MK539956	MK540087	MK540150b	MK540168	Present study
Nst. spinificis	BCRC FU30120	KP676045	LC055104	–	–	Yang et al. (2016)

¹BCRC: Bioresource Collection and Research Centre, Taiwan; CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Ria, Thailand. ^T indicates ex-type strains.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene. ^a and ^b in tef1 column indicate the primers used for sequencing: ^a: EF1-983F / EF1-2218R, ^b: EF1-728F / EF-2.

Fig. 34.

RAxML phylogram obtained from the combined ITS (571 bp), LSU (847 bp), rpb2 (337 bp) and tub2 (304 bp) sequence alignment of all accepted species of Neostagonospora. The tree was rooted to Parastagonospora avenae CBS 289.69 and Parastagonospora nodorum CBS 110109. The novelty proposed in this study is indicated in bold. RAxML bootstrap support (BS) values above 70 % and Bayesian posterior probability scores above 0.95 are shown at the nodes. GenBank accession numbers of LSU are listed in Fig. 28, and of the other loci in Tables 7 and 9. ^T indicates ex-type strains. TreeBASE: S23834.

Conidiomata immersed, pycnidial, globose, exuding a pale luteous to creamy conidial mass; conidiomatal wall composed of 2–3 layers of pale brown cells of textura angularis. Conidiophores reduced to conidiogenous cells. Conidiogenous cells phialidic, hyaline, smooth-walled, aggregated, lining the inner cavity, ampulliform to doliiform, tapering at apex with prominent periclinal thickening. Conidia hyaline, smooth-walled, granular, thin-walled, narrowly fusoid-ellipsoidal to subcylindrical, apex subobtusely rounded, base truncate, widest in middle, aseptate or transversely euseptate, becoming constricted with age (adapted from Quaedvlieg et al. 2013).



Culture characteristics: Colonies flat, spreading, erumpent, circular or undulate, smooth to velvety, even margins, with sparse to moderate aerial mycelium. On PDA, surface dirty white, greyish sepia to isabelline; reverse pale white to pale pink, pale pink with white edge, luteous or olivaceous grey to pale olivaceous grey.



Optimal media and cultivation conditions: PDA and sterilised Carex leaves or Anthriscus stem placed on 1.5 % water agar at 25 °C under continuous near-ultraviolet light to promote sporulation.



Distribution: Africa (South Africa), Asia (Russia and Taiwan), Australia and Europe (Italy and the Netherlands).



Hosts: Arrhenatherum elatius, Phragmites australis, Sorghum halepense and Spinifex littoreus (Poaceae), Carex acutiformis (Cyperaceae) and Elegia cuspidata (Restionaceae).



Disease symptoms: Leaf spots.



Notes: Neostagonospora was introduced by Quaedvlieg et al. (2013) to accommodate two taxa associated with leaf spots on Carex acutiformis (Nst. caricis) and Elegia cuspidata (Nst. elegiae). However, its pathogenicity remains unclear since Koch’s postulates have not been completed. Subsequently, another foliicolous fungus was included in this genus, Nst. spinificis (Yang et al. 2016), associated with green tissues and leaf spots of Spinifex littoreus. The most recently introduced species are both saprobes on members of Poaceae: Nst. arrhenatheri and Nst. phragmitis (Thambugala et al. 2017). Further studies are needed to prove the pathogenicity of members included in this genus.

 Neostagonospora is similar to Stagonospora since both produce pycnidial conidiomata with euseptate, hyaline, fusoid-ellipsoidal to subcylindrical conidia, but Neostagonospora is distinguished by having conidiogenous cells that are phialidic, with prominent periclinal thickening (Quaedvlieg et al. 2013).

 In our phylogenetic analysis based on ITS and LSU sequences of members of the family Phaeosphaeriaceae (Fig. 28), Nst. artemisiae, which was the most recently described species (Wanasinghe et al. 2018), is not included in the clade that represents the genus Neostagonospora, being located in the Septoriella clade. Therefore, this species is excluded from Neostagonospora and transferred to Septoriella (see Septoriella below).



References: Quaedvlieg et al., 2013, Yang et al., 2016, Thambugala et al., 2017 (morphology and phylogeny).



Neostagonospora sorghi Crous & Y. Marín, sp. nov. MycoBank MB829612. Fig. 35.



Fig. 35.

Neostagonospora sorghi (ex-type CBS 145366). A. Conidiomata sporulating on MEA. B, C. Conidiogenous cells. D. Conidia. Scale bars: A = 200 μm; others = 10 μm.

Etymology: Name refers to the genus Sorghum, the host from which this fungus was collected.



Conidiomata solitary, erumpent, pycnidial, brown, globose, 180–200 μm diam, with central ostiole; conidiomatal wall of 2–3 layers of brown textura angularis. Conidiophores reduced to conidiogenous cells lining the inner cavity. Conidiogenous cells hyaline to pale brown, smooth-walled, ampulliform, phialidic with visible periclinal thickening and collarette, 5–8 × 4–5 μm. Conidia solitary, aseptate, ellipsoid with obtuse ends, straight, guttulate, (4–)5–6 × (2–)2.5(–3) μm.



Culture characteristics: Colonies flat, spreading with moderate aerial mycelium and even, lobate margins, covering dish in 2 wk. On MEA surface hazel to isabelline, reverse isabelline; on PDA surface isabelline with scarlet outer margins, reverse brown vinaceous; on OA surface isabelline with patches of scarlet.



Typus: Australia, Western Australia, Denmark, Mount Lindesay Walk trail, on Sorghum halepense (Poaceae), 19 Sep. 2015, P.W. Crous, HPC 697A (holotype CBS H-23869, culture ex-type CBS 145366 = CPC 29239).



Notes: Neostagonospora sorghi is the first species of the genus reported from Sorghum, and occurring in Australia. It is closely related to Nst. caricis, which is associated with leaf spots on Carex acutiformis. However, Nst. sorghi can be distinguished from this species and from other species of the genus by its aseptate conidia. Moreover, Nst. sorghi produces smaller conidia than Nst. caricis [(4–)5–6 × (2–)2.5(–3) μm in Nst. sorghi vs. (10–)13–16(–19) × (3–)3.5(–4) μm in Nst. caricis].



Authors: Y. Marin-Felix & P.W. Crous



Nothophoma Q. Chen & L. Cai, Stud. Mycol. 82: 212. 2015. Fig. 36.



Fig. 36.

Nothophoma spp. A, B. Disease symptoms. A.Nothophoma quercina (CGMCC 3.19246) on Osmanthus fragrans. B.Nothophoma quercina (LC12187) on Jasminum mesnyi. C–I. Asexual morph. C, D. Conidiomata of Nothophoma anigozanthi (ex-epitype CBS 381.91) sporulating on OA. E–H. Conidia. E.Nothophoma infossa (ex-neotype CBS 123395). F.Nothophoma macrospora (ex-type CBS 140674). G.Nothophoma quercina (CGMCC 3.19246). H.Nothophoma variabilis (ex-type CBS 142457). I. Conidiogenous cells of Nothophoma macrospora (ex-type CBS 140674). Scale bars: C = 200 μm; D = 20 μm; E–I = 10 μm. Pictures C, D taken from Chen et al. (2015); E from Aveskamp et al. (2009); F, I from Crous et al. (2016b); H from Valenzuela-Lopez et al. (2018).

Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Didymellaceae.



Type species: Nothophoma infossa (Ellis & Everh.) Q. Chen & L. Cai, basionym: Phoma infossa Ellis & Everh., J. Mycol. 4: 102. 1888. Neotype and ex-neotype strain designated by Aveskamp et al. (2009): CBS H-20145, CBS 123395.



DNA barcodes (genus): LSU, ITS.



DNA barcodes (species): rpb2, tub2. Table 8. Fig. 37.



Table 8.

DNA barcodes of accepted Nothophoma spp.

Species	Isolates1	GenBank accession numbers2				References
		LSU	ITS	rpb2	tub2
Nothophoma anigozanthi	CBS 381.91ET	GU238039	GU237852	KT389655	GU237580	Aveskamp et al., 2010, Chen et al., 2015
Not. arachidis-hypogaeae	CBS 125.93	GU238043	GU237771	KT389656	GU237583	Aveskamp et al., 2010, Chen et al., 2015
Not. gossypiicola	CBS 377.67	GU238079	GU237845	KT389658	GU237611	Aveskamp et al., 2010, Chen et al., 2015
Not. infossa	CBS 123395NT	GU238089	FJ427025	KT389659	FJ427135	Aveskamp et al., 2009, Aveskamp et al., 2010, Chen et al., 2015
Not. macrospora	CBS 140674T	LN880537	LN880536	LT593073	LN880539	Crous et al. (2016b)
Not. quercina	CBS 633.92	EU754127	GU237900	KT389657	GU237609	Aveskamp et al., 2010, Chen et al., 2015
	CGMCC 3.19246	MK088581	MK088574	MK088588	MK088595	Present study
	LC12187	MK088582	MK088575	MK088589	MK088596	Present study
Not. raii	MCC 1082T	–	MF664467	–	MF664468	Crous et al. (2017b)
Not. variabilis	CBS 142457T	LN907428	LT592939	LT593078	LT593008	Valenzuela-Lopez et al. (2018)

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; CGMCC: Chinese General Microbiological Culture Collection Center, Beijing, China; LC: Dr Lei Cai's personal culture collection, housed at CAS, China; MCC: National Centre for Microbial Resources (formerly Microbial Culture Collection), Pune, India. ^T,ET and ^NT indicate ex-type, ex-epitype and ex-neotype strains, respectively.

²LSU: partial large subunit (28S) nrRNA gene; ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tub2: partial β-tubulin gene.

Fig. 37.

Phylogenetic tree generated from a maximum parsimony analysis based on the combined LSU (868 bp), ITS (490 bp), tub2 (336 bp) and rpb2 (845 bp) sequences of all accepted species of Nothophoma. The tree was rooted to Phoma herbarum CBS 615.75. Values above the branches represent parsimony bootstrap support values (> 50 %). GenBank accession numbers are indicated in Table 8. ^{T, ET} and ^NT indicate ex-type, ex-epitype and ex-neotype strains, respectively. TreeBASE: S23494.

Conidiomata pycnidial, globose to elongated, or irregular, superficial or immersed into the agar, solitary or confluent, ostiolate, sometimes with an elongated neck; conidiomatal wall pseudoparenchymatous, multi-layered, outer wall pigmented. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform to doliiform, sometimes flask-shaped. Conidia hyaline but incidentally brown, smooth- and thin-walled, aseptate, ovoid or ellipsoidal, eguttulate or guttulate. Chlamydospores elongated barrel-shaped, olivaceous brown, in chains. Sexual morph unknown (adapted from Chen et al., 2015, Crous et al., 2017b).



Culture characteristics: Colonies on OA yellow/green to olivaceous grey/brown, dull green, or translucent, aerial mycelium tenuous, sometimes margins irregular and whitish, flattened or effused, compact, floccose.



Optimal media and cultivation conditions: OA or sterile pine needles placed on OA under near-ultraviolet light (12 h light, 12 h dark) to promote sporulation at 25 °C.



Distribution: Worldwide.



Hosts: Wide host range, mainly occurring as pathogens, and also endophytes or saprobes, on Amaryllidaceae, Anacardiaceae, Fabeceae, Fagaceae, Haemodoraceae, Malvaceae, Oleaceae, Rosaceae, Rhamnaceae and Rutaceae. Also isolated from other substrates and environments, such as soil, fungi and human infections.



Disease symptoms: Leaf spots, stem cankers, brown spot of fruits, shoot canker.



Notes: Nothophoma was one of the genera established recently in order to delineate a more natural classification for the Ascochyta-Didymella-Phoma complex (Chen et al. 2015). Currently this genus comprises nine species, including five Phoma species previously classified in Phoma, and four species that were recently proposed (Crous et al., 2016b, Crous et al., 2017b, Valenzuela-Lopez et al., 2018). Within Nothophoma morphological differences between species are insignificant, and phylogenies based on multi-locus sequence data are primarily used to distinguish species.

 Species in this genus are seed- and soil-borne endophytes or pathogens mainly causing leaf spots and stem canker of cultivated crops and plants, such as groundnut and cotton. Some species are mycophylic on other fungi or occur in soil, as well as in the respiratory secretion of a patient with pneumonia or in a human bronchial wash sample (Boerema et al., 2004, Aveskamp et al., 2009, Aveskamp et al., 2010, Chen et al., 2015, Crous et al., 2016b, Crous et al., 2017b, Valenzuela-Lopez et al., 2018).



References: Boerema et al. 2004 (morphology and pathogenicity), Aveskamp et al., 2010, Chen et al., 2015, Crous et al., 2016b, Crous et al., 2017b, Valenzuela-Lopez et al., 2018 (morphology and phylogeny).



Authors: Q. Chen & L. Cai



Parastagonospora Quaedvl. et al., Stud. Mycol. 75: 362. 2013. Fig. 38.



Fig. 38.

Parastagonospora spp. A–D. Sexual morph of Parastagonospora nodorum (CBS H-13909). A, B. Ascomata. C, D. Asci and ascospores. E–M. Asexual morph. E, F. Conidiomata. E.Parastagonospora poagena (ex-type CBS 136776). F.Parastagonospora poae (CBS 135091). G–I. Conidiogenous cells. G.Parastagonospora caricis (ex-type CBS H-21304). H.Parastagonospora poae (CBS 135091). I.Parastagonospora poagena (ex-type CBS 136776). J–M. Conidia. J.Parastagonospora caricis (ex-type CBS H-21304). K.Parastagonospora nodorum (CBS H-13909). L.Parastagonospora poae (CBS 135091). M.Parastagonospora poagena (ex-type CBS 136776). Scale bars: C, D, J–M = 10 μm; G–I = 5 μm. Pictures A–D, F–H, J–L taken from Quaedvlieg et al. (2013); E, I, M from Crous et al. (2014b).

Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Phaeosphaeriaceae.



Type species: Parastagonospora nodorum (Berk.) Quaedvlieg et al., basionym: Depazea nodorum Berk. Reference strain: CBS 110109.



DNA barcode (genus): LSU. Fig. 28.



DNA barcodes (species): ITS, rpb2, tef1, tub2. Table 9. Fig. 39.



Table 9.

DNA barcodes of accepted Parastagonospora spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	rpb2	tef1	tub2
Parastagonospora allouniseptata	MFLUCC 13-0386T	KU058711	–	MG520914a	–	Li et al., 2015, Phookamsak et al., 2017
P. avenae	CBS 289.69	KF251174	KF252182	KF253132b	KF252669	Quaedvlieg et al. (2013)
	MFLUCC 13-0557T ofP. forlicesenica	KY769660	–	–	–	Thambugala et al. (2017)
P. caricis	CBS 135671T	KF251176	KF252184	KF253134b	KF252671	Quaedvlieg et al. (2013)
P. dactylidis	MFLUCC 13-0375T	KU058712	–	–	–	Li et al. (2015)
	MFLUCC 13-0376T ofP. minima	KU058713	–	MG520916a	–	Li et al., 2015, Phookamsak et al., 2017
	MFLUCC 13-0573T ofP. cumpignensis	KU842388	–	–	–	Li et al. (2016a)
P. fusiformis	MFLUCC 13-0215T	KX926418	KX863711	–	–	Thambugala et al. (2017)
P. italica	MFLUCC 13-0377T	KU058714	–	MG520915a	–	Li et al., 2015, Phookamsak et al., 2017
P. nodorum	CBS 110109	KF251177	KF252185	KF253135b	KF252672	Quaedvlieg et al. (2013)
P. novozelandica	CBS 145416T	MK539957	MK540088	MK540151	MK540169	Present study
P. phragmitis	CBS 143446T	MK539958	MK540089	MK540152	–	Present study
P. poaceicola	MFLUCC 15-0471T	KX926419	KX880499	–	–	Thambugala et al. (2017)
P. poae	CBS 135089T	KF251178	KF252186	KF253136b	KF252673	Quaedvlieg et al. (2013)
P. poagena	CBS 136776T	KJ869116	–	–	–	Crous et al. (2014b)
P. uniseptata	MFLUCC 13-0387T	KU058715	–	MG520917a	–	Li et al., 2015, Phookamsak et al., 2017

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Ria, Thailand. ^T indicates ex-type strains.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene. ^a and ^b in tef1 column indicate the primers used in sequencing: ^a: EF1-983F / EF1-2218R, ^b: EF1-728F / EF-2.

Fig. 39.

RAxML phylogram obtained from the combined ITS (575 bp), LSU (848 bp), rpb2 (337 bp) and tef1 (866 bp) sequence alignment of all accepted species of Parastagonospora. The tree was rooted to Neostagonospora carici CBS 135092 and Neostagonospora elegiae CBS 135101. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 % and Bayesian posterior probability scores above 0.95 are shown at the nodes. GenBank accession numbers of LSU are listed in Fig. 28, and of the others loci are indicated in Table 7, Table 9. ^T indicates ex-type strains. TreeBASE: S23834.

Ascomata perithecial, immersed, globose, becoming depressed, dark brown to black, with central ostiole with upper region slightly papillate; ascomatal wall thin- or thick-walled, composed of 2–6 layers of brown cells of textura angularis. Pseudoparaphyses filiform, hyaline, septate. Asci bitunicate, clavate, cylindrical, narrowly fusoid or curved, shortly stipitate, thick-walled, 8-spored. Ascospores fusoid or ellipsoidal, hyaline or subhyaline to pale brown, smooth-walled, transversely 3-euseptate, cells above central septum often broader than the lower ones, with acute rounded ends, constricted or not at each septum, sometimes with distinct oil droplets in each cell. Conidiomata pycnidial, brown to black, erumpent or immersed to semi-immersed, subepidermal, globose to subglobose, ampulliform, or obpyriform, with central papillate ostiole, exuding creamy or pinkish conidial mass; conidiomatal wall composed of 2–4 layers of brown cells of textura angularis, or composed of 1–5 outer layers of dark brown cells and 1–3 inner layers of hyaline cells of textura angularis, or composed of an outer layer of brown to dark brown cells of textura globosa and an inner layer of pale brown to hyaline cells of textura angularis. Conidiophores reduced to conidiogenous cells. Conidiogenous cells phialidic, hyaline, smooth-walled, aggregated, lining the inner cavity, ampulliform to subcylindrical, broadly cylindrical or broadly conical, with percurrent proliferation near apex. Conidia hyaline or subhyaline, smooth-walled, thin- or thick-walled, cylindrical, subcylindrical or fusiform, granular to multi-guttulate, with obtuse or subobtuse apex and truncate base, rarely rounded at both ends, straight to gently curved, sigmoid, transversely 1–9-euseptate, sometimes constricted at the septa (adapted from Quaedvlieg et al. 2013).



Culture characteristics: Colonies flat, with aerial mycelium, white to pink, olivaceous, grey or vinaceous buff.



Optimal media and cultivation conditions: Sterilised Carex leaves placed on 1.5 % WA at 25 °C under continuous near-ultraviolet light to promote sporulation.



Distribution: Worldwide.



Hosts: Pathogens or saprophytes of grass (Poaceae). Species of Parastagonospora are directly or indirectly responsible for significant annual crop losses worldwide on wheat, barley and rye.



Disease symptoms: Leaf, glume and node spots.



Notes: Parastagonospora was recently introduced in order to accommodate a clade of several common and serious cereal pathogens that had been previously been placed in the genera Septoria/Stagonospora or Leptosphaeria/Phaeosphaeria (Quaedvlieg et al. 2013). This genus differs from Stagonospora mainly in the sexual morph, being phaeosphaeria-like in Parastagonospora and didymella-like in Stagonospora.

 In the phylogenetic analysis based only on the ITS and LSU sequences of representative members of the family Phaeosphaeriaceae (Fig. 28), all the species of Parastagonospora were located in a well-supported clade (0.98 PP), except for P. phoenicicola. The ex-type strain of this latter species clustered in well-supported clade (84 % BS) representing the genus Phaeosphaeria. Therefore, a new combination is proposed for this taxon.

 In our phylogenetic analysis (Fig. 39), P. cumpignensis, P. dactylidis and P. minima grouped in the same well-supported clade (79 % BS / 0.96 PP) without significant phylogenetic distance. The three species all have been isolated from Thailand on dead stems of Dactylis (Li et al., 2015, Li et al., 2016a). Only ITS sequences are available for P. cumpignensis and P. dactylidis, and nucleotide similarity for this locus for all three species is 100 %. Therefore, these three species are reduced to synonymy. The same problem is found in P. forlicesenica, which is one of the most recently described species in the genus (Thambugala et al. 2017). Based on ITS, P. forlicesenica shares a nucleotide similarity of 99.8 % with P. avenae. Therefore, further studies should be done to confirm if P. forlicesenica represents a separate species or should be synonymised with P. avenae.

 Species of Parastagonospora are pathogens or saprophytes of grasses, being directly or indirectly responsible for significant annual crop losses worldwide. Parastagonospora avenae causes minor leaf blotch of barley and rye, while it is considered an important pathogen of oats (Cunfer 2000). Parastagonospora nodorum is known primarily as a major necrotrophic pathogen of wheat that causes leaf and glume blotch, but also infects barley, on which it is considered as not economically important (Cunfer, 2000, Oliver et al., 2012).



References: Cunfer 2000 (pathology and morphology), Oliver et al. 2012 (pathology, genomics and host resistence), Quaedvlieg et al., 2013, Li et al., 2015, Thambugala et al., 2017 (morphology and phylogeny).



Parastagonospora dactylidis W.J. Li et al., Mycosphere 6: 691. 2015.

Synonyms: Parastagonospora minima W.J. Li, et al., Mycosphere 6: 691. 2015.

Parastagonospora cumpignensis Tibpromma et al., Fungal Diversity 78: 48. 2016.



Typus: Italy, Province of Arezzo, Passo della Consuma, on dead stem of Dactylis sp. (Poaceae), 19 Jun. 2012, Erio Camporesi (holotype MFLU 15-0693, culture ex-type MFLUCC 13-0375 = ICMP 20774 = KUMCC15-0131).



Additional materials: Italy, Province of Arezzo, Passo della Consuma, on dead stem of Dactylis sp. (Poaceae), 19 Jun. 2012, Erio Camporesi, MFLUCC 13-0376 = ICMP 20776 = KUMCC15-0132; ibid., Campigna, Santa Sofia, ForlìCesena Province, on dead stem of Dactylis glomerata (Poaceae), 23 Jun. 2012, Erio Camporesi, MFLUCC 13-0573.



Notes: In our phylogenetic analysis (Fig. 39), the ex-type strains of P. cumpignensis (MFLUCC 13- 0573), P. dactylidis (MFLUCC 13-0375) and P. minima (MFLUCC 13-0376) grouped in the same well-supported clade (79 % BS / 0.96 PP) without significant phylogenetic distance. The ITS sequences of the three species showed a nucleotide similarity of 100 %. Moreover, all of them were isolated from from Thailand on dead stems of Dactylis (Li et al., 2015, Li et al., 2016a). Therefore, the three species are herewith reduced to synonymy.



Parastagonospora novozelandica Crous, Thangavel & Y. Marín, sp. nov. MycoBank MB829668. Fig. 40.



Fig. 40.

Parastagonospora novozelandica (ex-type CPC 29613). A–C. Conidiogenous cells. D. Conidia. Scale bars = 10 μm.

Etymology: Name refers to New Zealand, the country where this fungus was isolated.



Culture nearly sterile, with only a few conidiomata observed. Conidiomata solitary, pycnidial, dark brown, globose, 180–200 μm diam, with central ostiole; conidiomatal wall with 3–6 layers of pale brown textura angularis. Conidiophores reduced to conidiogenous cells lining the inner cavity. Conidiogenous cells hyaline, smooth, ampulliform to subcylindrical, 6–8 × 2.5–5 μm, proliferating percurrently at apex. Conidia solitary, hyaline to pale olivaceous, smooth, guttulate, subcylindrical, straight, apex subobtuse, base truncate, 1-septate, (9–)11–13(–16) × (2–)2.5(–3) μm.



Culture characteristics: Colonies flat, spreading, reaching 60 mm diam after 2 wk, with moderate aerial mycelium, and even, smooth margins. On MEA surface greenish olivaceous to umber, reverse olivaceous to umber; on OA surface brown vinaceous.



Typus: New Zealand, Browns Bay, on unidentified grass (Poaceae), Nov. 2015, R. Thangavel (holotype CBS H-23903, culture ex-type T15–06960B = CPC 29613 = CBS 145416).



Notes: Parastagonospora novozelandica is related to P. allouniseptata. Both species produce 1-septate conidia, but these can be easily distinguished based on their conidial dimensions [(9–)11–13(–16) × (2–)2.5(–3) μm in P. novozelandica vs. 16–22 × 2.5–3.5 μm in P. allouniseptata].



Parastagonospora phragmitis Crous & Y. Marín, sp. nov. MycoBank MB829667. Fig. 41.



Fig. 41.

Parastagonospora phragmitis (ex-type CPC 32075). A, B. Conidiogenous cells. C, D. Conidia. Scale bars = 10 μm.

Etymology: Name reflects the genus Phragmites from which this fungus was isolated.



Conidiomata solitary, pycnidial, brown, globose, 250–300 μm diam, with central ostiole; conidiomatal wall with 3–6 layers of pale brown cells of textura angularis. Conidiophores reduced to conidiogenous cells lining the inner cavity. Conidiogenous cells hyaline, smooth, ampulliform to doliiform, 7–10 × 8–9 μm, proliferating percurrently at apex. Conidia solitary, hyaline to pale olivaceous, smooth, guttulate, subcylindrical-fusoid, straight to slightly curved, with prominent taper in upper third to subobtuse apex, widest in middle to lower third, base truncate, 3-septate, (18–)23–25(–27) × (3–)4 μm.



Culture characteristics: Colonies flat, spreading, covering dish after 2 wk, with moderate aerial mycelium, and smooth, lobate margins. On MEA surface saffron, reverse sienna; on PDA surface saffron to sienna, reverse sienna; on OA surface pale luteous to saffron.



Typus: Australia, New South Wales, Sussex Inlet, on Phragmites sp. (Poaceae), 27 Nov. 2015, P.W. Crous, HPC 1785 (holotype CBS H-23902, culture ex-type CPC 32075 = CBS 143446).



Notes: Parastagonospora phragmitis is related to P. fusiformis. However, P. phragmitis produces an asexual morph, while in P. fusiformis only the sexual morph has been observed. Moreover, P. phragmitis is the first species of the genus reported on Phragmites.



Phaeosphaeria phoenicicola (Crous & Thangavel) Y. Marín & Crous, comb. nov. MycoBank MB829700.

Basionym: Parastagonospora phoenicicola Crous & Thangavel, Persoonia 37: 349. 2016.



Description and illustration: Crous et al. (2016a).



Typus: New Zealand, Auckland, Botany road, on leaves of Phoenix canariensis (Arecaceae), 2015, R. Thangavel (holotype CBS H-22892, culture ex-type CPC 28711 = CBS 142107).



Notes: In the phylogenetic analysis based on ITS and LSU sequences (Fig. 28), the ex-type strain of this species was located in the well-supported clade (84 % BS) representing the genus Phaeosphaeria. Morphologically, this species produces conidia more similar to Phaeosphaeria than to Parastagonospora, since these are subcylindrical, mostly straight, while in Parastagonospora the conidia tend to be sigmoid and longer than in P. phoenicicola. Based on morphology and molecular data, the new combination, Phaeosphaeria phoenicicola, is herewith proposed.



Authors: Y. Marin-Felix, R. Thangavel & P.W. Crous



Phaeosphaeriopsis M.P.S. Câmara et al., Mycol. Res. 107: 519. 2003. Fig. 42.



Fig. 42.

Phaeosphaeriopsis spp. A. Symptomatic leaves of Agapanthus precox caused by Phaeosphaeriopsis agapanthi. B. Asci and ascospores of Phaeosphaeriopsis agavacearum (ex-type CBS 142110). C–P. Asexual morph. C, D. Conidiomata sporulating on PNA and OA, respectively, of Phaeosphaeriopsis agapanthi (ex-type CBS 141287). E. Conidiomata sporulating on OA of Phaeosphaeriopsis agavacearum (ex-type CBS 142110). F. Conidioma of Phaeosphaeriopsis agavacearum (ex-type CBS 142110). G–L. Conidiogenous cells giving rise to conidia. G, H.Phaeosphaeriopsis agapanthi (ex-type CBS 141287). I–L.Phaeosphaeriopsis glaucopunctata (CBS 653.86). M–O. Conidia. M.Phaeosphaeriopsis agapanthi (ex-type CBS 141287). N.Phaeosphaeriopsis agavacearum (ex-type CBS 142110). O.Phaeosphaeriopsis glaucopunctata (CBS 653.86). P. Chlamydospores of Phaeosphaeriopsis agavacearum (ex-type CBS 142110). Scale bars: F = 100 μm; others = 10 μm; I applies to I–L. Pictures A, C, D, G, H, M taken from Crous et al. (2016b); B, E, F, N, P from Crous et al. (2016a); I–L, O from Quaedvlieg et al. (2013).

Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Phaeosphaeriaceae.



Type species: Phaeosphaeriopsis glaucopunctata (Grev.) M.P.S. Câmara et al., basionym: Cryptosphaeria glaucopunctata Grev. [as “glauco-punctata”]. Epitype and ex-epitype strain designated by Thambugala et al. (2014): MFLU 14-0029, MFLUCC 13-0265 = ICMP 20199.



DNA barcode (genus): LSU. Fig. 28.



DNA barcodes (species): ITS, rpb2, tef1, tub2. Table 10. Fig. 43.



Table 10.

DNA barcodes of accepted Phaeosphaeriopsis spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	rpb2	tef1	tub2
Phaeosphaeriopsis agapanthi	CBS 141287T	KX228260	MK540094	MK540157a	MK540173	Crous et al. (2016b), present study
Phs. agavacearum	CBS 142110T	KY173430	KY173591	MK540158a	KY173610	Crous et al. (2016a), present study
Phs. agavensis	CBS 102206	KY090635	KY090685	–	–	Ahmed et al. (2017)
Phs. aloes	CBS 145367T	MK539959	MK540090	MK540153a	–	Present study
Phs. aloicola	CBS 145368T	MK539960	MK540091	MK540154a	MK540170	Present study
Phs. amblyospora	CBS 110131T	AY188993	–	–	–	Câmara et al. (2003)
Phs. dracaenicola	MFLUCC 11-0157T	KM434273	KM434309	KM434301b	–	Phookamsak et al. (2014b)
Phs. glaucopunctata	MFLUCC 13-0265ET	KJ522473	–	MG520918b	–	Thambugala et al., 2014, Phookamsak et al., 2017
Phs. grevilleae	CBS 145369T	MK539961	MK540092	MK540155a	MK540171	Present study
Phs. nolinae	CBS 102205	KY090637	KY090686	–	–	Ahmed et al. (2017)
Phs. obtusispora	CBS 102204	KY090636	KY090687	–	–	Ahmed et al. (2017)
Phs. phacidiomorpha	T111	FJ462742	–	–	–	Zhang et al. (unpubl. data)
Phs. pseudoagavacearum	CBS 145370T	MK539962	MK540093	MK540156a	MK540172	Present study
Phs. triseptata	MFLUCC 13-0271T	KJ522475	KJ522485	MG520919b	–	Thambugala et al., 2014, Phookamsak et al., 2017
Phs. yuccae	MFLUCC 16-0558T	KY554482	–	MG520920b	–	Phookamsak et al. (2017)

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Ria, Thailand; T: isolate housed in China. ^T and ^ET indicate ex-type and ex-epitype strains.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene. ^a and ^b in tef1 column indicate the primers used in sequencing: ^a: EF1-728F / EF-2, ^b: EF1-983F / EF1-2218R.

Fig. 43.

RAxML phylogram obtained from the combined ITS (587 bp), LSU (849 bp), rpb2 (838 bp), tef1 (601 bp) and tub2 (519 bp) sequence alignment of all accepted species of Phaeosphaeriopsis. The tree was rooted to Neostagonospora caricis CBS 135092 and Neostagonospora elegiae CBS 135101. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 % and Bayesian posterior probability scores above 0.95 are shown at the nodes. GenBank accession numbers of LSU are listed in Fig. 28, and of the other loci in Tables 7 and 9. ^T and ^ET indicate ex-type and ex-epitype strains, respectively. TreeBASE: S23834.

Ascomata solitary or aggregated, immersed, subepidermal to erumpent, pushing up flaps of the epidermis, globose to pyriform, often papillate, solitary or gregarious in a stroma of scleroplectenchyma or dark brown cells of textura angularis, often surrounded by septate, brown hyphae extending into the host tissues. Asci 8-spored, bitunicate, cylindrical to broadly fusoid, short stipitate, with visible apical chamber. Ascospores uni- to triseriate, cylindrical, broadly rounded at apex, tapering to narrowly rounded base, 4–5-septate, first septum submedian, often constricted, medium brown, echinulate, punctate or verrucose. Asexual morph coniothyrium-like or phaeostagonospora-like. Conidiomata pseudoparenchymatous, sometimes of scleroplectenchyma. Conidiogenous cells lining locule, ampulliform, hyaline, proliferating percurrently, resulting in inconspicuous annellations. Conidia cylindrical, with bluntly rounded ends, 0–3-septate, yellowish brown, punctate (Quaedvlieg et al. 2013).



Culture characteristics: Colonies flat or rarely slightly raised, spreading, feathery, velvety or floccose, with sparse to moderate aerial mycelium, circular or lobate, margins smooth or rarely slightly radiating. On PDA, surface white, dirty white, pinkish white, primrose, pale grey or pale luteous; reverse dirty white, light to dark grey, luteous or olivaceous buff. On MEA, surface dirty white, pale luteous, or white to cream at the margins, pale yellowish to yellowish brown in the middle and pale brown to brown or orange-brown at the centre, with small white to grey droplets; reverse luteous, umber with patches of dirty white, isabelline in the middle and cinnamon in outer region, or white to cream at the margins, brown to orange-brown in the middle and pale yellowish at the centre.



Optimal media and cultivation conditions: On MEA, PDA or OA at 25 °C.



Distribution: Worldwide.



Hosts: Pathogens or saprophytes on Agapanthus praecox (Alliaceae), Agave spp. and Yucca spp. (Agavaceae), Aloe sp. (Aloaceae), Dracaena lourieri, Dracaena sp. and Nolina erumpens (Dracaenaceae), Grevillea sp. (Proteaceae), Phormium spp. (Phormiaceae) and Ruscus spp. (Ruscaceae).



Disease symptoms: Leaf spots and leaf blight.



Notes: The genus Phaeosphaeriopsis was introduced by Câmara et al. (2003) to accommodate some species of Paraphaeosphaeria that were not congeneric based on phylogenetic data. Phaeosphaeriopsis is characterised by having uni- or multi-loculate stromata and 4–5-septate ascospores, and coniothyrium-like and phaeostagonospora-like asexual morphs, while Paraphaeosphaeria produces 2-septate ascospores and has a microsphaeropsis-like asexual morph (Câmara et al., 2003, Quaedvlieg et al., 2013). Phaeosphaeriopsis is related to Acericola, which is a genus recently introduced to accommodate a saprobic fungus found on dead twigs of Acer campestre (Hyde et al. 2017). Unfortunately, it appears that the LSU sequence of Acericola is incorrect (Crous et al. 2019a).

 In our phylogenetic analysis based on ITS and LSU sequences, 11 species are accepted in the genus Phaeosphaeriopsis, and four strains located in independent branches are introduced as new species.

 Species included in Phaeosphaeriopsis are saprobes or presumed pathogens. The type species, Phaeosphaeriopsis glaucopunctata, is associated with leaf spot and necrosis of Ruscus aculeatus (Câmara et al., 2003, Golzar and Wang, 2012). Phaeosphaeriopsis agapanthi and Phs. dracaenicola are also associated with necrotic leaf spots of Agapanthus precox and Dracaena lourieri, respectively (Phookamsak et al., 2014b, Crous et al., 2016b).



References: Câmara et al., 2003, Quaedvlieg et al., 2013, Thambugala et al., 2014 (morphology and phylogeny).



Phaeosphaeriopsis aloes Crous & Y. Marín, sp. nov. MycoBank MB829642. Fig. 44.



Fig. 44.

Phaeosphaeriopsis aloes (ex-type CBS 145367). A. Conidiomata sporulating on MEA. B, C. Conidiogenous cells. D. Conidia. Scale bars: A = 180 μm; all others = 10 μm.

Etymology: Name refers to Aloe, the host from which this fungus was collected.



Conidiomata solitary, brown, pycnidial, globose, 150–180 μm diam, with central ostiole, 30–40 μm diam; conidiomatal wall of 3–4 layers of brown cells of textura angularis. Conidiophores reduced to conidiogenous cells lining the inner cavity, hyaline, smooth-walled, ellipsoid, phialidic, 4–6 × 3–4 μm. Conidia solitary, aseptate, straight, verruculose, golden-brown, subcylindrical, apex obtuse, base bluntly rounded, (4–)5(–6) × 3(–3.5) μm.



Culture characteristics: Colonies flat, spreading, with sparse to moderate aerial mycelium, covering dish in 2 wk. On MEA surface honey, reverse cinnamon; on PDA surface and reverse sepia; on OA surface saffron.



Typus: USA, California, on leaves of Aloe sp. (Aloaceae), 6 Aug. 2016, P.W. Crous, HPC 1326 (holotype CBS H-23870, culture ex-type CBS 145367 = CPC 31480).



Notes: Phaeosphaeriopsis aloes is related to Phs. obtusispora. This latter species only produces the sexual morph, while only the asexual morph has been observed in our new species.

 Phaesphaeriopsis aloes and Phs. aloicola, both described here, are the first species of the genus found on a member of the family Aloaceae, an Aloe sp. However, the two species are not related. Phaeosphaeriopsis aloes produces an asexual morph, while in Phs. aloicola only the sexual morph has been observed.



Phaeosphaeriopsis aloicola Crous & Y. Marín, sp. nov. MycoBank MB829643. Fig. 45.



Fig. 45.

Phaeosphaeriopsis aloicola (ex-type CBS 145368). A. Ascomata sporulating on SNA. B. Asci. C. Pseudoparaphyses. D. Ascospores. Scale bars: A = 200 μm; all others = 10 μm.

Etymology: Name refers to the host genus Aloe from which this fungus was collected.



Ascomata solitary, aggregated, erumpent, brown, globose, 150–200 μm diam, with papillate neck and central ostiole, 40–50 μm diam; ascomatal wall of 4–6 layers of brown cells of textura angularis. Pseudoparaphyses hyaline, smooth-walled, hyphae-like, 2–3 μm diam, anastomosing, branched, intermingled among asci. Asci bitunicate, subcylindrical, apex obtuse with well-defined apical chamber, 2 μm diam, fasciculate, short stipitate, 70–100 × 10–12 μm. Ascospores bi- to triseriate, subcylindrical, straight to slightly curved, (2–)3-septate, at times slightly swollen in second cell from apex, medium brown, verruculose, ends obtuse, (19–)22–25(–26) × (4–)5(–6) μm.



Culture characteristics: Colonies flat, spreading, with sparse to moderate aerial mycelium and even, lobate margins, reaching 30 mm diam on PDA, covering dish on MEA and OA. On MEA surface buff, outer region sienna, reverse sienna; on PDA surface and reverse buff to sienna; on OA surface scarlet.



Typus: USA, California, on leaves of Aloe sp. (Aloaceae), 6 Aug. 2016, P.W. Crous, HPC 1306 (holotype CBS H-23871, culture ex-type CBS 145368 = CPC 31454).



Notes: Phaeosphaeriopsis aloicola is related to Phs. agapanthi and Phs. triseptata. Morphologically, Phs. aloicola is similar to Phs. triseptata since both produce verruculose, 3-septate ascospores. However, both species differ in the size of ascomata (up to 200 μm in Phs. aloicola vs. up to 110 μm in Phs. triseptata), asci (70–100 × 10–12 μm in Phs. aloicola vs. 56−70 × 7.5−9 μm in Phs. triseptata) and ascospores [(19–)22–25(–26) × (4–)5(–6) μm in Phs. aloicola vs. 14.5−18 × 3−4 μm in Phs. triseptata]. Moreover, Phs. triseptata also produces an asexual morph, which has not been observed in Phs. aloicola. Phaeosphaeriopsis agapanthi only produces an asexual morph. The three species were isolated from different hosts in different families. Phaeosphaeriopsis agapanthi was isolated from Agapanthus precox (Amaryllidaceae), Phs. aloicola from Aloe sp. (Aloaceae), and Phs triseptata from Ruscus aculeatus (Asparagaceae). Moreover, Phs. aloicola was found in the USA while the other species have been reported from Europe. Phaeosphaeriopsis aloes was also isolated from Aloe in California. For comparison see notes of Phaeosphaeriopsis aloes.



Phaeosphaeriopsis grevilleae Crous & Y. Marín, sp. nov. MycoBank MB829644. Fig. 46.



Fig. 46.

Phaeosphaeriopsis grevilleae (ex-type CBS 145369). A. Conidiomata sporulating on PDA. B, C. Conidiogenous cells. D. Conidia. Scale bars = 10 μm.

Etymology: Name refers to the host genus Grevillea from which this fungus was collected.



Conidiomata solitary, pycnidial, scattered, globose, 180–250 μm diam, with central ostiole, exuding black mucoid conidial mass; conidiomatal wall of 2–3 layers of brown cells of textura angularis. Conidiophores reduced to conidiogenous cells lining inner cavity, hyaline, smooth-walled, ampulliform, phialidic, 5–7 × 3–5 μm. Conidia solitary, aseptate, medium brown, verruculose, ellipsoid to ovoid, (4–)5(–6) × (3–)3.5(–4) μm.



Culture characteristics: Colonies flat, spreading, with moderate aerial mycelium and feathery margins, reaching 35 mm diam on MEA, covering dish on PDA and OA. On MEA surface and reverse scarlet; on PDA surface ochreous, reverse sienna; on OA surface scarlet with patches of ochreous.



Typus: Australia, Queensland, leaves of Grevillea sp. (Proteaceae), 14 Jul. 2009, P.W. Crous, (holotype CBS H-23872, culture ex-type CBS 145369 = CPC 17003).



Notes: In the phylogenetic analysis based on ITS, LSU, rpb2, tef1 and tub2, this species was located in an independent branch. This is the first species reported on Grevillea, which is a member of the Proteaceae.



Phaeosphaeriopsis pseudoagavacearum Crous & Y. Marín, sp. nov. MycoBank MB829645. Fig. 47.



Fig. 47.

Phaeosphaeriopsis pseudoagavacearum (ex-type CBS 145370). A. Conidiomata sporulating on MEA. B, C. Conidiogenous cells. D. Conidia. Scale bars = 10 μm.

Etymology: Named after its similarity to Phaeosphaeriopsis agavacearum.



Conidiomata solitary, globose, brown, pycnidial, 200–250 μm diam, with central ostiole, 15–20 μm diam; conidiomatal wall of 2–3 layers of brown cells of textura angularis. Conidiophores reduced to conidiogenous cells lining the inner cavity, hyaline, smooth-walled, ampulliform, phialidic, 5–7 × 3–4 μm. Conidia solitary, golden-brown, verruculose, thick-walled, straight to slightly curved, 1-septate, subcylindrical, apex obtuse, base bluntly rounded, (6–)8–9(–10) × 4(–4.5) μm.



Culture characteristics: Colonies flat, spreading, with moderate aerial mycelium and even, smooth margins, covering dish in 2 wk. On MEA surface ochreous, reverse bay; on PDA surface sienna with bay outer region, reverse bay; on OA surface sienna with scarlet margins.



Typus: France, Domaine la Fraysse, Valgorge, on leaves of Agave sp. (Asparagaceae), 15 Jul. 2010, P.W. Crous (holotype CBS H-23873, culture ex-type CBS 145370 = CPC 18383).



Notes: Phaeosphaeriopsis pseudoagavacearum is closely related to Phs. agavacearum. Morphologically these species are also similar in producing verruculose, aseptate conidia. However, they differ in the size of their conidiomata (up to 180 μm diam in Phs. agavacearum vs. up to 250 μm diam in Phs. pseudoagavacearum) and conidia [(5–)6–7(–9) × 3(–4) μm in Phs. agavacearum vs. (6–)8–9(–10) × 4(–4.5) μm in Phs. pseudoagavacearum].



Authors: Y. Marin-Felix & P.W. Crous



Pleiocarpon L. Lombard & D. Aiello, IMA Fungus 8: 73. 2017. Fig. 48.



Fig. 48.

Pleiocarpon strelitziae (ex-type CBS 142251). A–F. Disease symptoms. A, B. Wilting and dying Strelitzia reginae plants in the nursery. C–F. Basal rot and wilting of plant induced during the pathogenicity test. G–L. Asexual morph. G, H. Simple conidiophores. I, J. Sporodochia. K. Microconidia. L. Macroconidia. Scale bars: 10 μm; G applies to G–L. Pictures taken from Aiello et al. (2017).

Classification: Sordariomycetes, Hypocreomycetidae, Hypocreales, Nectriaceae.



Type species: Pleiocarpon strelitziae L. Lombard & D. Aiello. Holotype and ex-type strain: CBS H-22967, CBS 142251.



DNA barcode (genus): LSU.



DNA barcodes (species): ITS, his3, rpb2, tef1, tub2. Table 11.



Table 11.

DNA barcodes of accepted Pleiocarpon spp.

Species	Isolates1	GenBank accession numbers2					References
		ITS	his3	rpb2	tef1	tub2
Pleiocarpon livistonae	CBS 145030T	MK539963	MK540234	MK540095	MK540165	MK540179	Present study
Pl. strelitziae	CBS 142251T	KY304644	KY304616	KY304697	KY304722	KY304750	Aiello et al. (2017)

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands. ^T indicates ex-type strains.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; his3: partial histone H3 gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene.

Conidiophores simple or aggregated, forming sporodochia; simple conidiophores arising laterally or terminally from aerial mycelium, solitary to loosely aggregated, unbranched or sparsely branched, septate, bearing up to two conidiogenous cells. Conidiogenous cells monophialidic, cylindrical, tapering slightly towards the apex. Macroconidia cylindrical to subcylindrical, hyaline, straight to curved, 1−6-septate, apex or apical cell typically slightly bent to one side and minutely beaked, base with sometimes visible, centrally located or laterally displaced hilum. Microconidia absent or abundant, aseptate, hyaline, ellipsoid to ovoid or subcylindrical, straight to slightly curved, with clearly laterally displaced hilum. Chlamydospores absent or solitary, globose, brown, thich-walled, guttulate. Sexual morph not observed (adapted from Aiello et al. 2017).



Culture characteristics: Colonies on PDA with sparse to moderate aerial mycelium, even, smooth, with lobate margins; surface and reverse umber or cinnamon to honey.



Optimal media and cultivation conditions: On PDA, MEA, OA or SNA with sterile filter paper and carnation leaf pieces at 25 °C.



Distribution: Italy and Sri Lanka.



Host: Livistona rotundifolia (Arecaceae) and Strelitzia reginae (Strelitziaceae).



Disease symptoms: Basal rot and wilt.



Notes: Pleiocarpon was recently introduced by Aiello et al. (2017) to accommodate a new species isolated from potted plants of Strelitzia reginae in an ornamental nursery located in eastern Sicily that had a new basal rot disease. This basal stem rot disease resulted in the detachment of the roots from the stem. Moreover, the diseased plants displayed symptoms of general wilting and rot of the internal foliage. Pathogenicity tests indicated that Pl. strelitziae, was highly aggressive, killing all inoculated test plants within 2 mo (Aiello et al. 2017).

 The phylogenetic analysis based on ITS, LSU, tef1 and tub2 demonstrated that Pleiocarpon is closely related to the genus Thelonectria, with both genera being characterised by cylindrocarpon-like asexual morphs (Aiello et al. 2017). Recently, Thelonectria was segregated by introducing three new genera, Cinnamomeonectria, Macronectria and Tumenectria (Salgado-Salazar et al. 2016). These four related genera are mostly found on bark of exposed wood of dead, dying or diseased trees, and are rarely associated with small cankers and root rots (Chaverri et al., 2011, Salgado-Salazar et al., 2016). Moreover, Pleiocarpon can be distinguished from Thelonectria and these three new genera by the absence of a sexual morph.

 Hitherto, Pleiocarpon was monospecific. Here we introduce a new species isolated from Livistona rotundifolia (Arecaceae) in Sri Lanka, causing root and corm rot.



References: Aiello et al. 2017 (morphology, pathogenicity and phylogeny).



Pleiocarpon livistonae Crous & Quaedvl., sp. nov. MycoBank MB829613. Fig. 49.



Fig. 49.

Pleiocarpon livistonae (ex-type CBS 145030). A. Sporodochium on SNA. B. Conidiophores with conidiogenous cells. C. Conidia. D. Chlamydospores. Scale bars = 10 μm.

Etymology: Name refers to Livistona, the host from which this fungus was collected.



Conidiophores simple, solitary or aggregated, forming sporodochia, arising from superficial hyphae, branched, 2–4-septate, 50–120 × 6–8 μm. Conidiogenous cells monophialidic, cylindrical, tapering slightly towards apex, 10–30 × 4–5 μm, forming conidia in false chains that eventually aggregate in a mucoid mass. Macroconidia hyaline, smooth-walled, subcylindrical, 1–6-septate, curved, apex subobtuse, with base sometimes visible as lateral hilum; 1–3 septate conidia (21–)28–34(–45) × (5–)6 μm; 4–6-septate conidia (45–)55–65(–70) × (5–)6 μm. Chlamydospores solitary, globose, brown, thick-walled, guttulate, 15–20 μm diam.



Culture characteristics: Colonies flat, spreading, with moderate aerial mycelium and smooth, lobate margins, reaching 60 mm diam after 2 wk at 25 °C. On MEA surface ochreous, reverse umber; on PDA surface and reverse umber; on OA surface umber.



Typus: Sri Lanka, on Livistona rotundifolia (Arecaceae), W. Quaedvlieg, NAK Tuinbouw, INS-17-20656D (holotype CBS H-23849, culture ex-type CBS 145030 = CPC 34576).



Notes: Pleiocarpon livistonae is distinguished from Pl. strelitziae by the absence of microconidia, the production of chlamydospores, and the septation and size of its macroconidia (1–6-septate, up to 70 μm in Pl. livistonae vs. 1–5-septate, up to 50 μm in Pl. strelitziae). Pleiocarpon livistonae is phylogenetically close but clearly differentiated from Pl. strelitziae based on ITS, his3, rpb2, tef1 and tub2 sequence similarity (96 %, 85 %, 92 %, 94 %, and 91 %, respectively). Moreover, Pl. livistonae was isolated from Livistona rotundifolia (Arecaceae) in Sri Lanka, while Pl. strelitziae was found on Strelitzia reginae (Strelitziaceae) in Italy.



Authors: Y. Marin-Felix, W. Quaedvlieg & P.W. Crous



Pyrenophora Fr., Summa veg. Scand. 2: 397. 1849. Fig. 50.

Fig. 50.

Pyrenophora spp. A–D. Sexual morph. A, B. Sterile ascomata of Pyrenophora campanulata (CBS 127927). C. Protoascomata of Pyrenophora erythrospila on PDA (CBS 312.69). D. Protoascoma of Pyrenophora erythrospila (CBS 108941). E–K. Asexual morph. E–H. Conidiophores. E.Pyrenophora fugax (CBS 509.77). F.Pyrenophora novozelandica (CBS 127934). G.Pyrenophora erythrospila (CBS 312.69). H.Pyrenophora fugax (CBS 509.77). I, J. Conidia. I.Pyrenophora erythrospila (CBS 312.69). J. Pyrenophora fugax (CBS 509.77). K. Chlamydospores of Pyrenophora tetrarrhenae (CBS 127924). Scale bars: A = 50 μm; D = 20 μm; G–K = 10 μm.

Synonyms: Polytrichia Sacc., Syll. fung. (Abellini) 1: 451. 1882.

Pleospora subgen. Scleroplea Sacc., Syll. fung. (Abellini) 2: 277. 1883.

Neilreichina Kuntze, Revis. gen. pl. (Leipzig) 2: 862. 1891.

Scleroplea (Sacc.) Oudem., Verslag. Meded. K. Akad. Wetensch., Afd. Natuurk., ser. 3 9: 152. 1900.

Drechslera S. Ito, Proc. Imp. Acad. Japan 6: 355. 1930.

Marielliottia Shoemaker, Canad. J. Bot. 76: 1559. 1999.



Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Pleosporaceae.



Type species: Pyrenophora phaeocomes (Rebent.) Fr., basionym: Sphaeria phaeocomes Rebent. Neotype specimen designated by Shoemaker (1961): UPS 170980. Representative strain: DAOM 222769.



DNA barcodes (genus): LSU, ITS.



DNA barcodes (species): ITS, gapdh, tef1. Table 12. Fig. 51.



Table 12.

DNA barcodes of accepted Pyrenophora spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	LSU	gapdh	rpb2
Pyrenophora avenicola	CBS 307.84T	MK539972	MK540042	MK540180	–	Present study
Py. biseptata	CBS 307.69	MK539973	MK540043	MK540181	–	Present study
	CBS 319.69	MK539974	MK540044	MK540182	MK540102	Present study
	CBS 108963	MK539975	JN712532	MK540183	–	Crous et al. (2011), present study
Py. bromi	CBS 311.68	MK539976	MH870851	MK540184	–	Vu et al. (2019), present study
	DAOMC 127414	JN943666	JN940074	AY004839	–	Zhang & Berbee (2001), Hambleton (unpubl. data)
Py. chaetomioides	CBS 279.31A	MK539977	MK540045	MK540185	MK540103	Present study
	CBS 195.31	MK539978	MH866633	MK540186	MK540104	Vu et al. (2019), present study
	CBS 314.68	MK539979	MK540046	MK540187	MK540105	Present study
Py. cynosuri	CBS 127918T	MK539980	MK540047	MK540188	MK540106	Present study
Py. dactylidis	DAOMC 92161	JN943667	JN940087	AY004812	–	Zhang & Berbee (2001), Hambleton (unpubl. data)
Py. dictyoides	DAOMC 63666	JN943653	JN940080	AY004836	–	Zhang & Berbee (2001), Hambleton (unpubl. data)
	CBS 258.80	MK539981	MK540048	MK540189	MK540107	Present study
	CBS 967.87	MK539982	MK540049	MK540190	MK540108	Present study
	CBS 127933	MH877971	MK540050	MK540191	MK540109	Vu et al. (2019), present study
Py. erythrospila	CBS 312.69	MK539983	MK540051	MK540192	–	Present study
	CBS 108941	MK539984	MK540052	MK540193	MK540110	Present study
Py. fugax	CBS 509.77	MK539985	MK540053	MK540194	MK540111	Present study
Py. grahamii	CBS 315.69	MK539986	MK540054	MK540195	–	Present study
	CBS 128043	MK539987	MH876230	MK540196	MK540112	Vu et al. (2019), present study
	CBS 128044	MK539988	MH876231	MK540197	MK540113	Vu et al. (2019), present study
Py. leucospermi	CBS 111083T	JN712467	JN712533	MK540198	MK540114	Crous et al. (2011), present study
	CBS 111505	MK539989	JN712542	MK540199	MK540115	Crous et al. (2011), present study
	CBS 114493	MK539990	JN712545	MK540200	MK540116	Crous et al. (2011), present study
Py. lolii	CBS 240.48	MK539991	MK540055	MK540201	MK540117	Present study
	CBS 318.69	MK539992	MH871050	MK540202	MK540118	Vu et al. (2019), present study
	CBS 128046	MK539993	MH876233	MK540203	MK540119	Vu et al. (2019), present study
Py. nisikadoi	CBS 190.29ET	KM257054	KM243296	KM257057	–	Manamgoda et al. (2014)
	CBS 119213	EU552124	MK540056	MK540204	MK540120	Marincowitz et al. (2008), present study
	CBS 127912	MH877963	MK540057	MK540205	MK540121	Vu et al. (2019), present study
Py. nobleae	CBS 259.80	MK539994	MK540058	MK540206	MK540122	Present study
	CBS 966.87	MK539995	MK540059	MK540207	MK540123	Present study
	CBS 127936	MK539996	MK540060	MK540208	MK540124	Present study
Py. novozelandica	CBS 127934T	MK539997	MK540061	MK540209	MK540125	Present study
Py. phaeocomes	DAOMC 222769	JN943649	JN940093	–	DQ497614	Hambleton (unpubl. data), James et al. (unpubl. data)
Py. poae	CBS 319.68A	MK539998	MK540062	MK540210	MK540126	Present study
	CBS 128045	MK539999	MH876232	MK540211	MK540127	Vu et al. (2019), present study
	DAOMC 145373	JN943650	JN940083	AY004832	JN993632	Zhang and Berbee, 2001, Schoch et al., 2012, Hambleton (unpubl. data)
Py. pseudoerythrospila	CBS 127931T	MK540000	MK540063	MK540212	–	Present study
Py. semeniperda	DAOMC 213153	JN943665	JN940088	AY004826	–	Zhang & Berbee (2001), Hambleton (unpubl. data)
	BRIP 10941	KJ415564	KJ415518	KJ415382	–	Tan et al. (2014)
	CBS 127927	MK540001	MK540064	MK540213	MK540128	Present study
Py. sieglingiae	CBS 127930	MK540002	MK540065	MK540214	MK540129	Present study
Py. teres	CBS 228.76T ofPy. teres f. maculata	MK540003	MK540066	MK540215	MK540130	Present study
	CBS 281.31A ofPy. japonica	MK540004	MK540067	MK540216	MK540131	Present study
	CBS 282.31	MK540005	MK540068	MK540217	MK540132	Present study
	CBS 314.69	MK540006	MK540069	MK540218	MK540133	Present study
	CBS 336.29	MK540007	MH877692	MK540219	MK540134	Vu et al. (2019), present study
	CBS 123929	MK540008	MK540070	MK540220	MK540135	Present study
	CBS 123932	MK540009	MK540071	MK540221	MK540136	Present study
Py. tetrarrhenae	DAOMC 171966	JN943663	JN940090	–	JN993620	Schoch et al. (2012), Hambleton (unpubl. data)
	CBS 127915	MK540010	MH877964	MK540222	MK540137	Vu et al. (2019), present study
	CBS 127924	MK540011	MH877965	MK540223	MK540138	Vu et al. (2019), present study
Py. trichostoma	CBS 328.53	MK540012	MK540072	MK540224	MK540139	Present study
	CBS 391.54	MK540013	MK540073	MK540225	–	Present study
	CBS 392.54	MK540014	MK540074	MK540226	MK540140	Present study
Py. triseptata	CBS 128047	MK540015	MH877983	MK540227	MK540141	Vu et al. (2019), present study
	CBS 128048	MK540016	MH876234	MK540228	MK540142	Vu et al. (2019), present study
Py. tritici-repentis	CBS 259.59SynT ofPy. tritici-vulgaris	MK540017	MK540075	AM884276	MK540143	Lepoint et al. (2010), present study
	CBS 191.29	MK540018	MK540076	MK540229	MK540144	Present study
	CBS 127922	MK540019	MK540077	MK540230	MK540145	Present study
Py. variabilis	CBS 127920T	MK540020	MK540078	MK540231	MK540146	Present study
Py. wirreganensis	CBS 109896	MK540021	MK540079	MK540232	MK540147	Present study

¹BRIP: Queensland Plant Pathology Herbarium, Brisbane, Australia; CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; DAOMC: Plant Research Institute, Department of Agriculture (Mycology), Ottawa, Canada. ^{A, ET, SynT and T} indicate authentic, ex-epitype, ex-syntype and ex-type strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; LSU: partial large subunit (28S) nrRNA gene; gapdh: partial glyceraldehyde-3-phosphate dehydrogenase gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene.

Fig. 51.

RAxML phylogram obtained from the combined ITS (788 bp), LSU (862 bp), gapdh (694 bp) and tef1 (860 bp) sequences of all the accepted species of Pyrenophora. Bipolaris panici-miliacei CBS 199.29 and Bipolaris yamadae CBS 202.29 were used as outgroup. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 % and Bayesian posterior probability scores ≥ 0.95 are shown in the nodes. GenBank accession numbers were indicated in Table 12 and Manamgoda et al. (2014). ^{A, ET, LT, SynT and T} indicate authentic, ex-epitype, ex-lectotype, ex-syntype and ex-type strains, respectively. TreeBASE: S23834.

Ascomata perithecial, immersed, becoming erumpent to near superficial, solitary or scattered, globose to subglobose, broadly or narrowly conical, smooth-walled, with central ostiole; necks papillate, covered with brown to reddish brown setae, which are darkened at the base; ascomatal wall comprising 2–4 layers of brown, thick-walled cells of textura angularis. Pseudoparaphyses not observed. Asci 8-spored, bitunicate, fissitunicate, clavate to subcylindrical, with a short, broad pedicel, with a distinct ocular chamber surrounded by a large apical ring. Ascospores 2–3-seriate, muriform, constricted at the septum, smooth-walled, surrounded by a mucilaginous sheath. Conidiophores semi- to macronematous, mononematous, sometimes caespitose, straight or flexuous, often geniculate, usually unbranched, sometimes branched, pale brown to brown, rarely subhyaline to pale brown. Conidiogenous cells polytretic, integrated, terminal, frequently becoming intercalary, sympodial, cylindrical, smooth-walled, or less frequently verruculose, cicatrised. Conidia solitary, in certain species also sometimes catenate or forming secondary conidiophores which bear conidia, acropleurogenous, simple, straight or curved, cylindrical, ellipsoidal or obclavate, less frequently subglobose, obpyriform or fusiform, tapering towards apex, straw-coloured or pale to dark brown or olivaceous brown, sometimes the end cells are paler than the intermediate ones, smooth-walled or verruculose, pseudoseptate; hila protuberant or flat, darkened, thickened (adapted from Ellis 1971, Ariyawansa et al. 2014).



Culture characteristics: Colonies flat or umbonate, cottony, sometimes granular or powdery, with moderate to abundant aerial mycelium, sometimes with sparse aerial mycelium, margins fringed, sometimes arachnoid. On PDA smoke-grey to olivaceous or olivaceous grey, primrose to greyish yellow-green, greenish grey to olivaceous black, olivaceous black with patches white for the aerial mycelium, honey to isabelline, orange to umber, cinnamon with centre white due to the aerial mycelium, greyish sepia to fuscous black, or fuscous grey with margins buff; reverse olivaceous, olivaceous black with or without margins, primrose or luteous, fuscous black with or without margins transparent or buff, honey to isabelline, sienna to umber with margins luteous, or cinnamon with centre brick to dark brick. On MEA white to pale greenish glaucous or buff, greyish sepia to pale mouse grey or mouse grey, smoke-grey to pale olivaceous grey, glaucous grey to greenish grey, pale vinaceous to vinaceous buff, purplish grey with margins vinaceous buff, luteous with margins white to pale smoke-grey, vinaceous buff to hazel with margins white and saffron, pale greenish grey to greenish grey, or fuscous black with margins luteous; reverse olivaceous black, smoke-grey to olivaceous grey with middle white due to the aerial mycelium, fuscous black with or without margins luteous or olivaceous or buff to cinnamon or honey to isabelline, chestnut with margins luteous to rust, blood colour with margins luteous or scarlet, chestnut with margins luteous, or orange to sienna. On OA smoke-grey, olivaceous, olivaceous black, hazel, buff, cinnamon, olivaceous grey with margins luteous, greyish sepia to fuscous black with margins brick, or orange to umber with margins transparent; reverse olivaceous to olivaceous black, smoke-grey to olivaceous grey, olivaceous black with margins transparent or luteous, leaden grey to leaden black, buff with centre fuscous black and margins olivaceous, isabelline with centre olivaceous, orange to umber or greyish sepia to fuscous black with margins transparent, olivaceous grey to olivaceous black with margins transparent, or fuscous black with margins brick, or transparent with centre brick to dark brick.



Optimal media and cultivation conditions: On PDA, PNA, OA and MEA to induce sporulation of the asexual morph, while for the sexual morph Sach's agar with sterilised rice or wheat straw at 25 °C is used.



Distribution: Worldwide, mainly in Australia, Europe, New Zealand and North America.



Hosts: Wide host range, occurring as pathogens, saprobes or endophytes. Mainly found in members of Poaceae, being pathogens of cereals and grasses, including barley, oats and wheat. The most common genera belonging to Poaceae which this genus is associated to are Agropyron, Agrostis, Avena, Bromus, Dactylis, Festuca, Hordeum, Lolium, Poa and Triticum, among others. Pyrenophora species are also reported from other genera outside this family, such as Protea and Leucospermum in the Proteaceae.



Disease symptoms: Leaf spots, leaf blight, leaf blotch, net blotch, melting out, head rot, foot rot, seed-borne diseases, among others.



Notes: Pyrenophora is characterised by immersed to semi-immersed ascomata with necks covered with brown to reddish brown setae, lack of pseudoparaphyses, clavate to saccate asci, usually with a large apical ring, and muriform terete (cylindrical, frequently circular in section but narrowing to one end) ascospores (Ariyawansa et al. 2014). The asexual morph was known as Drechslera and it is characterised by brown, transversely septate conidia similar to those found in Bipolaris and Curvularia. In order to properly delineate these three genera, phylogenetic analyses using sequence data of different loci (i.e. LSU, SSU, ITS, gapdh and rpb2) were performed (Zhang and Berbee, 2001, Ariyawansa et al., 2014, Manamgoda et al., 2014). The synonymy of Drechslera with Pyrenophora was recently discussed by Ariyawansa et al. (2014). However, there is still a large number of species which await treatment. Three new combinations are introduced here, i.e. Py. nisikadoi, Py. poae and Py. wirreganensis. The main problem encountered is the lack of type material of the already known species, and this resulted in few molecular studies being performed in the past.

 Species delimitation in Pyrenophora based on morphology alone is complicated since many species have overlapping characters, similar to what is observed in Bipolaris and Curvularia (Marin-Felix et al. 2017). Therefore, molecular data (ITS, gapdh and rpb2) are essential for an accurate identification of species of Pyrenophora. In our phylogenetic analysis, 21 species are accepted and an additional six are newly described.

 Pyrenophora includes saprobic and plant pathogenic species with a worldwide distribution, commonly associated with members of the family Poaceae. Some species are serious plant pathogens, e.g. Py. teres, which is a necrotrophic pathogen causing net blotch in barley (Crous et al., 1995, Louw et al., 1995, Campbell et al., 1999, Campbell et al., 2002), and Py. tritici-repentis, which causes tan spot of wheat (Lamari and Bernier, 1989, Balance et al., 1996, Abdullah et al., 2017) in all the major wheat growing areas of the world resulting in 3–50 % yield losses (Lamari & Bernier 1989).



References: Sivanesan 1987 (morphology and pathogenicity), Zhang and Berbee, 2001, Ariyawansa et al., 2014 (morphology and phylogeny).



Pyrenophora avenicola Y. Marín & Crous, sp. nov. MycoBank MB829614. Fig. 52.



Fig. 52.

Pyrenophora avenicola (ex-type CBS 307.84). A, B. Conidiophores and conidia. C–I. Conidia. Scale bars: A, B = 10 μm; C–I = 5 μm; C applies to C–I.

Etymology: Name refers to the host genus Avena, from which it was isolated.



Hyphae hyaline, branched, septate, verrucose, 2–6(–7.5) μm. Conidiophores arising in groups, septate, straight or flexuous, sometimes geniculate at upper part, usually cells decrease in size towards apex, sometimes branched, cell walls thicker than those of vegetative hyphae, semi- to macronematous, subhyaline to pale brown, usually paler towards apex, not swollen at the base, up to 350 μm long, 4.5–7 μm wide. Conidiogenous cells verruculose, terminal or intercalary, proliferating sympodially, subhyaline to pale brown, subcylindrical to swollen, 14–33.5(–43.5) × 6.5–9.5 μm. Conidia verruculose, straight, middle cells enlarged, cylindrical to obclavate, tapering towards apex, pale brown to brown, end cells rarely slightly paler, 1–4(–5)-distoseptate, 21.5–71.5 × 9.5–15 μm, forming secondary conidiophores or conidia; hila protuberant, darkened, thickened, 3–4.5 μm. Chlamydospores, microconidiation and sexual morph not observed.



Culture characteristics: Colonies on MEA covering dish after 1 wk at 25 °C, with abundant aerial mycelium, umbonate; surface fuscous black, margins luteous; reverse smoke-grey to olivaceous grey, centre white due to the aerial mycelium. Colonies on PDA covering dish, with abundant aerial mycelium; surface smoke-grey to olivaceous grey; reverse fuscous black to black, margins transparent. Colonies on OA covering all dish, with moderate to abundant aerial mycelium; surface smoke-grey to olivaceous grey; reverse olivaceous grey to olivaceous black, margins transparent.



Typus: Sweden, Uppsala, on seed of Avena sp. (Poaceae), unknown date, C. Svensson (holotype CBS H-23840, culture ex-type CBS 307.84).



Notes: Pyrenophora avenicola is closely related to Py. chaetomioides. Moreover, both species have been found on the same host, Avena. However, Py. avenicola can be easily distinguished by its shorter conidiophores (up to 350 μm in Py. avenicola vs. 1 mm in Py. chaetomioides) and smaller conidia (21.5–71.5 × 9.5–15 μm in Py. avenicola vs. 25–140 × 12–22 μm in Py. chaetomioides) with less septa [1–4(–5) in Py. avenicola vs. 2–9 in Py. chaetomioides]. The sexual morph has only been observed in Py. chaetomioides.



Pyrenophora cynosuri Y. Marín & Crous, sp. nov. MycoBank MB829615. Fig. 53.



Fig. 53.

Pyrenophora cynosuri (ex-type CBS 127918). A–C. Conidiophores and conidia. D. Conidium forming secondary conidium. E–M. Conidia. Scale bars: 10 μm; E applies to E–M.

Etymology: Name refers to the host genus Cynosurus, from which it was isolated.



Hyphae hyaline to pale brown, branched, septate, smooth-walled or verrucose, 1.5–5 μm. Conidiophores arising in groups, septate, straight or flexuous, usually geniculate in upper part, size of cells rarely decrease towards apex, rarely branched, cell walls thicker than those of vegetative hyphae, macronematous, rarely micronematous, pale brown to brown, slightly paler towards apex, not swollen at the base, (70–)95–700 × 4.5–8 μm. Conidiogenous cells smooth-walled to slightly verruculose, terminal or intercalary, proliferating sympodially, pale brown to brown, subcylindrical to swollen, 10–30(–37) × 5.5–10 μm. Conidia verruculose, mostly curved, middle cells sometimes enlarged, cylindrical to obclavate, tapering towards apex, subhyaline to pale brown, end cells rarely paler, 2–5-distoseptate, (25–)28–80(–83) × 9–16.5 μm, forming secondary conidiophores or conidia; hila protuberant, darkened, thickened, (3–)3.5–6 μm. Chlamydospores, microconidiation and sexual morph not observed.



Culture characteristics: Colonies on MEA reaching 55–60 mm diam after 1 wk at 25 °C, with moderate aerial mycelium, flat to umbonate, margins arachnoid; surface greyish sepia to mouse grey; reverse blood colour, margins luteous. Colonies on PDA reaching 60–65 mm diam, with sparse aerial mycelium, flat, margins arachnoid; surface greyish sepia to fuscous black; reverse fuscous black. Colonies on OA covering dish, with moderate aerial mycelium; surface greyish sepia to fuscous black, margins brick; reverse fuscous black, margins brick.



Typus: New Zealand, on seeds of Cynosurus cristatus (Poaceae), 1975, E.H.C. McKenzie (holotype CBS H-23841, culture ex-type CBS 127918 = BRIP 12355 a = NZ 14880).



Notes: Pyrenophora cynosuri was isolated from seeds of Cynosurus cristatum, a member of the Poaceae, which includes host genera commonly infected by species of Pyrenophora. However, Cynosurus represents a new host genus for Pyrenophora.

 Pyrenophora cynosuri is closely related and morphologically similar to Py. dictyoides. However, both species differ in the size of their conidiophore length (up to 700 μm in Py. cynosuri vs. up to 250 μm in Py. dictyoides) and conidial length (up to 83 μm in Py. cynosuri vs. up to 250 μm in Py. dictyoides), as well as conidial septation (up to 5 in Py. cynosuri vs. up to 15 in Py. dictyoides).



Pyrenophora dictyoides A.R. Paul & Parbery, Trans. Brit. Mycol. Soc. 51: 708. 1968.

Synonyms: Helminthosporium dictyoides Drechsler, J. Agric. Res. 24: 679. 1923.

Helminthosporium dictyoides var. dictyoides Drechsler, J. Agric. Res. 24: 679. 1923.

Helminthosporium dictyoides f. dictyoides Drechsler, J. Agric. Res. 24: 679. 1923.

Drechslera dictyoides (Drechsler) Shoemaker, Canad. J. Bot. 37: 881. 1959.

Helminthosporium dictyoides f. perenne Braverman & J.H. Graham, Phytopathology 50: 695. 1960.

Drechslera andersenii Scharif, Studies on Graminicolous Species of Helminthosporium (Tehran): 29. 1963. (nom. inval., Art. 36.1).

Drechslera andersenii A. Lam, Trans. Brit. Mycol. Soc. 85: 601. 1986.



Notes: Isolates belonging to Py. dictyoides (CBS 127933 and DAOM 63666) and Drechslera andersenii (CBS 258.80 and CBS 967.87) clustered together in a well-supported clade (100 % BS / 1 PP). Moreover, the morphology of the asexual morph is similar in both species, differing only in the production of conidia with much less tapered apices in D. andersenii (Sivanesan 1987). Therefore, we reduce these species to synonymy.



Pyrenophora nisikadoi Y. Marín & Crous, nom. nov. MycoBank MB829616. Fig. 54.

Fig. 54.

Pyrenophora nisikadoi (CBS 119213). A, B. Conidiophores and conidia. C. Chlamydospores. D–K. Conidia. Scale bars: A, B = 10 μm; C = 20 μm; D = 5 μm; D applies to D–K.

Replaced synonym: Helminthosporium brizae Y. Nisik., Ber. Ohara Inst. Landw. Biol.: 121, 133. 1928, non Pyrenophora brizae C. Massal. ex Sacc. 1911.

Additional synonyms: Bipolaris brizae (Y. Nisik.) Shoemaker, Canad. J. Bot. 37: 882. 1959.

Drechslera brizae (Y. Nisik.) Subram. & B.L. Jain, Curr. Sci. 35: 354. 1966.



Etymology: Named after the Japanese plant pathologist and mycologist, Y. Nisikado, who first described and named this fungus.



Hyphae hyaline to pale brown, branched, septate, verrucose, 2–5.5 μm. Conidiophores arising in groups, septate, mostly flexuous, rarely straight, geniculate at upper part, sometimes size of cells decrease towards apex, frequently branched, cell walls thicker than those of vegetative hyphae, macronematous, pale brown to brown, sometimes paler towards apex, rarely swollen at the base, 50–330 × 3.5–6.5(–8.5) μm. Conidiogenous cells smooth-walled to verruculose, terminal or intercalary, proliferating sympodially, pale brown to brown, subcylindrical to swollen, 7.5–20.5(–25) × 5–7.5 μm. Conidia verruculose, straight or curved, middle cells enlarged, cylindrical to obclavate, tapering towards apex, pale brown to brown, basal cell sometimes paler, less frequently apical cell also paler, (1–)2–4(–5)-distoseptate, (15–)17.5–42.5 × 8.5–12 μm, not forming secondary conidiophores or conidia; hila flat, darkened, thickened, 2–4 μm. Chlamydospores immersed in all media tested (MEA, OA and PDA), brown to dark brown, lineally or irregularly disposed, verrucose, globose to subglobose, up to 30 μm. Microconidiation and sexual morph not observed.



Culture characteristics: Colonies on MEA reaching 80–90 mm diam after 1 wk at 25 °C, with abundant aerial mycelium, cottony, lobate; surface pale greenish grey to greenish grey; reverse olivaceous black. Colonies on PDA covering dish, with moderate aerial mycelium, cottony, powdery at margins, flat; surface greenish grey to olivaceous black; reverse olivaceous black. Colonies on OA covering the dish, with sparse aerial mycelium, powdery to granular, flat; surface grey olivaceous to olivaceous black; reverse leaden grey to leaden black.



Typus: Japan, from Briza minor (Poaceae), Y. Nisikado [epitype designated by Manamgoda et al. (2014) CBS H-7218, culture ex-epitype CBS 190.29 = MUCL 9613].



Additional materials examined: South Africa, Western Cape Province, J.S. Marais Nature Reserve, from Protea burchellii senescent flowerheads (Proteaceae), 6 Jun. 2000, S. Lee, CBS 119213. New Zealand, Auckland, Waitakere Ranges, from Briza minor (Poaceae), 1 Nov. 1975, E.H.C. McKenzie, CBS 127912 = ICMP 6183.



Notes: This species was originally described in Helminthosporium as Hel. brizae (Nisikado 1928), then transferred to Bipolaris (Shoemaker 1959), and finally placed in Drechslera (Subramanian & Jain 1966). Type material was not available, thus Manamgoda et al. (2014) designated CBS 190.29 as ex-epitype since this strain was isolated by the original author from the same host and location. In our phylogenetic analysis based on ITS, gapdh and rpb2, CBS 190.29 together with other two strains were located in a well-supported clade (100 % BS / 1 PP) within the main clade representing the genus Pyrenophora. Therefore, we propose to transfer this species to Pyrenophora, changing the epithet to Py. nisikadoi since Py. brizae already exists.

 Isolate CBS 119213 sporulated, enabling us to conduct a morphological comparison and provide a modern description of this species in PDA. Moreover, Py. nisikadoi was formerly only recorded from Briza minor, a member of the Poaceae, while it is here also recorded from Protea birchellii, which belongs to the Proteaceae.



Pyrenophora novozelandica Y. Marín & Crous, sp. nov. MycoBank MB829620. Fig. 55.



Fig. 55.

Pyrenophora novozelandica (ex-type CBS 127934). A–D. Conidiophores and conidia. E–M. Conidia. Scale bars: A–D = 10 μm; E = 5 μm; E applies to E–M.

Etymology: Name refers to New Zealand, the country from where it was isolated.



Hyphae hyaline to pale brown, branched, septate, verrucose, 1–6(–8.5) μm. Conidiophores arising in groups, septate, straight or flexuous, sometimes geniculate at upper part, size of cells not decreasing towards apex, rarely branched, cell walls thicker than those of vegetative hyphae, macronematous, pale brown to brown, paler towards apex, not swollen at the base, 35–700 × 4.5–7.5 μm. Conidiogenous cells smooth-walled, terminal or intercalary, proliferating sympodially, brown, terminal conidiogenous cells hyaline, cylindrical to subcylindrical, 11–22 × 5–8.5 μm. Conidia smooth-walled, straight, rarely slightly curved, sometimes middle cells slightly enlarged, cylindrical to obclavate, tapering towards apex, pale brown to brown, sometimes basal cell slightly paler, (2–)3–5(–6)-distoseptate, 20.5–58 × 9.5–14 μm, not forming secondary conidiophores or conidia; hila usually inconspicuous, flat, slightly darkened, slightly thickened, 2–4 μm. Chlamydospores, microconidiation and sexual morph not observed.



Culture characteristics: Colonies on MEA reaching 27–30 mm diam after 1 wk at 25 °C, with sparse aerial mycelium, raised, margins fringed; surface grey olivaceous; reverse dark mouse grey, margins buff. Colonies on PDA reaching 38–40 mm diam, with sparse aerial mycelium, flat, margins fringed; surface smoke grey to olivaceous grey; reverse olivaceous black. Colonies on OA reaching 37–40 mm diam, with moderate aerial mycelium, flat, margins fringed; surface grey olivaceous; reverse olivaceous black.



Typus: New Zealand, Wanganui, Palmerston North, Seed Testing Station, on seed of Triticum sp. (Poaceae), 5 Oct. 1976, G.F. Laundon (holotype CBS H-23843, culture ex-type CBS 127934 = LEV 11079b = PDD 50697).



Notes: Pyrenophora novozelandica is similar and closely related to Py. fugax. However, both species can be easily distinguished based on the size of their conidiophores (up to 250 μm in Py. fugax vs. up to 700 μm in Py. novozelandica) and conidia (50–170 × 14–24 μm in Py. fugax vs. 20.5–58 × 9.5–14 μm in Py. novozelandica), as well as conidial septation [4–8(–10) in Py. fugax vs. (2–)3–5(–6) in Py. novozelandica]. Pyrenophora novozelandica is known to occur on Triticum in New Zealand, which is a common host of species belonging to Pyrenophora, including Py. fugax.



Pyrenophora poae (Baudyš) Y. Marín & Crous, comb. nov. MycoBank MB829617.

Basionym: Helminthosporium poae Baudyš, Lotos 63: 104. 1916.

Synonyms: Helminthosporium vagans Drechsler, J. Agric. Res., Washington 24: 688. 1923.

Drechslera vagans (Drechsler) Shoemaker, Canad. J. Bot. 37: 881. 1959.

Drechslera poae (Baudyš) Shoemaker, Canad. J. Bot. 40: 827. 1962.



Description and illustration: Sivanesan (1987).



Materials examined: Canada, Saskatchewan, Saskatoon, from Poa pratensis (Poaceae), Oct. 1973, J.D. Smith, DAOMC 145373. Germany, Husum, from P. pratensis, Aug. 1966, U.G. Schlösser, CBS 319.68. USA, Maryland, Beltsville, from P. pratensis, Apr. 1979, A. Hagan, CBS 128045 = BRIP 12969a.



Notes: Pyrenophora poae was introduced as Helminthosporium poae by Baudys (1916), then transferred to Drechslera (Shoemaker 1959). The original description was based on a specimen isolated from Poa trivialis in the Czech Republic. Type material is not available, but CBS 319.68 is considered here as an authentic strain since was isolated from the same host genus and continent. Unfortunately, it did not sporulate and thus we chose to not designate it as epitype. All the strains identified as D. poae were located in the main clade belonging to Pyrenophora, and a new combination is proposed here.



Pyrenophora pseudoerythrospila Y. Marín & Crous, sp. nov. MycoBank MB829675. Fig. 56.



Fig. 56.

Pyrenophora pseudoerythrospila (ex-type CBS 127931). A. Protoascomata on OA. B, C. Protoascomata. Scale bars = 10 μm.

Etymology: Named after its close phylogenetic relation to Py. erythrospila.



Only forming protoascomata in OA. Protoascomata composed of pale brown to brown cells of up to 100 μm diam, of textura angularis to textura globulosa. Pyrenophora pseudoerythrospila differs from its closest phylogenetic neighbour, Py. erythrospila by unique fixed alleles in three loci based on alignments of the separate loci deposited in TreeBASE (S23834): LSU positions 70 (G), 395 (C), 396 (T), 397 (T), 500 (G), 536 (C), 537 (T); ITS positions 141 (A), 146 (A), 147 (T), 148 (A), 149 (G), 152 (G), 153 (A), 154 (G), 155 (T), 164 (T), 168 (T), 169 (G), 173 (G), 174 (C), 176 (A), 178 (T), 179 (G), 184 (T), 187 (T), 189 (T), 197 (C), 198 (C), 199 (C), 205 (C), 206 (T), 208 (C), 223 (T), 224 (T), 225 (T), 226 (T), 234 (A), 252 (T), 264 (T), 268 (C), 279 (G), 288 (C), 289 (A), 293 (A), 302–304 (indels), 327 (T), 330–332 and 341 (indels),511 (T), 536–540 (indels), 558 (C), 591 (A), 594 (G), 601 (T), 621 (A), 630 (C), 641 (G), 643 (A), 644 (G), 645 and 646 (indels), 659 (T), 660 (G), 664 (T), 666 (A), 667 (T); gapdh positions 30 (C), 49 (A), 54 and 55 (indels), 59 (G), 60 (A), 69 (C), 71 (C), 74 (A), 85 (T), 87 (A), 177 (G), 178 (G), 179 (C), 180 (C), 182 (C), 187 (G), 189 (C), 190 (T), 191 (A), 192 (T), 193 (C), 194 (A), 195 (G), 196 (A), 197 (C), 201 (G), 203 (A), 204 (G), 205 (A), 256 (G), 319 (G), 373 (T), 406 (C), 487 (T), 493 (T), 496 (T), 523 (G), 526 (C), 532 (C), 538 (A).



Culture characteristics: Colonies on MEA reaching 55–60 mm diam after 1 wk at 25 °C, with sparse aerial mycelium, flat, margins fringed; surface pale vinaceous to vinaceous buff; reverse orange to sienna, margins transparent. Colonies on PDA reaching 56–59 mm diam, with sparse aerial mycelium, flat, margins fringed; surface cinnamon, white mycelium in the centre; reverse cinnamon, centre brick to dark brick. Colonies on OA reaching 50–55 mm diam, without aerial mycelium, flat; surface cinnamon; reverse transparent, centre brick to dark brick.



Typus: Germany, West Germany, on Lolium sp. (Poaceae), 9 Sep. 1968, U.G. Schlosser (holotype CBS H-23844, culture ex-type CBS 127931 = DAOMC 126772).



Notes: The ex-type strain of Pyrenophora pseudoerythrospila did not sporulate on any of the media tested, producing only few protoascomata in OA. However, these remained sterile after several months of incubation. Pyrenophora pseudoerythrospila is closely related to Py. erythrospila, which produces both sexual and asexual morphs. The protoascomata were also reported in Py. erythrospila, but these finally developed mature ascospores after 25 wk. Pyrenophora erythrospila is commonly found on Agrostis spp. in Australia and North America, but has also been reported on Lolium in Germany (Farr & Rossman 2019), having the same host and distribution as Py. pseudoerythrospila.



Pyrenophora sieglingiae Y. Marín & Crous, sp. nov. MycoBank MB829618. Fig. 57.



Fig. 57.

Pyrenophora sieglingiae (ex-type CBS 127930). A–C. Sterile ascomata. D. Neck of ascoma. E, F. Conidiophores and conidia. G–O. Conidia. Scale bars: C = 100 μm; D–F = 20 μm; G = 10 μm; G applies to G–O.

Etymology: Name refers to Sieglingia, the host genus from which this fungus was collected.



Hyphae hyaline to pale brown, branched, septate, verrucose, (1–)1.5–5.5 μm. Sterile ascomata solitary or arising in groups, brown to dark brown or black, sometimes apical part of neck yellowish brown, composed of cells of textura intricata, up to 1200 μm long, up to 300 μm wide, conidiophores arising from the body and neck; inside consisting of angular to globose, hyaline cells. Conidiophores arising in groups, septate, straight or flexuous, rarely geniculate in the upper part, cell size rarely decreases towards the apex, unbranched, cell walls thicker than those of vegetative hyphae, macronematous, brown, mostly paler towards apex, not swollen at the base, 100–700 × (5–)7–9(–11) μm. Conidiogenous cells verruculose, terminal or intercalary, proliferating sympodially, pale brown to brown, subcylindrical to slightly swollen, (12–)15–33.5(–36.5) × 9–12(–13.5) μm. Conidia verruculose, straight or curved, sometimes with middle cells enlarged, cylindrical to obclavate, tapering towards apex, pale brown to brown, end cells usually paler, 4–8-distoseptate, 56–108(–120) × 15–23(–25.5) μm, forming secondary conidiophores or conidia; hila not protuberant or flat, darkened, thickened, (4–)4.5–6.5(–7) μm. Chlamydospores, microconidiation and sexual morph not observed.



Culture characteristics: Colonies on MEA reaching 26–29 diam after 1 wk at 25 °C, with abundant aerial mycelium, raised, slightly lobate; surface white to buff; reverse fuscous black. Colonies on PDA reaching 27–30 diam, with abundant aerial mycelium, lobate; surface olivaceous black with patches of white due to aerial mycelium; reverse olivaceous black, margins luteous. Colonies on OA reaching 54–57 diam, with moderate to abundant aerial mycelium, flat; surface smoke-grey to olivaceous grey; reverse smoke-grey to olivaceous grey.



Typus: New Zealand, Auckland, Waikumete, from leaf of Sieglingia decumbens (Poaceae), E.H.C. McKenzie (holotype CBS H-23842, culture ex-type CBS 127930 = ICMP 6170 = PDDCC 6170).



Notes: Pyrenophora sieglingiae is closely related to Py. semeniperda and Py. wirreganensis. Morphologically, these species are similar, producing sterile ascomata with long necks. However, they can be distinguished by the size of their conidiophores (up to 700 μm in Py. sieglingiae vs. up to 180 μm in Py. semeniperda vs. up to 1 000 μm in Py. wirreganensis) and conidia [56–108(–120) × 15–23(–25.5) μm in Py. sieglingiae vs. 70–160 × 13–17 μm in Py. semeniperda vs. (30–)40–80(–100) × (10–)12–19(–22) μm in Py. wirreganensis). Moreover, Py. semeniperda produces conidia with more septa (up to 12 in Py. semeniperda vs. up to 8 in Py. sieglingiae vs. up to 9 in Py. wirreganensis), and it is the only one that produces a sexual morph. Pyrenophora sieglingiae has been isolated from Sieglingia from New Zealand while Py. wirreganensis occurs on Hordeum in Australia. Pyrenophora semeniperda has been isolated from both hosts in both locations, apart from other hosts that are widely distributed, i.e. Agropyron, Avena, Bromus, Cortaderia, Ehrhartia, Pennisetum and Triticum.



Pyrenophora teres Drechsler, J. Agric. Res., Washington 24: 656. 1923.

Synonyms: Helminthosporium secalis Fée, Mém. Soc. Mus. Hist. Nat. Strassbourg 3: 36. 1843.

Alternaria secalis (Fée) Sacc. & Traverso, Syll. fung. (Abellini) 20: 1184. 1911.

Helminthosporium gramineum Rabenh., Klotzschii Herb. Viv. Mycol., Edn Nov, Ser. Sec., Cent. 4: no. 332. 1857.

Brachysporium gracile var. gramineum (Rabenh. ex Schltdl.) Sacc., Syll. fung. (Abellini) 4: 430. 1886.

Drechslera graminea (Rabenh. ex Schltdl.) S. Ito, Proc. Imper. Acad. Tokyo 6: 355. 1930.

Drechslera teres subsp. graminea (Rabenh. ex Schltdl.) Simay, Barley Newsletter 36: 174. 1992.

Helminthosporium teres Sacc., Syll. fung. (Abellini) 4: 412. 1886.

Drechslera teres (Sacc.) Shoemaker, Can. J. Bot. 37: 881. 1959.

Drechslera teres f. teres (Sacc.) Shoemaker, Canad. J. Bot. 37: 881. 1959.

Drechslera teres subsp. teres (Sacc.) Shoemaker, Canad. J. Bot. 37: 881. 1959.

Helminthosporium hordei Eidam, Der Landw. (Schles. Landw. Ztg), Breslau 27: 509. 1891.

Helminthosporium tuberosum G.F. Atk., Bulletin of Cornell University 3: 47. 1897.

Drechslera tuberosa (G.F. Atk.) Shoemaker, Canad. J. Bot. 37: 881. 1959.

Helminthosporium fragosoi Bubák, Hedwigia 57: 13. 1915.

Pyrenophora teres f. teres Drechsler, J. Agric. Res., Washington 24: 656. 1923.

Pyrenophora teres subsp. teres Drechsler, J. Agric. Res., Washington 24: 656. 1923.

Helminthosporium japonicum S. Ito & Kurib., Proc. Imper. Acad. Tokyo 6: 353. 1930.

Pyrenophora japonica S. Ito & Kurib., Proc. Imper. Acad. Tokyo 6: 353. 1930.

Drechslera japonica (S. Ito & Kurib.) Shoemaker, Canad. J. Bot. 37: 881. 1959.

Pyrenophora graminea S. Ito & Kurib., Proc. Imp. Acad. Japan 6: 353. 1930.

Pyrenophora teres subsp. graminea (S. Ito & Kurib.) Simay, Barley Newsletter 36: 174. 1992.

Pyrenophora secalis M.D. Whitehead & J. Dicks., Mycologia 44: 752. 1952.

Drechslera teres f. maculata Smed.-Pet., Arb. Tiflis Bot. Gard.: 139. 1971.

Pyrenophora teres f. maculata Smed.-Pet., The Royal Veterinary and Agricultural University Yearbook: 139. 1971.



Description and illustrations: Sivanesan (1987).



Materials examined: Denmark, from Hordeum vulgare (Poaceae), unknown date, V. Smedegaard-Petersen (ex-type culture of Py. teres f. maculata CBS 228.76). Japan, from H. vulgare (Poaceae), unknown date, S. Ito, CBS 281.31; unkown substrate and date, S. Ito, CBS 282.31; from H. vulgare (Poaceae), unknown date, Y. Nisikado, CBS 336.29 = MUCL 9687. Germany, Niedersachsen, Rotenburg, from H. vulgare (Poaceae), Jul. 1968, U.G. Schlösser, CBS 314.69. Hungary, Eszteragpuszta, from Hordeum vulgare leaf (Poaceae), unknown date, col. M. Csosz, dep. J. Bakonyi, CBS 123929; Taplanszentkereszt, from Hordeum vulgare leaf (Poaceae), unknown date, col. A. Tomcsanyi, dep. J. Bakonyi, CBS 123932.



Notes: In our phylogenetic analysis, isolates identified as Py. teres and Py. graminea were located in the same well-supported clade (100 % BS / 1 PP), suggesting that these represent the same species. In fact, Py. graminea has been recently considered as a subspecies of Py. teres (Simay 1992) since its morphology is similar and both species share the same host, Hordeum. Therefore, we propose the synonymy of both species under the name of Py. teres, which is well established and the most commonly used name for this taxon. Moreover, an authentic strain of Py. japonica was also located in this clade, supporting the synonymy of Py. japonica with Py. teres proposed by Crous et al. (1995), which was based on their morphological, molecular and pathological similarity.

 Pyrenophora teres produces net blotch on barley worldwide, causing cell death and feeding off the nutrients released (Sivanesan, 1987, Louw et al., 1995, Campbell et al., 1999, Ellwood et al., 2012). Two different forms of Py. teres were recognised depending on the disease symptoms produced, i.e. Py. teres f. teres producing the net form of net blotch, characterised by elongated lesions where necrosis develops along leaf veins with occasional transverse striations, while Py. teres f. maculata produces the spot form of net blotch, typified by more ovoid lesions, often surrounded by a chlorotic zone (Campbell et al., 1999, Ellwood et al., 2012). However, both forms are considered the same species, Py. teres. This disease becomes systemic in plants infected from seed (Sivanesan 1987).



Pyrenophora variabilis Hern.-Restr. & Y. Marín, sp. nov. MycoBank MB829619. Fig. 58.



Fig. 58.

Pyenophora variabilis (ex-type CBS 127920). A–C. Conidiophores and conidia. D–N. Conidia. Scale bars = 10 μm; C applies to A–C; N applies to D–N.

Etymology: Name refers to the highly variable conidial morphology.



Hyphae hyaline to brown, branched, septate, smooth-walled to verrucose, 2.5–7 μm. Conidiophores arising in groups, septate, straight or flexuous, sometimes geniculate in upper part, simple, cell walls thicker than those of vegetative hyphae, semi- to macronematous, brown, not swollen at the base, up to 321 μm long, 5–10 μm wide. Conidiogenous cells smooth-walled, terminal or intercalary, proliferating sympodially, brown, subcylindrical, 18–27 × 8–10 μm. Conidia smooth-walled, straight to curved, cylindrical, subcylindrical, obclavate, obpyriform to subglobose, pale brown to brown, 1–3-distoseptate, 20–75 × 13–19.5 μm; hila flat, darkened, thickened, 4–7 μm. Chlamydospores and sexual morph not observed.



Typus: Canada, British Columbia, Agassiz Research Station, from leaves of Poa trivialis (Poaceae), Jul. 1972, J.D. Smith (holotype CBS H-23843, culture ex-type CBS 127920 = DAOMC 139513).



Notes: Pyrenophora variabilis was located on an independent branch far removed from the other species in the genus. It can be easily distinguished from all the species of the genus by its highly variable conidial morphology in size and shape, from cylindrical, subcylindrical or obclavate to subglobose or obpyriform. It was isolated from Poa trivialis (Poaceae) leaves in Canada, a common host of Pyrenophora spp.



Pyrenophora wirreganensis (Wallwork et al.) Y. Marín & Crous, comb. nov. MycoBank MB829621.

Basionym: Drechslera wirreganensis Wallwork et al., Mycol. Res. 96. 888. 1992.



Description and illustration: Wallwork et al. (1992).



Material examined: Australia, South Australia, from Hordeum sp. (Poaceae), unknown date, J. Bakonyi, CBS 109896.



Notes: Pyrenophora wirreganensis was introduced as Drechslera wirreganensis by Wallwork et al. (1992) to accommodate a specimen isolated from Hordeum in Australia. In the phylogenetic analysis, the strain CBS 109896 identified as Py. wirreganensis and isolated from the same host and location than the ex-type strain (IMI 348323), was located in an independent branch within the main clade representing the genus Pyrenophora. Therefore, this species is here transferred to the latter genus. For comparison with close species see notes of Py. sieglingiae.



Authors: Y. Marin-Felix, M. Hernández-Restrepo, P.W. Crous



Ramichloridium Stahel ex de Hoog, Stud. Mycol. 15: 59. 1977. Fig. 59.



Fig. 59.

Ramichloridium spp. A.Ramichloridium luteum on apple. B. Sporulating colonies of Ramichloridium luteum (ex-type CBS 132088) on PDA. C–G. Macronematous conidiophores with sympodially proliferating conidiogenous cells, which give rise to a conidium-bearing rachis with crowded and prominent scars. C.Ramichloridium apiculatum (ex-type CBS 156.59). D.Ramichloridium cucurbitae (ex-type CBS 132087). E, F.Ramichloridium luteum (ex-type CBS 132088). G.Ramichloridium punctatum (ex-type CBS 132090). H, I. Scanning electron micrographs of Ramichloridium luteum (ex-type CBS 132088) showing sympodial proliferation with scars on conidiogenous cells. J, K. Conidiophores reduced to conidiogenous cells. J.Ramichloridium cucurbitae (ex-type CBS 132087). K.Ramichloridium luteum (ex-type CBS 132088). L, M. Conidia. L.Ramichloridium apiculatum (ex-type CBS 156.59). M.Ramichloridium punctatum (ex-type CBS 132090). Scale bars: H = 2 μm; I = 1 μm; all others = 10 μm. Pictures C, L taken from Li et al. (2012); all others from Arzanlou et al. (2007).

Classification: Dothideomycetes, Dothideomycetidae, Capnodiales, Dissoconiaceae.



Type species: Ramichloridium apiculatum (J.H. Mill. et al.) de Hoog, basionym: Chloridium apiculatum J.H. Mill. et al. Ex-type strain: CBS 156.59 = ATCC 13211 = IMI 100716 = JCM 6972 = MUCL 15753 = MUCL 7991 = QM 7716.



DNA barcode (genus): LSU.



DNA barcodes (species): ITS, rpb2, tef1. Table 13. Fig. 60.



Table 13.

DNA barcodes of accepted Ramichloridium spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	LSU	rpb2	tef1
Ramichloridium apiculatum	CBS 156.59T	EU041791	EU041848	MF951416	–	Arzanlou et al. (2007), Videira et al. (2017)
R. cucurbitae	CBS 132087T	JQ622087	JQ622095	–	JQ622112	Li et al. (2012)
R. luteum	CBS 132088T	EU329730	JQ622099	MF951417	JQ622116	Li et al., 2012, Videira et al., 2017
R. malus	LQ73T	EF627452	–	–	–	Zhang et al. (2007)
R. punctatum	CBS 132090T	JQ622086	JQ622094	–	JQ622111	Li et al. (2012)

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; LQ: collection not specified in the work in which it was introduced. ^T indicates ex-type strains.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; LSU: partial large subunit (28S)nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial elongation factor 1-alpha gene.

Fig. 60.

RAxML phylogram obtained from the combined ITS (594 bp), LSU (761 bp), rpb2 (819 bp) and tef1 (470 bp) sequence alignment of all accepted species of Ramichloridium and related taxa. The tree was rooted to Parapenidiella tasmaniensis CBS 124991 and Stenella araguata CBS 105.75. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 % and Bayesian posterior probability scores above 0.95 are shown at the nodes. GenBank accession numbers are listed in Table 13, Li et al., 2012, Videira et al., 2017 and Chen & Kirschner (2018). ^T and ^NT indicate ex-type and ex-neotype strains, respectively. TreeBASE: S23834.

Mycelium consisting of hyaline, subhyaline, pale brown, or brown, smooth-walled, septate, branched, submerged and aerial hyphae. Conidiophores straight to gently curved, subcylindrical, unbranched, smooth- and thick-walled, brown to dark brown, 0–3-septate, or sometimes reduced to intercalary conidiogenous cells. Conidiogenous cells integrated, terminal, pale to medium brown, or golden-brown, apical part subhyaline to pale brown, subcylindrical, rarely somewhat clavate, sometimes with irregular, nodulose swellings along the length of the conidiogenous cells, tapering towards apex, with sympodial proliferation, forming a rachis with slightly thickened and darkened, circular, somewhat protruding scars. Conidia solitary, aseptate, pale brown, smooth-walled to finely verrucose, clavate or oblong to ellipsoid, or obovate to obconical, apex obtuse or subobtuse, base truncate, with a conspicuous, slightly darkened and thickened, not refractive hilum.



Culture characteristics: Colonies after 1 mo at 25 °C in the dark flat, spreading, with sparse to moderate aerial mycelium, margins smooth and even, or lobate and feathery. On SNA grey olivaceous, pale mouse grey, or smoke-grey. On PDA olivaceous grey or smoke-grey; reverse olivaceous grey or iron-grey. On OA olivaceous grey or iron-grey; reverse iron-grey, with pale luteous pigment diffusing into agar. On MEA olivaceous green; reverse olivaceous black, often with a diffusing citron-yellow pigment.



Optimal media and cultivation conditions: MEA, OA, PDA and SNA at 25 °C under near-ultraviolet light.



Distribution: Africa, America and Asia.



Hosts: Aloe sp. (Aloaceae), Cucumis sativus, Cucurbita maxima (Cucurbitaceae), Malus domestica, Malus pumila and Pyrus pyrifolia (Rosaceae). Also isolated from soil.



Disease symptoms: Sooty blotch and flyspeck diseases.



Notes: Ramichloridium was initially introduced by Stahel (1937), designating R. musae as type species. However, the name was invalid due to the lack of Latin description or diagnosis. Subsequently, de Hoog (1977) validated this genus to include species with erect, dark conidiophores and predominantly aseptate conidia, designating as new type species R. apiculatum. In that study, 13 species were recognised in Ramichloridium, and subsequently more species were included. However, several molecular studies demonstrated that some of them belonged to different genera, i.e. Myrmecridium, Pachyramichloridium, Pleurothecium, Radulidium, Rhinocladiella and Zasmidium, and were subsequently transferred (Arzanlou et al., 2007, Cheewangkoon et al., 2009, Videira et al., 2017). Some species still need to be molecularly studied to confirm their phylogenetic position. In the present study, only five species have been demonstrated to belong to Ramichloridium, which is characterised by aseptate, pale brown, smooth-walled to finely verrucose, clavate or oblong to ellipsoid, or obovate to obconical conidia. Based on molecular data, R. indicum is proposed here as a new genus, Globoramichloridium indicum, and R. ducassei as a new combination in Zasmidium (see Zasmidium below). Moreover, R. apiculatum, R. cucurbitae and R. mali were located in a well-supported clade (100 % BS / 1 PP) without phylogenetic distance. Unfortunately, the only loci available and common in the three species are the ITS and LSU. Therefore, other loci should be sequenced to verify their status as separate species.

 Species of Ramichloridium cause sooty blotch and flyspeck disease (SBFS) on members of the family Rosaceae, which produces blemishes on the epicuticular wax layer and is regarded as an economically serious disease (Wang et al. 2014). Ramichloridium cucurbitae and R. punctatum have been found as SBFS pathogens only in the USA (Li et al. 2012), while R. apiculatum, R. luteum and R. mali have been reported as causal agents of SBFS in China (Zhang et al., 2007, Li et al., 2012, Wang et al., 2014).



References: Arzanlou et al., 2007, Li et al., 2012 (morphology and phylogeny).



Globoramichloridium Y. Marín & Crous, gen. nov. MycoBank MB829622.



Etymology: Name reflects the characteristic globose conidia produced by this genus.



Illustration: Arzanlou et al. (2007).



Mycelium consisting of submerged and aerial hyphae; submerged hyphae smooth- and thin-walled, hyaline, with thin septa; aerial hyphae coarsely verrucose, olivaceous green, rather thick-walled, with thin septa. Conidiophores arising vertically from creeping hyphae at right angles, straight, unbranched, thick-walled, smooth-walled, dark brown, with up to 10 thin septa, often with inflated basal cells. Conidiogenous cells terminally integrated, smooth-walled, dark brown, sympodially proliferating, rachis straight or flexuose, geniculate or nodose, subhyaline; scars thickened and darkened, clustered at nodes. Microcyclic conidiation observed in culture. Conidia solitary, (0–)1-septate, not constricted at the septum, subhyaline to pale brown, smooth-walled or coarsely verrucose, rather thin-walled, broadly ellipsoidal to globose, with truncate base; hila conspicuous, slightly darkened, not thickened.



Culture characteristics: Colonies on MEA reaching 35 mm diam after 2 wks at 24 °C. Colonies velvety, rather compact, slightly elevated, with entire, smooth, whitish margins, dark olivaceous green in the central part.



Type species: Globoramichloridium indicum (Subram.) Y. Marín & Crous. Holotype: IMI 114625. Representative strain: CBS 171.96.



Notes: This genus is introduced to accommodate R. indicum, which differs from Ramichloridium spp. by its broadly ellipsoidal to globose, mostly 1-septate, smooth-walled or coarsely verrucose conidia, being clavate or oblong to ellipsoid, or obovate to obconical, aseptate, smooth-walled to finely verrucose in Ramichloridium. This genus is related to Dissoconium, but the latter can be easily distinguished by its percurrent and sympodial proliferation, and the ellipsoid to obclavate, smooth-walled conidia.



Globoramichloridium indicum (Subram.) Y. Marín & Crous, comb. nov. MycoBank MB829623.

Basionym: Chloridium indicum Subram., Proc. Indian Acad. Sci., Sect. B 42: 286. 1955.

Synonyms: Veronaea verrucosa Geeson, Trans. Brit. Mycol. Soc. 64: 349. 1975.

Veronaea indica (Subram.) M.B. Ellis, in Ellis, More Dematiaceous Hyphomycetes: 209. 1976.

Ramichloridium indicum (Subram.) de Hoog, Stud. Mycol. 15: 70. 1977.



Description and illustration: Arzanlou et al. (2007).



Material examined: Unknown collection details, Feb. 1996, L. Marvanová, CBS 171.96.



Notes: The strain examined and included in the phylogenetic analysis, CBS 171.96, was not derived from type material. However, the morphology of this strain fits perfectly with the morphology of the holotype IMI 114625 (de Hoog 1977). Therefore, CBS 171.96 is considered here as a representative strain, and we propose the new genus and combination based on the phylogenetic data derived from this isolate, as well as on the morphological differences observed.



Authors: Y. Marin-Felix, J.Z. Groenewald & P.W. Crous



Seifertia Partr. & Morgan-Jones, Mycotaxon 83: 348. 2002. Fig. 61.



Fig. 61.

Seifertia azalae. A, B. Disease symptoms caused on Rhododendron. C–G. Synnemata. H, I. Conidiogenous cells and conidia. J, K. Conidia. Scale bars: F = 100 μm; G = 50 μm; H–K = 10 μm.

Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Melanommataceae.



Type species: Seifertia azaleae (Peck) Partr. & Morgan-Jones, basionym: Periconia azaleae Peck. Representative strain: DAOM 239136.



DNA barcode (genus): LSU.



DNA barcodes (species): LSU, tef1. Table 14.



Table 14.

DNA barcodes of accepted Seifertia spp.

Species	Isolates1	GenBank accession numbers2			References
		LSU	ITS	tef1
Seifertia azaleae	DAOM 239136	EU030276	–	–	Seifert et al. (2007)
	CPC 35017	MK540034	MK539964	MK540166	Present study
Sei. shangrilaensis	MFLUCC 16-0238T	KU954100	–	KU954101	Li et al. (2016b)

¹CPC: Culture collection of Pedro Crous, housed at Westerdijk Fungal Biodiversity Institute; DAOM: Plant Research Institute, Department of Agriculture (Mycology), Ottawa, Canada; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Ria, Thailand. ^T indicates ex-type strains.

²LSU: partial large subunit (28S) nrRNA gene; ITS: internal transcribed spacers and intervening 5.8S nrDNA; tef1: partial translation elongation factor 1-alpha gene.

Mycelium superficial or immersed, composed of branched, septate, smooth- and thin-walled, pale white to white or brown hyphae. Synnemata erect, simple, unbranched or very rarely branched, greenish when young, becoming dark brown to black at maturity, capitate at the apex. Conidiophores macronematous, synnematous, straight or slightly flexuous, unbranched or branched toward the upper region, cylindrical, septate, smooth- and thin-walled, hyaline to pale brown or olivaceous brown to brown. Conidiogenous cells mono- or polyblastic, integrated, terminal, determinate, cylindrical to subclavate or doliiform, smooth-walled. Conidia acropleurogenous, holoblastic, in simple or branched acropetal chains, dry, sometimes aggregated into slimy masses at the apex of the synnema, aseptate or very rarely 1-septate, smooth- and thin-walled, oblong, ellipsoidal, subglobose or fusiform, hyaline to subhyaline, pale brown or olivaceous (adapted from Partridge & Morgan-Jones 2002).



Culture characteristics: Colonies effuse, powdery or cottony to fairy fluffy, grey to dark brown.



Optimal media and cultivation conditions: MEA, OA and PDA at 25 °C.



Distribution: North America, Europe and Asia.



Hosts: Species of Rhododendron.



Disease symptoms: Bud and twig blight; Rhododendron bud blight disease.



Notes: Seifertia was introduced by Partridge & Morgan-Jones (2002) to accommodate Pycnostysanus azaleae based on morphological differences. Seifertia azaleae is morphologically similar to Sorocybe resinae. However, Partridge & Morgan-Jones (2002) decided to erect the new genus Seifertia since Sei. azaleae produces much narrower conidia and has minute denticles on the conidiogenous cells. Seifertia is characterised by erect, simple, and dark synnemata, macronematous conidiophores, holoblastic, integrated, terminal and determinate conidiogenous cells, and unicellular or very rarely 1-septate, pale brown or olivaceous conidia. This cosmopolitan genus occurs on azaleas and rhododendrons causing a disease known as Rhododendron bud blight disease, in which the flower buds die, and twig blight occurs. Infected buds are easily recognisable by the blackening of the bud and the development of numerous synnemata which appear as tiny black spines over the entire surface (Partridge and Morgan-Jones, 2002, Glawe and Hummel, 2006).

 This genus, which is relatively poorly studied, was recently placed in Melanommataceae by Li et al. (2016b), when they introduced the second species belonging to Seifertia, Sei. shangrilaensis. However, the relation of Seifertia with Mycopappus and its synasexual morph Xenostigmina, which are foliar pathogens belonging to Melanommataceae, was demonstrated previously by Crous et al. (2009a).



References: Partridge & Morgan-Jones 2002 (morphology), Glawe & Hummel 2006 (pathogenicity), Seifert et al., 2007, Li et al., 2016b (morphology and phylogeny).



Authors: Y. Marin-Felix & P.W. Crous



Seiridium Nees, Das System der Pilze und Schwämme: 22. 1817. Fig. 62.

Fig. 62.

Seiridium spp. A–F. Disease symptoms on Cupressaceae hosts. A–C. Flagging of branches. D. Trunk canker with gummosis. E. Branch canker. F. Conidiomata. G–I.Seiridium pezizoides (CBS 145115). G, H. Acervuli on Cupressaceae sp. I. Conidial masses on artificial media. J, K. Conidiophores and conidiogenous cells. J.Seiridium neocupressi (CBS 142625). K.Seiridium eucalypti (CBS 343.97). L–R. Conidia. L.Seiridium cardinale (CBS 909.85). M.Seiridium spyridicola (CBS 142628). N.Seiridium unicorne (CBS 538.82). O.Seiridium neocupressi (CBS 142625). P.Seiridium eucalypti (CBS 343.97). Q.Seiridium kartense (CBS 142629). R.Seiridium pezizoides (CBS 145115). S–U.Seiridium cupressi (IMI 40096). S, T. Ascomata. U. Ascospores. Scale bars: F = 2 mm; G, H = 50 μm; J–U = 10 μm. Pictures J–U taken from Bonthond et al. (2018).

Synonym: Pestalotia De Not., Mém. Reale Accad. Sci. Torino 3: 80. 1841.

Additional synonyms in Bonthond et al. (2018).



Classification: Sordariomycetes, Xylariomycetidae, Xylariales, Sporocadaceae.



Type species: Seiridium marginatum Nees, Syst. Pilze (Würzburg): 23. 1817. Neotype designated by Shoemaker et al. (1966): K 200376. Epitype and ex-epitype culture designated by Jaklitsch et al. (2016): WU 33575, CBS 140403.



DNA barcode (genus): ITS.



DNA barcodes (species): ITS, rpb2, tef1, tub2. Table 15. Fig. 63.



Table 15.

DNA barcodes of accepted Seiridium spp.

Species	Isolates.1	GenBank accession numbers2				References
		ITS	rpb2	tef1	tub2
Seiridium camelliae	MFLUCC 12-0647T	JQ683725	–	JQ683741	JQ683709	Maharachchikumbura et al. (2015)
S. cancrinum	CBS 226.55T	LT853089	LT853137	LT853186	LT853236	Bonthond et al. (2018)
S. cardinale	CBS 909.85R	LT853064	LT853113	LT853161	LT853211	Bonthond et al. (2018)
S. ceratosporum	PHSI2001Pathcw07	AY687314	–	–	DQ534043	Liu et al. (2007)
S. cupressi	CBS 224.55ET	LT853083	LT853131	LT853180	LT853230	Bonthond et al. (2018)
S. eucalypti	CBS 343.97ET	LT853099	LT853146	LT853196	LT853246	Bonthond et al. (2018)
S. kartense	CBS 142629T	LT853100	LT853147	LT853197	LT853247	Bonthond et al. (2018)
S. kenyanum	CBS 228.55T	LT853098	LT853145	LT853195	LT853245	Bonthond et al. (2018)
S. marginatum	CBS 140403GT	KT949914	LT853149	LT853199	LT853249	Jaklitsch et al., 2016, Bonthond et al., 2018
S. neocupressi	CBS 142625T	LT853079	LT853127	LT853176	LT853226	Bonthond et al. (2018)
S. papillatum	CBS 340.97T	LT853102	LT853150	LT853200	LT853250	Bonthond et al. (2018)
S. persooniae	CBS 143445T	MG386033	–	–	MG386163	Crous et al. (2017b)
S. pezizoides	CBS 145115	MK079342	MK058475	MK058480	MK058485	Present study
S. phylicae	CBS 133587T	LT853091	LT853139	LT853188	LT853238	Bonthond et al. (2018)
S. podocarpi	CBS 137995T	LT853101	LT853148	LT853198	LT853248	Bonthond et al. (2018)
S. pseudocardinale	MFLUCC 13-0525T	KU848210	–	–	–	Wijayawardene et al. (2016)
	CBS 145114	MK079341	MK058479	MK058484	MK058489	Present study
S. rosarum	MFLUCC 17-0654T	MG828961	–	–	–	Wanasinghe et al. (2018)
S. spyridicola	CBS 142628T	LT853095	LT853142	LT853192	LT853242	Bonthond et al. (2018)
S. unicorne	CBS 143871ET	MK079339	MK058477	MK058482	MK058487	Present study
	CBS 143872	MK079338	MK058476	MK058481	MK058486	Present study
	CBS 143873	MK079340	MK058478	MK058483	MK058488	Present study
	CBS 538.82R	LT853088	LT853136	LT853185	LT853235	Bonthond et al. (2018)
S. venetum	MFLU 15-0369R	KT438836	–	–	KT438837	Maharachchikumbura et al. (2015)

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; MFLU and MFLUCC: Herbarium and culture collection of Mae Fah Luang University, Chiang Rai, Thailand, respectively; PHSI: from Liu et al. (2007). ^{T, ET, GT} and ^R indicate type or ex-type, ex-epitype, ex-generic type and reference strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene.

Fig. 63.

A–D. Boxplots of conidial measurement data in μm from S. unicorne and other Cupressaceae pathogens. The boxes show the lower and upper quantiles and whiskers extend to 1.5x the interquartile range. Except for the new epitype all measurements are adapted from Bonthond et al. (2018). The ex-epitype strain (CBS 143871), holotype (IMI 5816) and reference strain (CBS 538.82) of S. unicorne are highlighted in blue. E. The best Maximum Likelihood (ML) tree based on four loci (ITS: 616 bp, rpb2: 802 bp, tef1: 633 bp, tub2: 809 bp). Nodes are labelled with ML bootstrap values (BS > 49 %)/Bayesian posterior probabilities (PP > 0.49) using the same model selection, settings and software as in Bonthond et al. (2018). Strains are displayed by number, host and country of collection. GenBank accession numbers are listed in Bonthond et al. (2018) and in Table 15. ^{T, ET, GT} and ^R indicate ex-type, ex-epitype, ex-generic type and reference strains, respectively. TreeBASE: S23390.

Ascomata perithecial, immersed to semi-erumpent, depressed, globose to pyriform, scattered or confluent, with central ostiole; necks slightly papillate, black, periphysate; ascomatal wall dark brown, pseudoparenchymatous. Paraphyses hyaline, smooth-walled, filiform. Asci cylindrical, 8-spored, unitunicate, thin-walled, stipitate, with an apical amyloid ring. Ascospores cylindrical-oblong, euseptate, septa often thicker than the wall, yellow- to dark brown, guttulate. Conidiomata acervuloid to pycnidioid, semi-immersed to erumpent, uni- to plurilocular, brown or black, glabrous, dehiscing by irregular splits in the upper wall. Conidiophores lining the cavity of the conidioma, septate and sparsely branched at the base, or reduced to conidiogenous cells, hyaline, smooth-walled. Conidiogenous cells discrete, integrated, ampulliform to lageniform or subcylindrical, hyaline, smooth-walled, proliferating percurrently at the apex. Conidia fusiform, euseptate (septal pores present or not), end cells hyaline, median cells dark brown to brown, wall thick, smooth or with striations, constricted at septa or not; apical cell with single or multiple, unbranched or branched appendages; basal cell with or without a centric, unbranched or sometimes branched appendage (adapted from Bonthond et al. 2018).



Culture characteristics: Colonies on PDA circular to irregular, reaching 12–68 mm diam after 14 d at 22 °C, mostly flat, in some cultures elevated at margins, often white coloured or with other colours, sporulation rare, with pycnidioid conidiomata. On SNA circular to irregular to rhizoid, reaching 20–54 mm diam after 14 d at 22 °C, mostly flat, white coloured, with moderate to abundant aerial mycelium, sporulation for some species within and others after 2 wk, sporodochia often compact and scattered.



Optimal media and cultivation conditions: Colonies grow well on CMA, MEA, PDA and SNA at 22 °C. Most species sporulate on SNA and some species on CMA, MEA or PDA as well.



Distribution: Worldwide.



Hosts: A diversity of gymnosperms and angiosperms. The genus is most well-known from members of Cupressaceae.



Disease symptoms: Cankers on stems and twigs.



Notes: Pestalotia was introduced in 1841 and is similar to Seiridium (1817), one of the older names in the Sporocadaceae. The genus has been subjected to many rearrangements (reviewed in Sutton 1969) which eventually resulted in the genus accommodating only the type species, Pe. pezizoides. One of the important characters used to separate Pestalotia from the related genera Pestalotiopsis and Truncatella was the production of 5-septate (or 6-celled) conidia. However, this morphology is typical for Seiridium as well, and for this reason it was speculated that Pestalotia and Seiridium could be congeneric (Maharachchikumbura et al. 2014). A fresh collection of Pe. pezizoides from Vitis vinifera collected in the USA was recently obtained (Table 1), which matches in all respects with the type of Pe. pezizoides. DNA sequence data generated here confirm that Pe. pezizoides clusters within Seiridium (Fig. 63). Therefore, Pestalotia is reduced to synonymy with Seiridium. For Seiridium, the here synonymised Pestalotia and related genera, not only the number but also the type of conidial septation has been a commonly reported descriptor. Different authors have interpreted the appearance of the cell walls as either distoseptate (e.g. Nag Raj 1993) or euseptate (e.g. Sutton 1980). Although when examined by light microscopy, conidia can appear as distoseptate, electron microscopic studies on S. cupressi (Roberts & Swart 1980) and S. pezizoides (Griffiths & Swart 1974) have shown that the conidial cell walls are differentiated into multiple zones but arise from a single layered cell wall and are thus euseptate. Since the sexual morph is known for only a few species, the taxonomy in Seiridium has been based mainly on asexual morphology. However, the generic type (S. marginatum) is one of the exceptions where both morphs have been characterised. This species was re-described and epitypified by Jaklitsch et al. (2016), who also provided detailed illustrations of sexual and asexual morphology.



References: Nag Raj 1993 (morphology), Danti & Della Rocca 2017 (pathogenicity), Bonthond et al. 2018 (morphology and phylogeny),



Seiridium cupressi (Nattrass et al.) Bonthond, Sand.-Den. & Crous, comb. nov. MycoBank MB830554.

Basionym: Rhynchosphaeria cupressi Nattrass et al., Trans. Brit. Mycol. Soc. 46: 103. 1963.

Synonyms: Cryptostictis cupressi Guba, Monograph of Monochaetia and Pestalotia: 47. 1961. Nom. inval. Art. 40.3 (Shenzhen).

Lepteutypa cupressi (Nattrass et al.) H.J. Swart, Trans. Brit. Mycol. Soc. 61: 79. 1973.

Seiridium cupressi (Guba) Boesew, Trans. Brit. Mycol. Soc. 80: 545. 1983. Nom. inval. Art. 40.3 (Shenzhen).



Description: Sexual morph Nattrass et al. (1963). Asexual morph Bonthond et al. (2018).



Known distribution: Africa (Kenya, Uganda) and Europe (Greece).



Typus: Africa, Kenya, on Cupressus macrocarpa, July 1954, R.M. Nattrass (holotype of Rhynchosphaeria cupressi IMI 56917); from cankers in branches of Cupressus macrocarpa, 1949, D.R. Jones [epitype of Rhynchosphaeria cupressi designated here IMI 52254, MBT386544 (dried culture), culture ex-epitype CBS 224.55].



Additional materials examined: Europe, Greece, from Cupressus sp., A. Graniti, CBS 122616 = CMW 1646. Africa, Kenya, non-pathogenic isolate from Cupressus sp., collection data unknown, CBS 320.51; on Cupressus macrocarpa, July 1948, R.M. Nattrass, IMI 37158; on Cupressus macrocarpa, Dec. 1949, R.M. Nattrass, IMI 40096; from cankers in branches of Cupressus forbesii, 1949, D.R. Jones, IMI 52255 (dried culture); CBS 225.55.



Notes: This species has been a source of confusion since its introduction (Guba 1961). Bonthond et al. (2018) showed that Guba’s diagnosis included three different species (S. cancrinum, S. cupressi and S. kenyanum) and selected an epi- and lectotype for Cryptosticis cupressi. The latter name, however, was invalidly published (article 40.1). Nattrass et al. (1963) re-examined the material from Guba (1961) and synonymised C. cupressi with Monochaetia unicornis. Despite noting small morphological differences between the asexual stage of R. cupressi and the type of M. unicornis (i.e. smaller and slender conidia), they were not able to confirm the exogenous origin of the basal appendage, which was the main argument for Guba (1961) to place the species in Cryptostictis instead of Monochaetia. In the same study, Nattrass et al. (1963) described the sexual morph of M. unicornis as Rhynchosphaeria cupressi based on three specimens: IMI 37158, IMI 40096 and the holotype IMI 56917. Bonthond et al. (2018) examined each of these specimens but incorrectly cited the holotype as IMI 37158. While only the sexual morph was found in these materials, the original description from Nattrass et al. (1963) includes drawings, photographs and measurements of the conidia. These measurements (22–32 × 6–9.5 μm) fall perfectly within the range documented for the lineage currently assigned to S. cupressi (Guba) Boesew. (18–36 × 5–11.5 μm) (Bonthond et al. 2018). Consequently, being the oldest valid name for this lineage and in accordance with the rule of priority Ry. cupressi is recombined in Seiridium, as S. cupressi (Nattrass et al.) Bonthond, Sand.-Den. & Crous, and an epitype is designated (IMI 52254). The similar species S. cancrinum and S. unicorne show smaller conidia (20–30.5 μm and 19–28 μm, respectively), whereas conidia of S. kenyanum are considerably larger (24–39 μm).



Seiridium pezizoides (De Not.) Crous, comb. nov. MycoBank MB828021. Fig. 64.

Fig. 64.

Seiridium pezizoides (CBS 145115). A–D. Colony morphology in 90-mm-diam Petri dishes after 10 d at 22 °C on MEA, SNA, PDA and CMA, respectively. E–K. Conidiomata on Vitis vinifera. L, M. Conidiophores. N. Conidia. Scale bars: E = 1 mm; F–K = 100 μm; L–N = 10 μm.

Basionym: Pestalotia pezizoides De Not., Mém. Reale Accad. Sci. Torino 2, 3: 80. 1839.



Caulicolous. Isolated from branches of Vitis vinifera. On the host (described in more detail by Nag Raj 1993): Conidiomata irregularly scattered over the surface, gregarious to confluent, discoid to cupulate and occasionally globose, erumpent from tissue, acervular to sporodochial, occasionally with aerial mycelium, black to brown, (300–)350–500(–650) μm. On SNA: Conidiophores tightly aggregated in the conidioma, cylindrical, irregularly branched, hyaline or pale brown at the base, smooth- and thin-walled. Conidiogenous cells discrete, hyaline, cylindrical, smooth- and thin-walled. Conidia lunate to falcate, often curved, 5-septate, not striate, bearing a basal and two or more apical appendages, euseptate with pores sometimes visible, (24–)28–33.5(–38.5) × (6–)7–8(–9) μm, mean ± SD = 30.7 ± 2.8 × 7.5 ± 0.4 μm; basal cell obconic with truncate base, hyaline, smooth-walled, bearing marginal frills, 4–7 μm; four median cells pale brown, smooth-walled, cylindrical to doliiform; second cell from base 3.5–8 μm; third cell 3.5–7 μm; fourth cell 3.5–6.5 μm; fifth cell 3.5–7.5 μm; apical cell conical, hyaline, smooth-walled, 4.5–8.5 μm long; apical appendages single or multiple, centric, branched or unbranched, 8.5–27 μm; basal appendage single, cylindrical, centric, occasionally branched, 5.5–14 μm.



Culture characteristics: Colonies on PDA circular, reaching 34–37 mm diam after 10 d at 22 °C, flat, olivaceous to luteous in the centre, white to brown at the margins, with abundant aerial mycelium at the margins, not sporulating within 10 d. On CMA circular, reaching 39–41 mm diam after 10 d at 22 °C, flat at centre and margins, dark brown to black, without aerial mycelium, not sporulating within 10 d. On MEA circular to slightly irregular, reaching 25–27 mm diam after 10 d at 22 °C, flat, olivaceous to pale green, with a white outer ring, with moderate aerial mycelium, massive spore production in the centre. On SNA circular, reaching 31–33 mm diam after 10 d at 22 °C, raised in the centre, flat at the margins, with moderate aerial mycelium, no sporulation within 10 d.



Distribution: Europe (France, Italy), USA.



Typus: Italy, near Mailand, twig of Vitis vinifera (Vitaceae), leg. Oct. 1838, De Notaris, holotype, RO.



Additional material examined: USA, Virginia, Charlottesville, from a complex hybrid of Vitis æstivalis × Vitis cinerea × Vitis vinifera, 2018, L. Morton, CBS 145115 = CPC 35011.



Notes: After several rearrangements and the introduction of the genera Pestalotiopsis and Truncatella (see Sutton 1969 and references therein), the generic type Pe. pezizoides was the only remaining species in Pestalotia. A specimen of Pe. pezizoides (IMI 83642, from branches of Vitis vinifera, Italy, non-type) was examined and redescribed by Sutton (1980). A more detailed description was provided by Nag Raj (1993), based on several materials, including this specimen. The present study is the first to provide DNA sequence data on this species. We sequenced four loci (ITS, rpb2, tef1 and tub2) and included Pe. pezizoides in an updated phylogeny of Seiridium (Fig. 63) which supports the conclusion that Pestalotia and Seiridium are congeneric. Consequently, the species is transferred to Seiridium as S. pezizoides. The S. pezizoides strain (CBS 145115 = CPC 35011) that was included in this analysis conforms morphologically with the description and was isolated from the same host, Vitis. However, since the specimen was collected in Virginia (USA) and the holotype is from Italy, it is not suitable for epitypification. The phylogeny generated here suggests that S. pezizoides is most closely related to S. rosarum (Rosa canina, Italy).



Seiridium unicorne (Cooke & Ellis) B. Sutton, Mycol. Pap. 138: 74. 1975. Fig. 65.

Fig. 65.

Seiridium unicorne (ex-epitype CBS 143871). A–D. Colony morphology in 90-mm-diam Petri dishes after 10 d at 22 °C on MEA, SNA, PDA and CMA, respectively. E. Symptoms on naturally infected host. F, G. Conidiomata on artificially infected Cupressaceae sp. H. Sporulation on PDA. I. Conidioma on SNA partially immersed in agar. J–O. Conidiophores and conidia. P. Conidia. Scale bars: F–H = 100 μm; I–P = 10 μm.

Basionym: Pestalotia unicornis Cooke & Ellis, Grevillea 7: 6. 1878, as "Pestalozzia".

Synonym: Monochaetia unicornis (Cooke & Ellis) Sacc. & D. Sacc., Syll. Fung. 18: 485. 1906.



Caulicolous. Most commonly isolated from cankers on branches of species from Cupressaceae. Conidiomata on PDA numerous, sporodochial, globose or clavate, mostly solitary, erumpent from agar, partially immersed in mycelium, producing large black spore masses; on SNA, sporodochial, mostly aggregated, erumpent from agar, producing large black spore masses. On SNA: Conidiophores septate, cylindrical, irregularly branched, hyaline or brown, thin-walled, 22–68 μm long, ex-epitype: 22–50 μm long. Conidiogenous cells discrete, hyaline, cylindrical, smooth- and thin-walled, 3.5–29.5 × 1.5–3.5 μm, ex-epitype: 16.2–28.9 × 1.7–3.5 μm, proliferating percurrently, with visible collarettes and minute periclinal thickenings. Conidia lunate to falcate, curved, 5-septate, rarely 4- or 6-septate, not striate, bearing two appendages, euseptate with no visible pores, (19–)22.5–26.5(–28) × (6.5–)7.5–8.5(–9.5) μm, mean ± SD = 24.5 ± 1.8 × 7.9 ± 0.5 μm, ex-epitype: (19–)22.5–26.5(–28) × (6.5–)7.5–8.5(–9) μm, mean ± SD = 24.4 ± 1.9 × 7.8 ± 0.4 μm; basal cell obconic with a truncate base, hyaline, walls smooth, bearing minute marginal frills, 2.5–9.5 μm, ex-epitype: 2.5–6 μm (n = 119); four median cells colour varying from pale to dark brown, smooth-walled, cylindrical to doliiform; second cell from base 3.5–6 μm (n = 152); third cell 3–5.5 μm; fourth cell 3–5.5 μm; fifth cell 3–5.5 μm, ex-epitype: second cell from base 3.5–6 μm; third cell 3–5.5 μm; fourth cell 3–5 μm; fifth cell 3–5.5 μm; apical cell conical, hyaline, smooth-walled, 2–5.5 μm long, ex-epitype: 2–5.5 μm long; apical appendage single, mostly centric, 5–10 μm, ex-epitype: 5–9.5 μm; basal appendage single, cylindrical, mostly excentric, 2.7–7.1 μm, ex-epitype: 4–6.5 μm (adapted from Bonthond et al. 2018).



Culture characteristics: Colonies on PDA irregular, reaching 65–68 mm diam after 14 d at 22 °C, slightly umbonate, colour citrine, olivaceous buff to olivaceous, with compact aerial mycelium on the surface, abundant sporulation surrounding centre and at the margins of the colony. On CMA circular or irregular, reaching 58–59 mm diam after 14 d at 22 °C, flat at the centre and margins, citrine to olivaceous coloured, with moderate aerial mycelium on the surface, sporulating abundantly. On MEA irregular, reaching 35–40 mm diam after 14 d at 22 °C, flat to crateriform, slightly sunk into the agar, buff to olivaceous coloured at the centre becoming white at the margins, with dense mycelium on the surface, sporulating near the centre. On SNA circular to slightly irregular, reaching 20–21 mm diam after 14 d at 22 °C, umbonate, with moderate aerial mycelium, sporulation abundant between centre and margins.



Distribution: New Zealand, South Africa and USA.



Typus: USA, Maryland, Pocomoke City, 38.072952N, 75.555852W, from branch canker of Cupressus sp., 2017, S.A. Krueger-Hadfield (epitype of Pestalotia unicornis designated here CBS H-23739, MBT383596, cultures ex-epitype CBS 143871 = CPC 34650, CBS 143872 = CPC 34649, CBS 143873 = CPC 34651); New Jersey, from Chamaecyparis thyoides, 1878, J.B. Ellis (holotype of Pestalotia unicornis IMI 5816).



Additional materials examined: New Zealand, from Cryptomeria japonica, 1981, H.J. Boesewinkel (CBS H-23151 reference specimen, culture CBS 538.82 = CPC 23783 = NBRC 32684). South Africa, from Cupressus sempervirens, 1999, I. Barnes (culture CBS 120306 = CMW 5596).



Notes: Seiridium unicorne (basionym: Pestalotia unicornis) is the earliest described cypress pathogen (Cooke & Ellis 1878) of Seiridium and was isolated from “cedar wood” collected in New Jersey (USA). The host was later identified by W.W. Wagener as Chamaecyparis thyoides, as indicated on the holotype label (see Bonthond et al. 2018). The genus Seiridium accommodates multiple species infecting Cupressaceae and S. unicorne has traditionally been regarded as a mild pathogen but capable of infecting a broad range of hosts, including plant species beyond the Cupressaceae (Guba 1961). The holotype (IMI 5816) was obtained and examined during a preceding study (Bonthond et al. 2018) and found to be limited to two microscope slides. Therefore, the selection of an epitype for S. unicorne is important to consolidate a stable taxonomic concept for this taxon. Given the occurrence of related species which are pathogenic on the same hosts (i.e. S. cancrinum, S. cardinale, S. cupressi and S. neocupressi) the availability of ex-epitype DNA sequence data provides a valuable reference for the identification of future collections. The specimen we introduce here as epitype (CBS H-23739) was collected from necrotic lesions of a Cupressus sp. in Maryland, USA and matches morphologically in all respects with the holotype (IMI 5816) and the reference strain (CBS 538.82) of S. unicorne. Furthermore, in the four-locus phylogeny (Fig. 63E) the ex-epitype strain clusters under a fully supported node in the clade that was assigned to S. unicorne based on morphology (Bonthond et al. 2018). Conidial measurements strongly overlap between the selected epitype, holotype and reference strain (Fig. 63A–D), although the median width of the epitype being slightly narrower in comparison to the holotype and reference strain. Measurements of basal and apical appendages and distributions of those measurements are highly similar between epitype and reference strain. For both appendages, the variation in measurements is higher for the holotype compared to the reference strain and the epitype, which, however, likely results from the age and condition of the material as we observed that conidial appendages from the holotype were often damaged.



Authors: G. Bonthond, M. Sandoval-Denis, S.A. Krueger-Hadfield, L. Morton, C. Ambers & P.W. Crous



Septoriella Oudem., Ned. kruidk. Archf, ser. 2, 5: 504. 1889. Fig. 66.

Fig. 66.

Septoriella spp. A. Conidiomata on OA of Septoriella hirta (ex-neotype CBS 536.77). B. Conidiomata in vivo of Septoriella phragmitis (ex-epitype CBS 140065). C. Conidial cirrhus of Septoriella phragmitis (ex-epitype CBS 140065). D. Conidioma of Septoriella hirta (ex-neotype CBS 536.77). E, F. Section through conidiomata of Septoriella hirta (ex-neotype CBS 536.77). G–I. Conidiogenous cells. G.Septoriella oudemansii (ex-type CBS 138012). H, I.Septoriella phragmitis (ex-epitype CBS 140065). J. Developing conidia of Septoriella hirta (ex-neotype CBS 536.77). K–O. Conidia. K.Septoriella hirta (ex-neotype CBS 536.77). L.Septoriella oudemansii (ex-type CBS 138012). M.Septoriella poae (ex-type CBS 136766). N, O.Septoriella phragmitis (ex-epitype CBS 140065). Scale bars: D, E = 100 μm; F = 50 μm; all others = 10 μm. Pictures A–F, H–K, N, O taken from Crous et al., 2015a, Crous et al., 2015b, Crous et al., 2015c; G, L from Crous et al. (2014b).

Synonyms: Allophaeosphaeria Ariyaw. et al., Fungal Diversity 72: 137. 2015.

Poaceicola W.J. Li et al., Mycosphere 6: 696. 2015.

Vagicola Chethana & K.D. Hyde, Fungal Diversity 75: 113. 2015.



Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Phaeosphaeriaceae.



Type species: Septoriella phragmitis Oudem. Epitype and ex-epitype strain designated by Crous et al. (2015a): CBS H-22281, CBS 140065.



DNA barcode (genus): LSU. Fig. 28.



DNA barcodes (species): ITS, rpb2, tef1, tub2. Table 16. Fig. 67.



Table 16.

DNA barcodes of accepted Septoriella spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	rpb2	tef1	tub2
Septoriella agrostina	MFLU 18-0113HT	MG828945	–	MG829227a	–	Wanasinghe et al. (2018)
Sep. allojunci	MFLUCC 15-0701T	KU058718	–	MG520935a	–	Li et al., 2015, Phookamsak et al., 2017
Sep. artemisiae	MFLUCC 17-0693T	MG828929	–	–	–	Wanasinghe et al. (2018)
Sep. arundinicola	MFLU 16-0225HT	MG828946	MG829261	MG829228a	–	Wanasinghe et al. (2018)
Sep. arundinis	MFLUCC 15-0702T	KU058716	–	MG520921a	–	Li et al., 2015, Phookamsak et al., 2017
Sep. bromi	MFLUCC 13-0739T	KU058717	–	–	–	Li et al. (2015)
Sep. chlamydospora	MFLUCC 15-0177T	KU163658	–	–	–	Hyde et al. (2018)
Sep. dactylidicola3	MFLUCC 14-0002T	–	–	–	–	–
Sep. dactylidis	MFLU 15-2720HT	KU163657	–	–	–	Jayasiri et al. (2015)
Sep. elongata	MFLUCC 12-4444T	KM491546	–	–	–	Li et al. (2015)
Sep. forlicesenica	MFLUCC 15-0470T	KX926422	KY131966	MG520922a	–	Phookamsak et al., 2017, Thambugala et al., 2017
Sep. garethjonesii	MFLUCC 15-0469T	KX926425	KX898363	MG520923a	–	Phookamsak et al., 2017, Thambugala et al., 2017
Sep. germanica	CBS 145372T	MK539965	MK540096	MK540159b	MK540174	Present study
Sep. hibernica	CBS 145371T	MK539966	MK540097	–	–	Present study
Sep. hirta	CBS 536.77ET	KR873249	KR873324	–	–	Crous et al. (2015a)
Sep. hollandica	CBS 145374T	MK539967	MK540098	MK540160b	MK540175	Present study
Sep. hubertusii	CBS 338.86T	KF251230	KF252235	–	KF252717	Quaedvlieg et al. (2013)
Sep. italica	MFLUCC 13-0267T	KX926421	KX891169	MG520924a	–	Phookamsak et al., 2017, Thambugala et al., 2017
Sep. leuchtmannii	CBS 459.84IsoT	KF251188	KF252195	KF253144b	KF252682	Quaedvlieg et al. (2013)
Sep. muriformis	MFLUCC 13-0277T	KX926415	KX863710	–	–	Thambugala et al. (2017)
Sep. neoarundinis	MFLUCC 15-0027T	KY706139	–	MG520936a	–	Phookamsak et al., 2017, Thambugala et al., 2017
Sep. neodactylidis	MFLUCC 13-0618T	KP744432	–	–	–	Liu et al. (2015)
Sep. oudemansii	CBS 138012T	KR873250	–	–	–	Crous et al. (2015a)
Sep. phragmitis	CBS 140065ET	KR873251	–	–	–	Crous et al. (2015a)
Sep. poae	CBS 136766T	KJ869111	KJ869233	–	–	Crous et al. (2014b)
Sep. pseudophragmitis	CBS 145417T	MK560161	MK559450	MK559452b	MK559451	Present study
Sep. rosae	MFLU 18-0114HT	MG828948	–	MG829230a	–	Wanasinghe et al. (2018)
Sep. subcylindrospora	MFLUCC 13-0380T	KT314184	–	–	–	Ariyawansa et al. (2015a)
Sep. tridentina	MFLUCC 15-0475T	KX926424	KX891171	–	–	Thambugala et al. (2017)
Sep. vagans	CBS 604.86	KF251193	KF252200	KF253149b	KF252687	Quaedvlieg et al. (2013)

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; MFLU and MFLUCC: Herbarium and culture collection of Mae Fah Luang University, Chiang Rai, Thailand, respectively. ^{T, ET, HT} and ^IsoT indicate ex-type, ex-epitype, holotype and ex-isotype strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene. ^a and ^b in tef1 column indicate the primers used in sequencing: a: EF1-983F, EF1-2218R, b: EF1-728F, EF-2.

³Only LSU and SSU sequences available: KY657264 and KY657265, respectively (Thambugala et al. 2017).

Fig. 67.

RAxML phylogram obtained from the combined ITS (580 bp), LSU (849 bp) and rpb2 (1083 bp) sequence alignment of all accepted species of Septoriella. The tree was rooted to Neostagonospora caricis CBS 135092 and Neostagonospora elegiae CBS 135101. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 % and Bayesian posterior probability scores above 0.95 are shown at the nodes. GenBank accession numbers of LSU are listed in Fig. 28, and of the other loci in Tables 7 and 16. ^{T, ET, HT} and ^IsoT indicate ex-type, ex-epitype, holotype and ex-isotype strains, respectively. TreeBASE: S23834.

Ascomata ostiolate, solitary to gregarious, immersed to semi-immersed or superficial, broadly ellipsoidal to globose, subglobose, or obpyriform, brown to dark brown or black, smooth-walled, coriaceous, uni- to biloculate; necks central, flush to papillate, brown to dark brown or black, with or without periphyses, rarely comprising short, hyaline setae; ascomatal wall thin-walled, outer layers composed of brown to dark brown or blackish cells of textura angularis, inner layers composed of brown cells of textura prismatica, or of hyaline or brown cells of textura angularis, rarely composed of hyaline gelatinous cells. Hamathecium composed of numerous, 1–3 μm wide, filiform to broadly cylindrical, septate, cellular pseudoparaphyses, or lacking pseudoparaphyses. Asci 8-spored, bitunicate, fissitunicate, cylindrical, broadly cylindrical, cylindrical-fusiform, cylindrical-clavate, clavate, or broadly clavate, pedicellate, apically rounded with an ocular chamber. Ascospores overlapping, 1–3-seriate, hyaline to yellowish brown or pale brown, brown, golden brown, or reddish brown, narrowly or broadly fusiform or oblong to narrowly oblong, straight or slightly curved, smooth-walled or echinulate, multi-septate, with transverse septa, with or without longitudinal septa, sometimes with enlarged medium cells, constricted or not at septa, conical or obtuse, rounded ends, with or without sheath. Conidiomata pycnidial, solitary or aggregated, immersed to semi-immersed, globose to subglobose, unilocular, pale brown to brown or dark brown, with central, papillate, circular ostiole; conidiomatal wall of brown cells of textura angularis, rarely of textura oblita, inner layers becoming hyaline. Conidiophores lining the inner cavity, reduced to conidiogenous cells, invested in mucus. Conidiogenous cells ampulliform to lageniform, hyaline, smooth-walled, proliferating via inconspicuous percurrent proliferations near apex. Conidia cylindrical to subcylindrical, fusiform, or subfusiform, apex obtuse to subobtuse, base truncate, straight or curved, euseptate, pale brown to brown, thin-walled, smooth-walled or minutely verruculose, bearing mucoid appendages at both ends (type H sensu Nag Raj 1993) (description of asexual morph adapted from Crous et al. 2015a).



Culture characteristics: Colonies with moderate to abundant aerial mycelium, variable in colour, circulate or lobate. On PDA surface white to iron-grey or grey olivaceous, greyish white, pale olivaceous grey, or dull green margins, mouse grey in the middle and pale mouse grey at the center; reverse grey, olivaceous grey, dull green, buff to dark brown, olivaceous to pale brown or black, brown or olivaceous brown to black. On MEA surface white, dirty white, or white to pale yellow or iron-grey; reverse yellow, umber, buff, or dark grey to black.



Optimal media and cultivation conditions: CMA, MEA, OA and PDA at 25 °C.



Distribution: Mostly Europe, but also reported in Asia and North America.



Hosts: Mostly saprophytes of grasses (Poaceae), including Arundo spp., Agrostis stolonifera, Bromus sterilis, Calamagrostis spp., Dactylis glomerata, Elymus glaucus, E. repens, Poa sp., Phragmites spp. and Setaria verticillata. Also found on Rosa canina (Rosaceae) and Juncus sp. (Juncaceae), and others hosts not molecularly corroborated. Septoriella hirta is considered and important secondary pathogen of grasses, including Agropyron spp., Bromus spp., Dactylis glomerata, Festuca spp., Poa spp., Stipa spp., and Triticum spp., among others.



Disease symptoms: Secondary foot rot and rot of mature straw. Discoloured culms and predisposition of the plant to premature collapse.



Notes: Septoriella was considered an asexual genus characterised by pycnidial, unilocular conidiomata, and cylindrical to fusoid, euseptate conidia bearing mucoid appendages at both ends (Crous et al. 2015a). However, in our phylogenetic studies based on ITS and LSU, and on the combined dataset, the ex-type strains of the sexual genera Allophaeosphaeria, Poaceicola and Vagicola were located in the clade representing the genus Septoriella. Therefore, these genera are synonymised with Septoriella in the present study.

 Allosphaeosphaeria was recently introduced by Liu et al. (2015) to incorporate two new saprophytic species found on Dactylis glomerata from Italy, i.e. Al. dactylidis and Al. muriformia, the latter designated as type species. These species only produce the sexual morph characterised by ascospores with transverse and longitudinal septa, and a gelatinous sheath. Subsequently, three other new species were introduced in the genus, i.e. Al. clematidis, Al. cytisi and Al. subcylindrospora. Allosphaeosphaeria clematidis and Al. cytisi only produce the sexual morph, while Al. subcylindrospora only produces an asexual morph. The morphology of this asexual morph fits perfectly in the description of Septoriella, corroborating the synonymy proposed in the present study based on the phylogenetic data. Allosphaeosphaeria clematidis was recently excluded from the genus and transferred to the new genus Embarria (Wanasinghe et al. 2018). Moreover, in our phylogenetic studies, Al. cytisi formed an independent lineage in Phaeosphaeriaceae far from the clade representing Septoriella. Therefore, a new genus is proposed to accommodate this species.

 The genus Poaceicola was introduced by Li et al. (2015) to accommodate Phaeosphaeria elongata and two new species, i.e. Po. arundinis and Po. bromi. The two latter species are characterised by the production of an asexual morph similar to Septoriella. Poaceicola elongata produces a sexual morph characterised by ascospores with transverse septa. The presence of only transverse septa could be a morphologic difference from Allophaeosphaeria. However, seven more new species have been included in the genus, including one species presenting ascospores with transverse and longitudinal septa, Po. arundinis, demonstrating that the longitudinal septation of the ascospores is not phylogenetically informative in these genera.

 Vagicola was recently introduced by Ariyawansa et al. (2015a), in the same year as the other two genera. Ariyawansa et al. (2015a) raised the subgenus Vagicola (Shoemaker & Babcock 1989) to generic rank to accommodate Phaeosphaeria vagans, a species characterised by a sexual morph similar to the species of Poaceicola, having ascospores with transverse septa only. Subsequently, Jayasiri et al. (2015) introduced two new species: V. chlamydospora, which presents both morphs, and V. dactylidis, which produces only the sexual morph. The sexual morph of V. chlamydospora is similar to the two former species of the genus, while V. dactylidis produces ascospores with transverse and longitudinal septa as seen in species of Allophaeosphaeria, indicating again that the longitudinal septation of ascospores is not phylogenetically informative. Vagicola chlamydospora was recently transferred to Septoriella based on phylogenetic data (Jayasiri et al. 2015). Surprisingly, the asexual morph reported in that species does not fit with the morphology of Septoriella, since it produces micro- to macronematous conidiophores and chlamydospore-like conidia. Recently, Thambugala et al. (2017) introduced the last species of the genus, V. arundinis, which produces both morphs and is characterised by ascospores with transverse septa and an asexual morph similar to Septoriella, which demonstrates the link of Vagicola with Septoriella. This last species was invalid because two holotypes were designated. Therefore, this taxon is validated in the present study.

 Moreover, in our phylogenetic analyses, the ex-type strain of the most recently described species of Neostagonospora was located in the clade representing Septoriella. This species is characterised by the production of conidia that are subcylindrical or fusiform, euseptate, with a subobtuse apex and truncate base. However, the presence of mucoid appendages at both ends, as the other species of Septoriella, has not been reported. Septoriella artemisiae is saprobic or weakly necrotrophic on dead and dying stems of Artemisia austriaca.

 Most of the species now included in Septoriella are saprophytes, except for Sep. hirta, which is an important secondary pathogen of grasses (Sprague 1950). This species is often found in association with other fungi such as Gaeumannomyces graminis (Johnston et al. 2014) and Oculimacula yallundae causing foot rot of wheat (Crous et al., 2003, Crous et al., 2015a). Other disease symptoms observed in plants affected by Sep. hirta are discoloured culms and predisposition to premature collapse, especially in rainy and windy seasons, since this species produces a weakness in the culms of plants with ripe grains. The result of all these symptoms resulted in the increasing of the cost of harvesting and decreasing of the grain quality (Sprague 1950).



References: Sprague 1950 (pathogenicity), Crous et al., 2014b, Ariyawansa et al., 2015a, Li et al., 2015, Liu et al., 2015, Thambugala et al., 2017 (morphology and phylogeny).



Septoriella agrostina (Mapook et al.) Y. Marín & Crous, comb. nov. MycoBank MB829676.

Basionym: Poaceicola agrostina Mapook et al., Fungal Diversity 89: 132. 2018.



Description and illustration: Wanasinghe et al. (2018).



Septoriella artemisiae (Wanas. et al.) Y. Marín & Crous, comb. nov. MycoBank MB829677.

Basionym: Neostagonospora artemisiae Wanas. et al, Fungal Diversity 89: 130. 2018.



Description and illustration: Wanasinghe et al. (2018).



Septoriella arundinicola (Wanas. et al.) Y. Marín & Crous, comb. nov. MycoBank MB829678.

Basionym: Poaceicola arundinicola Wanas. et al., Fungal Diversity 89: 135. 2018.



Description and illustration: Wanasinghe et al. (2018).



Septoriella arundinis (W.J. Li et al.) Y. Marín & Crous, comb. nov. MycoBank MB829679.

Basionym: Poaceicola arundinis W.J. Li et al., Mycosphere 6: 698. 2015.



Description: Li et al. (2015).



Septoriella bromi (Wijayaw. et al.) Y. Marín & Crous, comb. nov. MycoBank MB829680.

Basionym: Poaceicola bromi Wijayaw. et al., Mycosphere 6: 698. 2015.



Description and illustration: Li et al. (2015).



Septoriella dactylidicola Y. Marín & Crous, nom. nov. MycoBank MB829681.

Replaced synonym: Poaceicola dactylidis Tibpromma et al., Mycosphere 8: 755. 2017, non Septoriella dactylidis (Wanas. et al.) Y. Marín & Crous. 2019.



Description and illustration: Thambugala et al. (2017).



Septoriella dactylidis (Wanas. et al.) Y. Marín & Crous, comb. nov. MycoBank MB829682.

Basionym: Vagicola dactylidis Wanas. et al., Phytotaxa 6: 725. 2015.



Description and illustration: Jayasiri et al. (2015).



Septoriella elongata (Wehm.) Y. Marín & Crous, comb. nov. MycoBank MB829683.

Basionym: Leptosphaeria elongata Wehm., Mycologia 44: 633. 1952.

Synonym: Poaceicola elongata (Wehm.) W.J. Li et al., Mycosphere 6: 701. 2015.



Description and illustration: Wehmeyer (1952).



Septoriella forlicesenica (Thambug. et al.) Y. Marín & Crous, comb. nov. MycoBank MB829684.

Basionym: Poaceicola forlicesenica Thambug et al., Mycosphere 8: 756. 2017.



Description and illustration: Thambugala et al. (2017).



Septoriella garethjonesii (Thambug. et al.) Y. Marín & Crous, comb. nov. MycoBank MB829685.

Basionym: Poaceicola garethjonesii Thambug et al., Mycosphere 8: 756. 2017.



Description and illustration: Thambugala et al. (2017).



Septoriella germanica Crous, R.K. Schumach. & Y. Marín, sp. nov. MycoBank MB829701. Fig. 68.



Fig. 68.

Septoriella germanica (ex-type CBS 145372). A. Conidiomata sporulating on PNA. B, C. Conidiogenous cells. D. Conidia with mucoid caps. Scale bars: A = 200 μm; all others = 10 μm.

Etymology: Name refers to Germany, from where this fungus was isolated.



Conidiomata solitary, pycnidial, erumpent, globose, brown, 180–220 μm diam, in vivo gregarious, caespitose or in rows, but also pseudostromatic, up to 300 μm diam, with central ostiole, 30–40 μm diam; conidiomatal wall of 3–4 layers of brown cells of textura angularis. Conidiophores reduced to conidiogenous cells lining the inner cavity, hyaline, smooth-walled, globose to ampulliform, phialidic, 4–6 × 4–5 μm. Conidia solitary, scolecosporous, fusoid to subcylindrical, apex subobtuse, base truncate, straight to sligthly curved, 3–6-septate, golden-brown, smooth-walled, granular with mucoid caps at each end, (35–)37–42(–46) × 3(–3.5) μm, in vivo 29–46 × 3–4.5 μm.



Culture characteristics: Colonies flat, spreading, with moderate aerial mycelium, covering dish in 2 wk. On MEA, PDA and OA surface olivaceous grey, reverse iron-grey.



Typus: Germany, near Berlin, on dead culm of Phragmites australis (Poaceae), 16 Apr. 2016, R.K. Schumacher, HPC 1168 (holotype CBS H-23875, culture ex-type CBS 145372 = CPC 30511).



Notes: Septoriella germanica is related to Sep. artemisiae. However, both species differ in the size of the conidia [15–25 × 2–2.5 μm in Sep. artemisiae vs. (35–)37–42(–46) × 3(–3.5) μm in Sep. germanica], as well as in the conidial septation (2–4 in Sep. artemisiae vs. 3–6 μm in Sep. germanica). Septoriella germanica was isolated from Phragmites australis (Poaceae), while Sep. artemisiae was found on Artemisia austriaca (Asteraceae).



Septoriella hibernica Crous, Quaedvl. & Y. Marín, sp. nov. MycoBank MB829703.



Etymology: Name refers to Ireland, where this fungus was collected.



Culture sterile. Septoriella hibernica differs from its closest phylogenetic neighbour, Septoriella subcylindrispora by unique fixed alleles in the ITS locus based on the alignment deposited in TreeBASE (S23834): positions 5 (T), 33 (T), 34 (A), 46 (T), 61 (A), 89 (T), 477 (A), 479 (T), 480 (A), 512 (T), 528 (G), 534 (G).



Culture characteristics: Colonies erumpent, spreading, covering dish in 2 wk, with fluffy aerial mycelium and even margins. On MEA, PDA and OA surface and reverse olivaceous grey.



Typus: Ireland, on unidentified grass species (Poaceae), Mar. 2014, W. Quaedvlieg (holotype CBS H-23874, culture ex-type CBS 145371 = CPC 24290).



Notes: Septoriella hibernica remained sterile on all media tested. It is related to Sep. subcylindrispora, but the ITS sequences of both species showed only 97.75 % of nucleotide similarity (Identities = 522/538, 3 gaps).



Septoriella hollandica Crous, Quaedvl. & Y. Marín, sp. nov. MycoBank MB829702. Fig. 69.



Fig. 69.

Septoriella hollandica (ex-type CBS 145374). A. Ascomata sporulating on PNA. B, C. Asci. D. Ascospores. Scale bars = 10 μm.

Etymology: Name refers to the Netherlands, where this fungus was collected.



Ascomata solitary, erumpent, globose, brown, 150–180 μm diam with central ostiole; conidiomatal wall of 3–4 layers of brown cells of textura angularis. Pseudoparaphyses hyphae-like, hyaline, smooth-walled, branched, septate, 1.5–2 μm diam. Asci subcylindrical, flexuous, bitunicate, with well-defined apical chamber, 1–1.5 μm diam, fasciculate, short stipitate, 70–90 × 8–10 μm. Ascospores bi- to triseriate, fusoid-ellipsoid, 5-septate, constricted at median septum, medium brown, smooth-walled, guttulate, widest above median septum, (27–)28–30(–32) × (4–)4.5(–5) μm.



Culture characteristics: Colonies flat, spreading, covering dish in 2 wk with moderate aerial mycelium. On MEA surface vinaceous buff, reverse sienna; on PDA surface isabelline, reverse hazel; on OA surface saffron.



Typus: The Netherlands, Oosterbeek, on leaves of Phragmites australis (Poaceae), 24 Jan. 2014, W. Quaedvlieg (holotype CBS H-23877, culture ex-type CBS 145374 = CPC 24109).



Notes: Septoriella hollandica is related to Sep. chlamydospora and Sep. tridentina. Septoriella hollandica, as well as Sep. chlamydospora and Sep. tridentina, produce sexual morphs in culture. Septoriella hollandica can be easily distinguished from Sep. chlamydospora by its 5-septate ascospores, being 9-septate in Sep. chlamydospora. Septoriella tridentina is the only species of this complex that produces ascospores surrounded by a mucilaginous sheath. The asexual morph was reported only for Sep. chlamydospora. However, as it was mentioned above, the asexual morph described in Sep. chlamydospora (Jayasiri et al. 2015) corresponds to chains of chlamydospores instead of scolecosporous conidia typical of Septoriella. Septoriella hollandica was isolated from Phragmites australis, while the other two species were found on Dactylidis spp.



Septoriella italica (Thambug. et al.) Y. Marín & Crous, comb. nov. MycoBank MB829704.

Basionym: Poaceicola italica Thambug. et al., Mycosphere 8: 759. 2017.



Description: Thambugala et al. (2017).



Septoriella muriformis (Ariyaw. et al.) Y. Marín & Crous, comb. nov. MycoBank MB829705.

Basionym: Allophaeosphaeria muriformis Ariyaw. et al., Fungal Diversity 72: 137.



Descriptions and illustrations: Liu et al., 2015, Thambugala et al., 2017.



Septoriella neoarundinis Y. Marín & Crous, nom. nov. MycoBank MB829706.

Replaced synonym: Vagicola arundinis Phukhams., Camporesi & K.D. Hyde, sp. nov. MycoBank MB831056, non Septoriella arundinis (W.J. Li et al.) Y. Marín & Crous. 2019.

Synonym: Vagicola arundinis Phukhams. et al. Mycosphere 8: 763. 2017. (nom. inval., Art. 40).



Etymology: Name reflects the host genus Arundo from which it was isolated.



Description and illustration: Thambugala et al. (2017).



Typus: Italy, Province of Marsignano, Predappio, on a dead stem of Arundo plinii (Poaceae), 10 Nov. 2014, E. Camporesi IT 2223A (holotype MFLU 17-0016, ex-type living culture MFLUCC 15-0027).



Notes: This species was initially introduced by Thambugala et al. (2017) as Vagicola arundinis. However, it was invalid since two different holotype numbers were cited. Therefore, this species is validated here and a new name in Septoriella is proposed, using a new epithet since Sep. arundinis is occupied.



Septoriella neodactylidis Y. Marín & Crous, nom. nov. MycoBank MB829707.

Replaced synonym: Allophaeosphaeria dactylidis Wanas. et al., Fungal Diversity 72: 137. 2015, non Septoriella dactylidis (Wanas. et al.) Y. Marín & Crous. 2019.



Description and illustration: Liu et al. (2015).



Septoriella pseudophragmitis Crous, Quaedvl. & Y. Marín, sp. nov. MycoBank MB829708. Fig. 70.



Fig. 70.

Septoriella pseudophragmitis (ex-type CPC 24166). A. Conidiomata sporulating on MEA. B, C. Conidiogenous cells. D. Conidia. Scale bars: A = 250 μm; all others = 10 μm.

Etymology: Name refers to its morphological similarity with Sep. phragmitis, which occurs on the same host.



Conidiomata solitary, pycnidial, erumpent, globose, brown-black, 200–250 μm diam with central ostiole; conidiomatal wall of 6–8 layers of brown textura angularis. Conidiophores reduced to conidiogenous cells lining the inner cavity, hyaline, smooth-walled, globose to ampulliform, phialidic, 4–10 × 4 μm. Conidia solitary, subcylindrical, golden-brown, guttulate, smooth-walled, apex obtuse, base truncate, 3(–6)-septate, with mucoid caps at each end, (20–)24–28(–32) × (3–)3.5(–4) μm.



Culture characteristics: Colonies erumpent, spreading, covering dish after 2 wk at 25 °C, with moderate aerial mycelium and feathery margins. On MEA surface olivaceous grey, reverse iron-grey.



Typus: The Netherlands, on leaves of Phragmites sp. (Poaceae), 5 Mar. 2014, W. Quaedvlieg (holotype CBS-H 23904, culture ex-type CBS 145417 = CPC 24166).



Notes: Septoriella pseudophragmitis is similar to Sep. phragmitis, which is reported from the same host, Phragmites (Poaceae). These species differ in the size of their conidiomata (up to 250 μm diam in Sep. pseudophragmitis vs. 350 μm diam in Sep. phragmitis) and conidia [(20–)24–28(–32) × (3–)3.5(–4) μm in Sep. pseudophragmitis vs. (29–)32–40(–46) × 3(–3.5) μm diam in Sep. phragmitis], as well as in the conidial septation, being mostly 3-septate in Sep. pseudophragmitis and 5-septate in Sep. phramitis. Based on our phylogenetic analysis, Septoriella pseudophragmitis is related to Sep. allojunci. However, Sep. allojunci produces smaller conidiomata (up to 150 μm) and larger conidia (48–70 × 3–6.6 μm). Moreover, Sep. allojunci was isolated from Juncus (Juncaceae).



Septoriella rosae (Mapook et al.) Y. Marín & Crous, comb. nov. MycoBank MB829713.

Basionym: Poaceicola rosae Mapook et al., Fungal Diversity 89: 136. 2018.



Description and illustration: Wanasinghe et al. (2018).



Septoriella subcylindrospora (W.J. Li et al.) Y. Marín & Crous, comb. nov. MycoBank MB829709.

Basionym: Allophaeosphaeria subcylindrospora W.J. Li et al., Fungal Diversity 75: 100. 2015.



Description and illustration: Ariyawansa et al. (2015a).



Septoriella vagans (Niessl) Y. Marín & Crous, comb. nov. MycoBank MB829710.

Basionym: Pleospora vagans Niessl, Verh. nat. Ver. Brünn 14: 174. 1876.

Synonym: Vagicola vagans (Niessl) O.E. Erikss. et al., Fungal Diversity 75: 115. 2015.



Description and illustration: Jayasiri et al. (2015).



Arezzomyces Y. Marín & Crous, gen. nov. MycoBank MB829711.



Etymology: Name reflects the Italian province Arezzo where it was collected.



Ascomata solitary, scattered, immersed to erumpent, obpyriform, dark brown to black, coriaceous, with ostiole filled with hyaline cells, appearing as a white ring around ostiole; necks papillate, black, smooth; ascomatal wall comprising 6–8 layers, outer layer heavily pigmented, comprising blackish to dark brown, thick-walled cells of textura angularis, inner layer composed of brown, thin-walled cells of textura angularis. Hamathecium comprising numerous, filamentous, branched, septate pseudoparaphyses. Asci 8-spored, bitunicate, fissitunicate, cylindrical, pedicel furcate, rounded and thick-walled at the apex, with an ocular chamber. Ascospores mostly uniseriate, initially hyaline, becoming yellowish brown at maturity, ellipsoidal, muriform, with 6–8 transverse septa, 3–7 vertical septa, strongly constricted at the central septa, weakly constricted at the other septa, with conical and narrowly rounded ends, lacking a mucilaginous sheath. Asexual morph not observed.



Culture characteristics: Colonies spreading, surface erumpent, with moderate aerial mycelium, and feathery margins. On MEA, PDA and OA surface dirty white; reverse dirty white to luteous.



Type species: Arezzomyces cytisi (Wanas. et al.) Y. Marín & Crous. Holotype and ex-type cultures: MFLU 15-1502, MFLUCC 15-0649.



Notes: Arezzomyces is introduced to accommodate Allophaeosphaeria cytisi since, based on phylogenetic data, it is located in an independent lineage distant to the clade representing the genus Septoriella. Moreover, based on a megablast search using the ITS sequence, the closest matches in NCBIs GenBank nucleotide database were Ophiosimulans tanaceti [GenBank KU738890; Identities = 534/586 (91 %), 11 gaps (1 %)], Ophiobolus cirsii [GenBank KM014664; Identities = 514/566 (91 %), 22 gaps (1 %)], and Chaetosphaeronema hispidulum [GenBank KX096655; Identities 535/588 (91 %), 22 gaps (3 %)]. Arezzomyces cytisi is a saprobe found on dead herbaceous branches of Cytisus.



Arezzomyces cytisi (Wanas. et al.) Y. Marín & Crous, comb. nov. MycoBank MB829712.

Basionym: Allophaeosphaeria cytisi Wanas. et al., Fungal Diversity 75: 97. 2015.



Description and illustration: Ariyawansa et al. (2015a).



Typus: Italy, Arezzo Province, Casuccia di Micheli in Quota, dead and hanging branches of Cytisus sp. (Fabaceae), 20 Jun. 2012, E. Camporesi (holotype MFLU 15-1502, culture ex-type MFLUCC 15-0649).



Authors: Y. Marin-Felix, W. Quaedvlieg, R.K. Schumacher & P.W. Crous



Setophoma Gruyter et al., Mycologia 10: 1077. 2010. Fig. 71.



Fig. 71.

Setophoma spp. A, B. Conidioma forming in culture. A.Setophoma chromolaenae (ex-type CBS 135105). B.Setophoma vernoniae (ex-type CBS 137988). C–E. Conidiomata with setae of Setophoma chromolaenae (ex-type CBS 135105). F–H. Conidiogenous cells. F, G.Setophoma chromolaenae (ex-type CBS 135105). H.Setophoma vernoniae (ex-type CBS 137988). I, J. Conidia. I.Setophoma chromolaenae (ex-type CBS 135105). J.Setophoma vernoniae (ex-type CBS 137988). Scale bars: C–E = 20 μm; all others = 10 μm; F applies to F and G.

Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Phaeosphaeriaceae.



Type species: Setophoma terrestris (H.N. Hansen) Gruyter et al., basionym: Phoma terrestris H.N. Hansen. Lectotype and ex-lectotype strain designated by de Gruyter et al. (2010): CBS H-20311, CBS 335.29.



DNA barcode (genus): LSU. Fig. 28.



DNA barcodes (species): ITS, rpb2, tef1, tub2. Table 17. Fig. 72.



Table 17.

DNA barcodes of accepted Setophoma spp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	rpb2	tef1	tub2
Setophoma brachypodii	CBS 145418T	MK539968	MK540099	MK540161	–	Present study
Set. chromolaenae	CBS 135105T	KF251244	KF252249	KF253195	KF252728	Quaedvlieg et al. (2013)
Set. pseudosacchari	CBS 145373T	MK539969	MK540100	–	MK540176	Present study
Set. sacchari	CBS 333.39ET	KF251245	KF252250	–	–	Quaedvlieg et al. (2013)
Set. terrestris	CBS 335.29LT	KF251246	KF252251	KF253196	KF252729	Quaedvlieg et al. (2013)
Set. vernoniae	CBS 137988T	KJ869141	–	MK540162	MK540177	Crous et al. (2014b), present study

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands. ^{T, ET} and ^LT indicate ex-type strains, ex-epitype and ex-lectotype, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene.

Fig. 72.

RAxML phylogram obtained from the combined ITS (589 bp), LSU (835 bp), tef1 (788 bp) and tub2 (532 bp) sequence alignment of all accepted species of Setophoma. The tree was rooted to Neostagonospora caricis CBS 135092 and Neostagonospora elegiae CBS 135101. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 % and Bayesian posterior probability scores above 0.95 are shown at the nodes. GenBank accession numbers of LSU are listed in Fig. 28, and of the other loci in Table 7, Table 17 and 18. ^{T, ET} and ^LT indicate ex-type strains, ex-epitype and ex-lectotype, respectively. TreeBASE: S23834.

Ascomata scattered, gregarious, immersed, visible as raised, minute black dots on host surface, uniloculate, globose to subglobose, glabrous, brown to dark brown, ostiole central, with minute papilla; ascomatal wall thin, of equal thickness, composed of pseudoparenchymatous cells, arranged in flattened textura angularis to textura prismatica. Hamathecium composed of numerous, filiform, broad cellular pseudoparaphyses, with distinct septa, anastomosing at apex. Asci 8-spored, bitunicate, fissitunicate, cylindrical to cylindric-clavate, short pedicellate, apically rounded, with well-developed narrowly ocular chamber. Ascospores overlapping, 2-seriate, phragmosporous, cylindrical to cylindrical-clavate, hyaline, 3-septate, usually enlarged at the second cell from apex, smooth-walled with large guttules. Conidiomata pycnidial, solitary to confluent, superficial or submerged in agar, globose to subglobose, setose, with papillate necks, honey to olivaceous or olivaceous black, with 2–7(–11) layers of pseudoparenchymatal cells. Conidiogenous cells hyaline, monophialidic. Conidia aseptate, ellipsoidal to subcylindrical or subfusoid, guttulate (adapted from Quaedvlieg et al., 2013, Phookamsak et al., 2014a).



Culture characteristics: Colonies spreading with sparse to moderate aerial mycelium, smooth or folded surface, even or lobate margins. On PDA surface iron-grey or grey olivaceous with outer region iron-grey; reverse olivaceous grey or iron-grey. On MEA surface olivaceous grey or umber with patches of apricot and dirty white; reverse ochreous or cinnamon with patches of olivaceous grey. On OA surface isabelline or iron-grey surrounded by orange to apricot diffuse pigment layer in agar.



Optimal media and cultivation conditions: OA and SNA at 25 °C under continuous near-ultraviolet light to promote sporulation. Sterile bamboo pieces on WA to induce sporulation of the sexual morph.



Distribution: Worldwide.



Hosts: Mainly on members of Poaceae, but also of Amaryllidaceae and Asteraceae, among others.



Disease symptoms: Leaf spots and necrosis, leaf dieback, and pink root.



Notes: Setophoma was introduced by de Gruyter et al. (2010) to accommodate two species previously placed in Pyrenochaeta, i.e. Pyr. sacchari and Pyr. terrestris. Setophoma is characterised by pycnidial conidiomata covered by setae, phialidic conidiogenous cells, and hyaline, ellipsoidal to subcylindrical, aseptate, guttulate conidia (de Gruyter et al., 2010, Quaedvlieg et al., 2013). When Setophoma was introduced, the sexual morph had not been observed. Subsequently, Phookamsak et al. (2014a) reported the sexual morph of this genus. It was found causing leaf spots of sugarcane (Saccharum officinarum), and based on the phylogenetic data it was shown to be the sexual morph of Set. sacchari. This sexual morph is similar to Phaeosphaeria species, producing ascospores with three septa with the second cell from the apex being swollen; these cells differ in colour (hyaline in Setophoma vs. yellowish to brown in Phaeosphaeria).

 Setophoma encompasses pathogenic or saprobic species associated with monocotyledonous plants (de Gruyter et al. 2010). The type species, Set. terrestris, causes pink root on Allium spp., and also on Zea mays and Oryza sativa, but it is asymptomatic on other hosts (Farr & Rossman 2019). Setophoma vernoniae produces leaf spots on Vernonia polyanthes (Crous et al. 2014b), while Set. sacchari is considered a weak pathogen of members of the Poaceae that is only noticeable when conditions are favourable for disease spread, and causes leaf spots and necrosis and leaf dieback (Farr & Rossman 2019).

 In our phylogenetic analysis based on ITS and LSU (Fig. 28), the clade representing the genus Setophoma is well-supported (95 % BS / 1 PP). However, the most recently described species, Set. cyperi, is not located in that clade, representing a new genus in the family Phaeosphaeriaceae.

At the proof stage of this paper, a new publication appeared on Setophoma (Liu et al. 2019), which contains four new species.



References: de Gruyter et al., 2010, Quaedvlieg et al., 2013, Phookamsak et al., 2014a (morphology and phylogeny).



Setophoma brachypodii Crous, R.K. Schumach. & Y. Marín, sp. nov. MycoBank MB829669.



Etymology: Name reflects the host genus Brachypodium from which it was isolated.



Culture sterile. Setophoma brachypodii differs from its closest phylogenetic neighbour, Setophoma terrestris by unique fixed alleles in two loci based on alignments of the separate loci deposited in TreeBASE (S23834): LSU positions 42 (G), 67 (C), 75 (C), 77 (T), 79 (G), 81 (C), 82 (A), 89 (C), 133 (C), 144 (G), 145 (C), 146 (C), 147 (T), 150 (G), 302 (C), 348 (T), 380 (C), 392 (A), 437 (T), 445 (T), 446 (C), 473 (A), 477 (G), 601 (G), 636 (T), 637 (T), 638 (A); ITS positions 32 (C), 34 and 35 (indels), 36 (T), 37 (T), 38 (T), 42 (G), 43 (T), 44 (A), 54 (C), 56 (G), 57 (T), 58 (T), 59 (C), 60 (G), 61 (C), 62 (T), 63 (G), 64 (T), 66 (G), 67 (T), 72 (T), 77 (G), 78 (T), 80 (T), 99 (T), 100 (G), 101 (A), 103 (C), 114 (C), 117 (G), 118 (T), 119 (A), 121 (C), 122 (T), 124 (C), 130 (A) 138 (C), 140 (A), 143 (T), 146 (A), 148 (C), 172 (A), 176 (T), 178 (A), 180 (T), 182 (A), 186 (indel), 354 (T), 379 (T), 381 (indel), 388 (T), 389 (G), 390 (G), 391 (T), 392 (C), 393 (C), 394 (T), 395 (C), 396 (T), 399 (G), 400 (A), 401 (C), 402 (C), 409 (A), 418 (A), 419 (T), 433 (G), 434 (T), 435 (A), 441 (G), 444 (T), 467 (A), 470 (indel), 473 (T), 475 (C), 477 (A), 478 (C), 479 (T), 482 (A), 485 (C), 486 (C), 490 (A), 495–498 (indels), 499 (C), 500 (C), 502 (T), 504 (A), 506 (T), 507 (A), 511 (C).



Culture characteristics: Colonies flat, spreading, with moderate aerial mycelium and even, lobate margins, reaching 60 mm diam after 2 wk. On MEA, PDA and OA, surface and reverse olivaceous grey.



Typus: Belgium, Dinant, 173 m a.s.l., on border of calcareous meadow, on a dead and attached leaf of Brachypodium sylvaticum (Poaceae), 2 Nov. 2016, L. Bailly & R.K. Schumacher, HPC 1503, RKS 1 (holotype CBS H-23905, culture ex-type CBS 145418 = CPC 32492).



Notes: Setophoma brachypodii remained sterile on all media tested, and the original specimen was depleted, hence we could not describe it based on morphology. This is the first species of Setophoma reported on Brachypodium.



Setophoma pseudosacchari Crous & Y. Marín, sp. nov. MycoBank MB829670. Fig. 73.



Fig. 73.

Setophoma pseudosacchari (ex-type CBS 145373). A. Ascomata sporulating on OA. B. Asci with ascospores. C. Conidia. Scale bars: A = 300 μm; all others = 10 μm.

Etymology: Named after its closely phylogenetic relation to Setophoma sacchari.



Ascomata developing on OA, solitary, erumpent, brown, 200–300 μm diam, globose, with large central ostiole, 30–40 μm diam; ascomatal wall of 3–4 layers of brown cells of textura angularis, ascomata setose; setae brown, flexuous, thick-walled, septate, base verruculose, with slight taper to obtuse apex, up to 150 μm long. Pseudoparaphyses hyphae-like, anastomosing, branched, septate, hyaline, occurring intermingled among asci. Asci bitunicate, ellipsoid to subcylindrical, hyaline, curved to straight, fasciculate, apex obtuse, with well-defined ocular chamber, 2 μm diam, stipitate, 70–100 × 10–13 μm. Ascospores bi- to triseriate, fusoid-ellipsoid with subobtuse ends, straight, 3-septate, widest in second cell from apex, prominently guttulate, hyaline, smooth-walled, (22–)25–30 × (5.5–)6 μm. Conidiomata developing on SNA, solitary to aggregated, erumpent, brown, globose, 200–300 μm diam, with 1–2 ostioles, lacking setae; conidiomatal wall of 2–3 layers of brown textura angularis. Conidiophores reduced to conidiogenous cells lining inner cavity, dissolving at maturity, hyaline, smooth-walled, globose to ampulliform, phialidic, 4–6 × 5–6 μm. Conidia solitary, aseptate, straight to slightly curved, subcylindrical to fusoid-ellipsoid, apex obtuse, base truncate, hyaline, smooth-walled, guttulate, (8–)11–12(–14) × (3–)4 μm.



Culture characteristics: Colonies erumpent, spreading, surface folded, with moderate aerial mycelium and even, lobate margins, reaching 55 mm diam. On MEA surface peach, outer region scarlet, reverse sienna; on PDA surface umber, outer region saffron, reverse sienna with patches of saffron; on OA surface sienna with patches of saffron.



Typus: France, La Réunion Island, leaf spots on Saccharum officinarum (Poaceae), May 2015, P.W. Crous, HPC 296 (holotype CBS H-23876, CBS 145373 = CPC 26421).



Notes: This species is closely related to Nph. sacchari, which is a species also isolated from sugarcane. However, the ITS sequences of the type material of both species showed only a 97.68 % of nucleotide similarity. Unfortunately, tef1 and tub2 sequences of Nph. sacchari are not available in order to compare both species. These species produce both the sexual and asexual morphs, with morphological differences most obvious in the sexual morph. Neosetophoma pseudosacchari can be easily distinguished by its larger ascomata (up to 300 μm diam in Nph. pseudosacchari vs. up to 180 μm diam in Nph. sacchari), asci [70–100 × 10–13 μm in Nph. pseudosacchari vs. 60–75(–85) × 12–15(–17) μm in Nph. sacchari] and ascospores [(22–)25–30 × (5.5–)6 μm in Nph. pseudosacchari vs. 20–23(–25) × 5–6 μm in Nph. sacchari].



Wingfieldomyces Y. Marín & Crous, gen. nov. MycoBank MB829671. Table 18. Fig. 74.



Table 18.

DNA barcodes of the accepted Wingfieldomyces sp.

Species	Isolates1	GenBank accession numbers2				References
		ITS	rpb2	tef1	tub2
Wingfieldomyces cyperi	CBS 141450T	KX228286	MK540101	MK540163	MK540178	Crous et al. (2016b), present study

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands. ^T indicates ex-type strain.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene.

Fig. 74.

Wingfieldomyces cyperi (ex-type CBS 141450). A. Symptomatic leaf of Cyperus sphaerocephala. B–D. Asci. E. Pseudoparaphyses. F–I. Ascospores. Scale bars: 10 μm; F applies to F–I. Pictures B, C, E–I taken from Crous et al. (2016b).

Etymology: Named in honour of its collector, Prof. dr M.J. Wingfield, who contributed greatly to the elucidation of African fungal biodiversity.



Ascomata immersed on host, erumpent in culture, black, globose, with central ostiole; ascomatal wall of 3–4 layers of dark brown cells of textura angularis. Pseudoparaphyses intermingled among asci, hyaline, septate, branched prominently, constricted at septa. Asci bitunicate with apical chamber, subcylindrical, hyaline, smooth, fasciculate, stipitate, 8-spored. Ascospores tri- to multiseriate, fusoid with subobtusely rounded ends, finely verruculose, red-brown, guttulate, 2-septate, slightly constricted at septa, with central cell somewhat swollen.



Culture characteristics: Colonies spreading, erumpent surface, with moderate aerial mycelium, margins feathery. On MEA, PDA and OA surface dirty white; reverse dirty white to luteous.



Type species: Wingfieldomyces cyperi (Crous & M.J. Wingf.) Y. Marín & Crous. Holotype and ex-type cultures: CBS H-22622, CBS 141450 = CPC 25702.



Notes: Wingfieldomyces is introduced to accommodate Set. cyperi since, based on phylogenetic data, it is located in an independent lineage distant to the clade representing the genus Setophoma. Moreover, based on a megablast search using the ITS sequence, the closest matches in NCBIs GenBank nucleotide database were Pringsheimia euphorbiae [GenBank NR_145344; Identities = 456/500 (91 %), 8 gaps (1 %)] and Phaeosphaeria caricis [GenBank KY090633; Identities 439/485 (91 %), 12 gaps (2 %)]. It only produces a sexual morph in culture, characterised by tri- to multiseriate, 2-septate, red-brown ascospores, while Setophoma produces both morphs and 2-seriate, 3-septate, hyaline ascospores with the second cell from the apex becoming swollen. Wingfieldomyces is associated with leaf scorch symptoms on Cyperus.



Wingfieldomyces cyperi (Crous & M.J. Wingf.) Y. Marín & Crous, comb. nov. MycoBank MB829672. Fig. 74.

Basionym: Setophoma cyperi Crous & M.J. Wingf., Persoonia 36: 385. 2016.



Description: Crous et al. (2016b).



Typus: South Africa, Eastern Cape Province, Haga Haga, on leaves of Cyperus sphaerocephala (Cyperaceae), Dec. 2014, M.J. Wingfield (holotype CBS H-22622, culture ex-type CPC 25702 = CBS 141450).



Authors: Y. Marin-Felix & P.W. Crous



Stagonosporopsis Died., Ann. Mycol. 10: 142. 1912. Emend. Aveskamp et al., Stud. Mycol. 65: 44. 2010. Fig. 75.



Fig. 75.

Stagonosporopsis spp. A, B. Disease symptoms of Stagonosporopsis tanaceti (ex-type CBS 131484). A. Leaf necrosis. B. Drooping flower heads. C–G. Sexual morph of Stagonosporopsis inoxydabilis (ex-type CBS 425.90). C. Close-up of ascoma with darkened ostiolar area. D, E. Stipitate, bitunicate asci. F, G. Ascospores (arrows denote sheath). H–T. Asexual morph. H, I. Colony sporulating on OA. H.Stagonosporopsis chrysanthemi (CBS 500.63). I.Stagonosporopsis tanaceti (ex-type CBS 131484). J. Close-up of pycnidial conidiomata of Stagonosporopsis tanaceti (ex-type CBS 131484). K. Close-up of darkened ostiolar area of Stagonosporopsis chrysanthemi (CBS 500.63). L–Q. Conidiogenous cells. L–N.Stagonosporopsis chrysanthemi (CBS 500.63). O–Q.Stagonosporopsis tanaceti (ex-type CBS 131484). R, S. Conidia. R.Stagonosporopsis chrysanthemi (CBS 500.63). S.Stagonosporopsis tanaceti (ex-type CBS 131484). T. Chain of chlamydospores of Stagonosporopsis tanaceti (ex-type CBS 131484). Scale bars: C = 35 μm; J = 150 μm; all others = 10 μm; D applies to D and E; L applies to L–N; O applies to O–Q. Pictures taken from Vaghefi et al. (2012).

Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Didymellaceae.



Type species: Stagonosporopsis boltshauseri (Sacc.) Died., designated as lectotype by Clements & Shear (1931), basionym: Ascochyta boltshauseri Sacc. = Stagonosporopsis hortensis (Sacc. & Malbr.) Petr., basionym: Hendersonia hortensis Sacc. & Malbr. Representative strain of Sta. hortensis: CBS 572.85 = PD 79/269.



DNA barcode (genus): LSU.



DNA barcodes (species): ITS, rpb2, tub2. Table 19. Fig. 76.



Table 19.

DNA barcodes of accepted Stagonosporopsis spp.

Species	Strain1	GenBank accession numbers2					References
		ITS	LSU	act	rpb2	tub2
Stagonosporopsis actaeae	CBS 106.96T	GU237734	GU238166	JN251974	KT389672	GU237671	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. ailanthicola	MFLUCC 16-1439T	KY100872	KY100874	–	KY100876	KY100878	Tibpromma et al. (2017)
Sta. ajacis	CBS 177.93NT	GU237791	GU238168	JN251962	KT389673	GU237673	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. andigena	CBS 101.80	GU237714	GU238169	JN251958	–	GU237674	Aveskamp et al., 2010, de Gruyter et al., 2012
Sta. artemisiicola	CBS 102636	GU237728	GU238171	JN251971	KT389674	GU237676	Aveskamp et al. (2010), de Gruyter et al. (2012), Chen et al. (2015)
Sta. astragali	CBS 178.25	GU237792	GU238172	JN251963	–	GU237677	Aveskamp et al., 2010, de Gruyter et al., 2012
Sta. bomiensis	CGMCC 3.18366T	KY742123	KY742277	–	KY742189	KY742365	Chen et al. (2017)
Sta. centaureae	MFLUCC 16-0787T	KX611240	KX611238	–	–	–	Hyde et al. (2016)
Sta. citrulli	ATCC TSD-2T	KJ855546	–	–	–	KJ855602	Stewart et al. (2015)
Sta. caricae	CBS 248.90	GU237807	GU238175	JN251969	–	GU237680	Aveskamp et al., 2010, de Gruyter et al., 2012
	DAR 28714	MK253236	MK253237	MK255065	MK255066	MK255067	Present study
Sta. chrysanthemi	ATCC 10748ET	JQ897484	JQ897460	JQ897508	–	JQ897504	Vaghefi et al. (2012)
Sta. crystalliniformis	CBS 713.85T	GU237903	GU238178	JN251960	KT389675	GU237683	Aveskamp et al. (2010), de Gruyter et al. (2012), Chen et al. (2015)
Sta. cucurbitacearum	CBS 133.96	GU237780	GU238181	JN251968	KT389676	GU237686	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. dennisii	CBS 631.68ET	GU237899	GU238182	Q-bank3	KT389677	GU237687	Aveskamp et al., 2010, Chen et al., 2015
Sta. dorenboschii	CBS 426.90T	GU237862	GU238185	JN251980	KT389678	GU237690	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. helianthi	CBS 200.87T	KT389545	KT389761	–	KT389683	KT389848	Chen et al. (2015)
Sta. heliopsidis	CBS 109182	GU237747	GU238186	JN251980	KT389679	GU237691	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. hortensis	CBS 572.85	GU237730	GU238198	JN251966	KT389680	GU237703	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. inoxydabilis	CBS 425.90T	GU237861	GU238188	JN251972	KT389682	GU237693	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. loticola	CBS 562.81IsoT	GU237890	GU238192	JN251978	KT389684	GU237697	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. lupini	CBS 101494T	GU237724	GU238194	JN251967	KT389685	GU237699	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. oculo-hominis	CBS 634.92T	GU237901	GU238196	JN251976	KT389686	GU237701	Aveskamp et al. (2010), de Gruyter et al. (2012), Chen et al. (2015)
Sta. papillata	CGMCC 3.18367T	KY742125	KY742279	–	KY742191	KY742367	Chen et al. (2017)
Sta. rudbeckiae	CBS 109180	GU237745	GU238197	Q-bank3	–	GU237702	Aveskamp et al. (2010)
Sta. tanaceti	CBS 131484T	JQ897481	JQ897461	JQ897512	–	JQ897496	Vaghefi et al. (2012)
Sta. trachelii	CBS 379.91	GU237850	GU238173	JN251977	KT389687	GU237678	Aveskamp et al., 2010, de Gruyter et al., 2012, Chen et al., 2015
Sta. valerianellae	CBS 329.67IsoT	GU237832	GU238201	JN251965	–	GU237706	Aveskamp et al., 2010, de Gruyter et al., 2012

¹ATCC: American Type Culture Collection, Virginia, USA; CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; CGMCC: Chinese General Microbiological Culture Collection Center, Beijing, China; DAR: New South Wales Plant Pathology Herbarium, NSW, Australia; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Rai, Thailand. ^{T, ET, IsoT} and ^NT indicate ex-type, ex-epitype, ex-isotype and ex-neotype strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; LSU: partial large subunit (28S) nrRNA gene; act: partial actin gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit; tub2: partial β-tubulin gene.

³Q-bank: Sequences retrieved from Q-bank Fungi database (http://www.q-bank.eu/fungi/).

Fig. 76.

The majority rule consensus phylogram of Stagonosporopsis spp. inferred from the concatenated LSU (876 bp), ITS (459 bp), tub2 (299 bp) and rpb2 (596 bp) sequence alignment using Bayesian Inference. The tree is rooted to Boeremia exigua var. exigua CBS 431.74. Bootstrap support values > 75 % and PP values > 0.90 are shown above or below the branches. ^T,ET,IsoT and ^NT indicate ex-type, ex-epitype, ex-isotype and ex-neotype strains, respectively. Genbank accession numbers are indicated in Table 19, Aveskamp et al. (2010) and Vaghefi et al. (2012). TreeBASE: S23800.

Ascomata pseudothecial, globose to subglobose, sometimes with a somewhat conical neck. Asci cylindrical or subclavate, 8-spored, biseriate. Ascospores ellipsoid, fusoid or obovoid, uniseptate, guttulate, sometimes with a gelatinous sheath. Conidiomata pycnidial, globose to subglobose, glabrous or with hyphal outgrowths, superficial on agar surface or immersed, solitary or confluent, ostiolate or poroid, occasionally papillate; conidiomatal wall pseudoparenchymatous, 2–6 layered, with an outer wall composed of 1–3 layers of brown to olivaceous cells. Conidiogenous cells phialidic, hyaline, simple, smooth-walled, ampulliform or doliiform. Conidia often dimorphic: mainly aseptate, hyaline, ellipsoid to subglobose, thin-walled, smooth-walled, eguttulate or with several polar or scattered guttules; second type of conidia larger in size, can be produced both in vivo and in vitro in the same pycnidia as the other type of conidia, 0–3-septate.



Culture characteristics: Colonies on OA regular to somewhat irregular, colourless, buff, luteous to ochraceous or amber, or olivaceous grey to greenish grey, with scarce or abundant floccose white to pale salmon, or olivaceous grey aerial mycelium.



Optimal media and cultivation conditions: On OA at 20–24 °C under near-ultraviolet light (13 h light, 11 h dark) to induce sporulation of the asexual morph, while MEA stimulates pigmentation and crystal formation. Changes in colour of the fungal cultures upon a sudden increase of pH (NaOH spot test), which may be used for taxonomic characterisation, are best observed on OA.



Distribution: Worldwide.



Hosts: Associated with at least 30 plant genera in Asteraceae, Brassicaceae, Campanulaceae, Caricaceae, Cucurbitaceae, Fabaceae, Lamiaceae, Ranunculaceae, Solanaceae and Valerianaceae as saprobes or pathogens. Stagonosporopsis oculo-hominis is the only species that is not associated with a plant host and was isolated from human corneal ulcer in the USA.



Disease symptoms: Plant stunting, seedling damping-off, leaf spots and dieback, crown rot, stem canker, flower blight, and fruit rot.



Notes: Many species of Stagonosporopsis are phytopathogens, causing devastating diseases on plants from various families. Some species have a worldwide distribution, e.g., Sta. cucurbitacearum on Cucurbitaceae, and Sta. hortensis on Fabaceae, while others represent important quarantine plant pathogens limited to certain geographical areas. For example, Sta. andigena and Sta. chrysanthemi are classified as A1 and A2 quarantine pathogens, respectively, by the European and Mediterranean Plant Protection Organisation (EPPO; 2016). Stagonosporopsis tanaceti is a destructive pathogen of pyrethrum (Tanacetum cinerariifolium) in Australia but has not been reported elsewhere in the world (Vaghefi et al. 2012). Some Stagonosporopsis species have been isolated from plants but their pathogenicity has not been established. For example, Sta. dennisii has been reported from dead stems of Solidago spp. but no data are available on its pathogenicity (Boerema et al. 2004).

 Species identification based on only morphology is unreliable. Stagonosporopsis was originally separated from Ascochyta based on occasional formation of multi-septate (stagonospora-like) conidia (Diedicke 1912). However, later phylogenetic studies revealed that some Stagonosporopsis spp. lack the stagonospora-like spores or any features except for globose pycnidial conidiomata, and aseptate, hyaline conidia (Aveskamp et al. 2010). Thus, multi-locus sequence typing is essential for identification of Stagonosporopsis species. The emended description of the genus Stagonosporopsis by Aveskamp et al. (2010) states that the sexual morph of Stagonosporopsis, if present, occurs only in vivo. However, some strains of Sta. chrysanthemi, Sta. caricae and Sta. inoxydabilis have been shown to produce pseudothecial ascomata intermingled with pycnidial conidiomata on agar media (Boerema et al., 2004, Vaghefi et al., 2012).

 Currently, more than 40 species are linked to the genus Stagonosporopsis. However, only 27 species are recognised based on molecular data (Table 19). Previous phylogenetic studies have used one locus (act in De Gruyter et al. 2012), three loci (LSU, ITS and tub2 in Aveskamp et al. 2010), four loci (LSU, ITS, tub2 and act in Hyde et al. 2014; LSU, ITS, tub2 and rpb2 in Chen et al. 2015; ITS, tub2, chs and cal in Stewart et al. 2015) and five loci (LSU, ITS, tub2, act and tef1 in Vaghefi et al. 2012) for phylogenetic species recognition in Stagonosporopsis. However, in most cases, ITS and tub2 sequences are sufficient for achieving resolution to species level. While ITS sequences alone may be used to distinguish Stagonosporopsis as a monophyletic clade within Didymellaceae, tub2 fails to distinguish Stagonosporopsis and, thus, needs to be always combined with ITS (Chen et al. 2015). A phylogeny produced by rpb2 alone is highly similar to the combined four-locus phylogeny based on LSU, ITS, tub2 and rpb2. However, amplification of rpb2 has not been successful for many Stagonosporopsis spp. (Chen et al. 2015). Likewise, while partial cal sequences provide high resolution for Stagonosporopsis species delineation, it has not been successfully amplified in some strains (Aveskamp et al., 2010, Vaghefi et al., 2012). Thus, the use of ITS and tub2 is recommended as they will provide sufficient resolution for almost all Stagonosporopsis species, are easier to amplify, and are available for the majority of Stagonosporopsis spp. described to date (Table 19). The only two species that cannot be separated based on the LSU-ITS-tub2 phylogeny are S. bomiensis and S. papillata, for which sequencing of rpb2 was necessary (Chen et al. 2017).



References: Boerema et al. 2004 (morphology and distribution); Aveskamp et al., 2010, Chen et al., 2015 (morphology and phylogeny).



Stagonosporopsis chrysanthemi (F. Stevens) Crous et al., Australas. Pl. Pathol. 41: 681. 2012.

Basionym: Ascochyta chrysanthemi F. Stevens, Bot. Gaz. 44: 246. 1907.

Synonyms: Mycosphaerella ligulicola, K.F. Baker et al., Phytopathology 39: 799. 1949.

Didymella ligulicola (K.F. Baker et al.) Arx, Beitr. Kryptfl. Schweiz 11: 364. 1962.

Didymella ligulicola var. ligulicola (K.F. Baker et al.) Arx, Stud. Mycol. 32: 199. 1990.

Phoma ligulicola var. ligulicola Boerema, Stud. Mycol. 32: 9. 1990.

Stagonosporopsis ligulicola var. ligulicola (K.F. Baker et al.) Aveskamp et al., Stud. Mycol. 65: 46. 2010.



Typus: USA, North Carolina, West Raleigh, on Chrysanthemum indicum, Dec. 1906, F.L. Stevens (Bartholomew, Fungi Columbiani no. 2502, Field Museum of Natural History, C0004169F; designated here as lectotype, MBT385563); on Chrysanthemum morifolium, 1949, L.H. Davis [epitype of Ascochyta chrysanthemi designated here ATCC 10748, MBT385567 (preserved in a metabolically inactive state)].



Notes: Stevens (1907) described Ascochyta chrysanthemi on Chrysanthemum indicum from North Carolina; however, he did not refer to a holotype specimen in the original description. A specimen at Field Museum of Natural History (C0004169F) is chosen as lectotype, among numerous other duplicates deposited at BPI, CUP, NYBG, MSC, and various other herbaria that include collections distributed as E. Bartholomew, Fungi Columbiani 2502. Since no living cultures derived from these specimens are available, we designate ATCC 10748, isolated from Chrysanthemum morifolium from North Carolina, as ex-epitype culture of Ascochyta chrysanthemi here.



Authors: N. Vaghefi, Y. Marin-Felix, P.W. Crous & P.W.J. Taylor



Stemphylium Wallr., Flora Cryptogamica Germaniae 2: 300. 1833. Fig. 77.

Fig. 77.

Stemphylium spp. A. Disease symptoms caused by Stemphylium vesicarium (BRIP 65181) on pyrethrum leaves. B, C. Pseudothecial ascomata of Stemphylium vesicarium (BRIP 65181) on pyrethrum flower stems in vivo and in vitro respectively. D–H. Conidia of Stemphylium spp. D, H.Stemphylium vesicarium (BRIP 65181). E.Stemphylium truncatulae (holotype BRIP 14850). F, G.Stemphylium waikerieanum (ex-type VPRI 21969). I–K. Conidiophores of Stemphylium spp. I. 1-branched conidiophore of Stemphylium vesicarium (BRIP 65181). J. Simple conidiophore of Stemphylium truncatuale (holotype BRIP 14850). K. Branched and immature conidiophores of Stemphylium waikerieanum (ex-type VPRI 21969). L–N. Sexual morphs. L, M. Asci and ascospores of Stemphylium vesicarium isolated from the dead flower stems of pyrethrum. N. Immature pseudothecial ascomata of Stemphylium truncatulae on SNA after 1 wk. Scale bars: D–K = 20 μm; L, M = 100 μm. Pictures A–D, H, I, M taken from Moslemi et al. (2017).

Synonyms: Scutisporium Preuss, Linnaea 24: 112. 1821.

Epochniella Sacc., Michelia 2: 127. 1880.

Soreymatosporium Sousa da Câmara, Proposta Stemphylium: 18. 1930.

Thyrodochium Werderm., Annls mycol. 22: 188. 1942.



Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Pleosporaceae.



Type species: Stemphylium botryosum Wallr. = Pleospora tarda E.G. Simmons. Holotype of Ste. botryosum: "Ad sparagam" in herb. Wallroth, STR. Ex-type strain of Ple. tarda: CBS 714.68.



DNA barcode (genus): ITS.



DNA barcodes (species): cmdA, gapdh. Table 20. Fig. 78.



Table 20.

DNA barcodes of accepted Stemphylium spp.

Species	Isolates1	GenBank accession numbers2			References
		ITS	gapdh	cmdA
Stemphylium amaranthi	CBS 124746T	KU850505	KU850652	KU850793	Woudenberg et al. (2017)
Ste. armeriae	CBS 338.73	KU850511	KU850658	KU850799	Woudenberg et al. (2017)
Ste. astragali	CBS 116583ET	KU850512	KU850659	KU850800	Woudenberg et al. (2017)
Ste. beticola	CBS 141024T	KU850520	KU850667	KU850808	Woudenberg et al. (2017)
	VPRI 42502	MK336834	MK336880	MK336857	Present study
Ste. botryosum	CBS 714.68T	KC584238	AF443881	KU850826	Woudenberg et al. (2017)
Ste. callistephi	CBS 527.50T	KU850539	KU850686	KU850828	Woudenberg et al. (2017)
Ste. canadense	CBS 116602T	KU850641	KU850782	KU850932	Woudenberg et al. (2017)
Ste. chrysanthemicola	CBS 117255T	KU850640	KU850781	KU850931	Woudenberg et al. (2017)
	VPRI 10316	MK336835	MK336881	MK336858	Present study
Ste. drummondii	CBS 346.83T	GQ395365	KU850687	KU850829	Woudenberg et al. (2017)
Ste. eturmiunum	CBS 109845T	KU850541	KU850689	KU850831	Woudenberg et al. (2017)
	BRIP 27557	MK336820	MK336866	MK336843	Present study
	BRIP 27560	MK336821	MK336867	MK336844	Present study
	BRIP 55702	MK336826	MK336872	MK336849	Present study
	BRIP 60383	MK336827	MK336873	MK336850	Present study
	BRIP 62759	MK336830	MK336876	MK336853	Present study
	BRIP 63689	MK336831	MK336877	MK336854	Present study
Ste. gracilariae	CBS 482.90T	KU850549	AF443883	KU850839	Woudenberg et al. (2017)
Ste. halophilum	CBS 337.73T	KU850553	KU850700	KU850843	Woudenberg et al. (2017)
Ste. ixeridis	CBS 124748T	KU850590	KU850737	KU850881	Woudenberg et al. (2017)
Ste. lancipes	CBS 133314ET	KU850596	KU850742	KU850887	Woudenberg et al. (2017)
Ste. loti	CBS 407.54T	KU850597	KU850743	KU850888	Woudenberg et al. (2017)
Ste. lucomagnoense	CBS 116601T	KU850629	KU850770	KU850920	Woudenberg et al. (2017)
Ste. lycii	CBS 125241T	KU850602	KU850748	KU850893	Woudenberg et al. (2017)
Ste. lycopersici	CBS 122639NT	KU850611	KU850756	KU850902	Woudenberg et al. (2017)
	BRIP 13821	MK336813	MK336859	MK336836	Present study
	BRIP 13902	MK336814	MK336860	MK336837	Present study
	BRIP 15113	MK336817	MK336863	MK336840	Present study
	BRIP 62317	MK336828	MK336874	MK336851	Present study
Ste. majusculum	CBS 717.68T	KU850618	AF443891	KU850909	Woudenberg et al. (2017)
Ste. novae-zelandiae	CBS 138295T	KU850631	KU850772	KU850922	Woudenberg et al. (2017)
Ste. paludiscirpi	CBS 109842T	KU850620	KU850762	KU850911	Woudenberg et al. (2017) Present study
Ste. rombundicum	BRIP 27486HT	MK336819	MK336865	MK336842
Ste. sarciniforme	CBS 110049	KU850591	KU850738	KU850882	Woudenberg et al. (2017)
Ste. simmonsii	CBS 133518T	KU850637	KU850778	KU850928	Woudenberg et al. (2017)
Ste. solani	CBS 116586ET	KU850627	KU850768	KU850918	Woudenberg et al. (2017)
Ste. symphyti	CBS 115268T	KU850643	KU850784	KU850934	Woudenberg et al. (2017)
Ste. trifolii	CBS 116580T	KU850647	KU850788	KU850938	Woudenberg et al. (2017)
Ste. triglochinicola	CBS 718.68T	KU850648	KU850789	KU850939	Woudenberg et al. (2017)
Ste. truncatulae Ste. vesicarium	BRIP 14850HT	MK336815	MK336861	MK336838	Present study
	CBS 715.68	KU850565	KU850712	KU850855	Woudenberg et al. (2017)
	BRIP 5891	MK336829	MK336875	MK336852	Present study
	BRIP 14857	MK336816	MK336862	MK336839	Present study
	BRIP 26714	MK336818	MK336864	MK336841	Present study
	BRIP 40125	MK336822	MK336868	MK336845	Present study
	BRIP 40155	MK336823	MK336869	MK336846	Present study
	BRIP 52457	MK336824	MK336870	MK336847	Present study
	BRIP 53984	MK336825	MK336871	MK336848	Present study
	VPRI 31963	MK336833	MK336879	MK336856	Present study
Ste. waikerieanum	VPRI 21969HT	MK336832	MK336878	MK336855	Present study

¹BRIP: Queensland Plant Pathology Herbarium, Brisbane, Queensland, Australia; CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; VPRI: Victorian Plant Pathology Herbarium, Bundoora, Victoria, Australia. ^{T, ET, HT} and ^NT indicate ex-type, ex-epitype, holotype and ex-neotype strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; gapdh: partial glyceraldehyde-3-phosphate dehydrogenase gene; cmdA: partial calmodulin gene.

Fig. 78.

Bayesian phylogenetic tree inferred from ITS (565 bp), gapdh (613 bp) and cmdA (863) using partitioned analysis with N92+G+I substituition model for ITS and gapdh and GTR+G+I for cmdA. Highest log likelihood -34098.05. The analysis involved 122 nucleotide sequences including 98 sequences obtained from GenBank and 24 sequences obtained in the present study. Scale bar indicates expected changes per site. The tree was rooted to Alternaria alternata (GV14 634a1). The novel species described in this study are shown in bold. Bayesian posterior probability scores above 0.95 are shown at the nodes. GenBank accession numbers are indicated in Table 20. ^{T, ET, HT} and ^NT indicate ex-type, ex-epitype, ex-holotype and ex-neotype strains, respectively. TreeBASE:S23794.

Ascomata pseudothecial, globose or ovoid, membranous, dark brown to black, sometimes with a slender neck. Asci oblong to clavate, with distinct outer and inner walls. Ascospores elongate to oval, with 7 horizontal and 3–5 longitudinal septa, yellowish to brown, muriform on maturity. Conidiophores dark due to percurrent proliferation forming phaeodictyospores, mostly solitary, straight or flexuous, short or long, branched or unbranched, aseptate or septate. Conidiophores proliferate further after a conidium is produced, producing new cells and new conidia. Conidiogenous cells swollen at apex, single or in group. Conidia olive, dark or pale brown, verrucose, oblong or muriform, with 3 or more constricted transverse and 1–2 longitudinal or oblique septa.



Culture characteristics: Stemphylium colonies grow rapidly on a variety of media. On most media, the colonies are velvety to cottony in texture with a pale or dark olivaceous grey, brown or brownish black colour and black pigmentation on the colony reverse. Conidial density is low in cultures produced under laboratory conditions even when the isolate is grown under alternate cycle of 12 h light and 12 h darkness on PDA. Aerial mycelia flat/effuse, woolly or compact. Margins smooth and sharp or crenate and lobate.



Optimal media and cultivation conditions: SNA for pigmentation and morphological identification, PCA for morphological identification and alternatively PDA for pigmentation and morphological identification. Incubation for 1–2 wk at moderate temperatures from 23–27 °C (depending on the species) under cool white florescent light with an 8-hr or 12-hr photoperiod.



Distribution: Worldwide.



Hosts: Many Stemphylium species are saprophytes and grow on plant debris and cellulose material. However, plant pathogenic species, such as Ste. beticola, Ste. botryosum, Ste. loti, Ste. solani and Ste. vesicarium, can cause devastating damage and significant loss of agriculturally important crops annually. Stemphylium spp. are pathogenic to a wide range of hosts, such as tomato, garlic, asparagus, alfalfa, lupin, lentil and cotton. The ability of pathogens to infect a wide range of crops reflects its adaptability to wide range of climatic conditions and provides better survival chances.



Disease symptoms: Leaf spot, defoliation, curling and bending of the leaf margins and stems. Lesion size differs in various hosts and can grow to encompass the entire leaf and reduce photosynthesis.



Notes: Simmons (1967) established criteria for morphological identification of various Stemphylium spp. and introduced Pleospora herbarum as the sexual morph of Ste. botryosum. However, Simmons (1985) subsequently reclassified Stemphylium/Pleospora holomorphs and reported P. tarda as the sexual morph of Ste. botryosum and P. herbarum the sexual morph of Ste. herbarum (Moslemi et al. 2017). The asexual morph Stemphylium has been well studied, though the sexual morph Pleospora is poorly defined. The number of Pleospora spp. identified may be as many as 1000 and they are reported to be polyphyletic. Stemphylium is morphologically similar to the closely related genus Alternaria. However, unlike Alternaria in which its conidia remain attached and form a chain, Stemphylium conidia are always solitary, arising from a conidiogenous cell with a swollen apex (Inderbitzin et al. 2009). Morphological features such as spore shape and size, conidiophores, ascospores and the size and time of pseudothecial maturation are important characteristics in species identification. Other features such as variation in conidial wall ornamentation and septum development are not considered as important parameters in Stemphylium identification (Câmara et al. 2002).

For phylogenetic analyses of Stemphylium species, cmdA and gapdh were identified as the most informative genes, and rpb2 and actA as the least informative (Woudenberg et al. 2017). Among ITS, cmdA and gapdh, cmdA provides the highest resolution; however, more significant support is obtained when all three loci are combined.

Environmental factors such as temperature and moisture are key in Stemphylium disease development. Plant debris and seeds are primary sources of inoculum of Stemphylium in most host plant species. When environmental conditions are favourable, the pathogen can cause significant loss to various agricultural crops such as lupin and cotton (Boshuizen et al. 2004).



References: Simmons, 1967, Ellis, 1971, Bayaa and Erskine, 1998, Câmara et al., 2002 (morphology); Bashi and Rotem, 1975, Mwakutuya, 2006 (culture characteristics); Boshuizen et al. (2004) (biology and life cycle); Wang et al. (2010) (host range); Woudenberg et al., 2017, Crous et al., 2019b (optimal media and growing conditions).



Stemphylium rombundicum Moslemi, Y.P. Tan & P.W.J. Taylor, sp. nov. MycoBank MB829291. Fig. 79.



Fig. 79.

Stemphylium rombundicum (ex-type BRIP 27486). A–J. Conidia. K–S. Verrucose conidiogenous cells and straight and simple conidiophores with conidia attached. Scale bars: A–N, P = 20 μm; others 100 μm.

Etymology: Named after the famous beverage, Bundaberg Rum (Bundy Rum), produced in Bundaberg, Queensland, Australia, where the fungus was first isolated.



Conidiophores long, solitary, straight, septate, verrucose, light or dark brown, (62–)111–258(–307) μm, bearing one thickened, darkened, percurrent rejuvenation site. Conidiogenous cells swollen at apex, darkened, (5–)6–9(–10) μm wide. Conidia solitary, conidium body light brown to golden, turning into dark brown around longitudinal and transverse septa, verrucose, oblong or cylindrical, occasionally ovoid with curved apex, (27.5–)35–55.5(–61) × (10–)12.5–24(–26.5) μm, with 3–4 transverse septa, 1–2(–3) longitudinal or oblique septa per transverse sector. Sexual morph not observed.



Culture characteristics: Colonies on SNA after 1 wk reaching 35 mm diam, effuse, hairy or velvety, white, colourless, mycelia mostly immersed in the agar. On PDA reaching 35 mm diam, fast growing, with compact, entire, aerial mycelium, fine, woolly on the surface; reverse dark orange to dark brown in the centre with central pale brown rings growing towards the sides; thick yellow margins, and grey zones can also be seen.



Typus: Australia, Queensland, Bundaberg (Burnett Heads), from fruit lesions of Solanum lycopersicum (Solanaceae), 9 Aug. 2000, J. Maltby (holotype BRIP 27486, culture ex-type BRIP 27486).



Notes: Colonies of Ste. lycopersici produce a yellow dark red pigmentation diffusing out in PDA and other media (Yamamoto 1960). As Ste. rombundicum is closely related to species in the Ste. lycopersici complex, similar physiological characters can be observed on PDA. Colonies only sporulated at 23 °C under 12 h photoperiod on PDA. Against Ste. lycopersici in which the conidia are mostly ovoid with a pointed apex, Ste. rombondicum mostly contains cylindrical or oblong conidia. It is difficult to observe the longitudinal septa in conidia of Ste. rombundicum. Conidiophores are significantly long compared to the type Ste. lycopersici in which the conidiophores length do not exceed 140 μm. Conidia of Ste. lycopersici are significantly longer (50–74 μm × 16–23 μm) than those of Ste. rombundicum.



Stemphylium truncatulae Moslemi, Y.P. Tan & P.W.J. Taylor, sp. nov. MycoBank MB829282. Fig. 80.



Fig. 80.

Stemphylium truncatulae (ex-type BRIP 14850). A–H. Asexual morph. A–D. Conidia on SNA. E–H. Straight and simple or multibranched conidiophores and conidiogenous cells. I–J. Sexual morph. I. Immature pseudothecium. J. Ascomatal wall. Scale bars: I = 100 μm; others 20 μm.

Etymology: Named after the host species, Medicago truncatula, from which it was first collected.



Immature ascomata observed on SNA and PDA embedded in the agar. Ascomata pseudothecial, dark brown to black, globose or flask shaped, solitary or aggregated in groups of 3–5, (83.5–)185.5–186(–304) × (351–)453–483(–603) μm, with outgrowing dark mycelia; ascomatal wall 27–32 μm thick. Conidiophores solitary, straight to flexuous, mostly branched, septate or occasionally aseptate, smooth-walled, light brown, mostly 7–11 μm length, some 17–39 μm in length, bearing 2–6 thickened, pale, percurrent rejuvenation sites. Conidiogenous cells slender or slightly swollen at apex, pale, (5.5–)6.5–7(–9.5) μm. Conidia solitary, conidium body pale brown to golden or olivaceous brown, mostly smooth-walled, sometimes minutely verrucose, usually ovoid, occasionally with pointed apex, (8–)9.5–18(–21) × (14–)15.5–29.5(–32) μm, with 2–4 transverse septa, one longitudinal or oblique septa per transverse sector.



Culture characteristics: Colonies on SNA reaching 21–25 mm diam after 1 wk, with white and fluffy aerial mycelia in the centre; reverse colourless with pale olivaceous grey centre. Colonies on PDA reaching 25 mm diam after 1 wk, with white fluffy mycelia in the centre; reverse dark green to grey with thin white margins.



Typus: Australia, Victoria, from seeds of Medicago truncatula (Fabaceae), 10 Sep. 1982, M. Mebalds (holotype BRIP 14850, culture ex-type BRIP 14850).



Notes: Differs from the type species Ste. botryosum described by Simmons (1969) by producing significantly smaller conidia. According to Simmons (1969), conidia of Ste. botryosum are 24–26 μm wide and 33–35 μm long. Additionally, colonies of Ste. botryosum grow rapidly to 48 mm diam after 6 d of incubation at 25 °C (Hosen et al. 2013), while Ste. truncatulae is slow growing. The morphological identifications along with sequence analyses support Ste. truncatulae as a unique taxon closely related to the type species Ste. botryosum (CBS 714.68).



Stemphylium waikerieanum Moslemi, Jacq. Edwards & P.W.J Taylor, sp. nov. MycoBank MB829283. Fig. 81.



Fig. 81.

Stemphylium waikerieanum (ex-type VPRI 21969). A. Dried leaf of Allium cepa showing leaf lesions caused by the pathogen. B. Dried type culture. C. Revived colony after 1 wk on PDA. D–K. Asexual morph. D–H. Simple or 1-branched conidiophores on PDA and SNA. I–K. Phaeodictyospores. L–N. Sexual morph. L, M. Immature ascomata on SNA after 1 wk. N. Ascomatal wall. Scale bars: N = 100 μm; others 20 μm.

Etymology: Named after the location, Waikerie in South Australia, from where it was collected.



Immature ascomata observed on SNA after 2 wk embedded in the agar. Ascomata pseudothecial, dark brown to black, mostly flask-shaped or occasionally globose, solitary or aggregated in groups of 4–6, (267.5–)292–349.5(–374) × (191.5–)235.5–337(–381) μm, with outgrowing mycelia; ascomatal wall thin, 10–15 μm thick. Conidiophores solitary, straight, simple or occasionally 1-branched, septate, smooth-walled, pale brown, (29–)42–85(–98) μm long, cylindrical, enlarging apically to the site of conidium production. Conidiogenous cells swollen at apex, darkened, (6–)6.5–7(–7.5) μm wide. Conidia solitary, dark reddish brown, verrucose, ovoid, oblong or cylindrical, (18–)25–49(–52) × (10.5–)14–26(–30) μm, with 2–5 transverse septa, 1–2(–3) longitudinal or oblique septa per transverse sector, constricted at multiple darkened transverse septa.



Culture characteristics: Colonies on SNA reaching 28 mm diam after 1 wk with flat, entire and fluffy aerial mycelia in the centre, sub-hyaline. On PDA reaching 20 mm diam after 1 wk, compact, entire, aerial mycelium white, woolly, with rings of light olivaceous grey in the centre and dark olivaceous grey to black on the reverse side, margins regular, thick and white.



Typus: Australia, South Australia, Waikerie, from leaf spots on Allium sativum (Alliaceae), 14 Nov. 1997, H. Suheri (holotype VPRI 21969, culture ex-type VPRI 21969).



Notes: Stemphylium waikerieanum is morphologically similar to species in the Ste. vesicarium species complex. However, the conidium length in Ste. vesicarium complex does not exceed 45 μm (Simmons 1969), whereas conidia of Ste. waikerieanum were observed up to 49 μm long. The multigene phylogenetic analysis of ITS, gapdh and cmdA also support (PP value =1) this species as a novel taxon.



Authors: A. Moslemi, J. Edwards, Y.P. Tan & P.W.J. Taylor



Tubakia B. Sutton, Trans. Brit. Mycol. Soc. 60: 164. 1973. Fig. 82.

Fig. 82.

Tubakia spp. A–E. Disease symptoms. A.Tubakia californica on Tanoak tree (Notholithocarpus densiflorus). B.Tubakia californica on California black oak (Quercus kelloggii). C.Tubakia sierrafriensis (holotype CFNL 2944) on Quercus eduardi. D.Tubakia japonica (epitype NBRC H-11611) on Castanea crenata. E.Tubakia melnikiana (holotype HAL 3179 F) causing necrotic leaf lesion. F–N. Asexual morph. F. Scutellum of Tubakia paradryinoides (holotype TFM:FPH 3923). G. Central columella of Tubakia oblongispora (holotype NBRC H-11881). H–J. Conidiophores. H.Tubakia japonica (epitype NBRC H-11611). I.Tubakia oblongispora (holotype NBRC H-11881). J.Tubakia paradryinoides (holotype TFM:FPH 3923). K–M. Conidia. K.Tubakia dryinoides (holotype NBRC H-11618). L.Tubakia oblongispora (holotype NBRC H-11881). M.Tubakia paradryinoides (holotype TFM:FPH 3923). N. Microconidia of Tubakia dryinoides (holotype NBRC H-11618). Scale bars: 10 μm. Pictures taken from Braun et al. (2018).

Synonyms: Actinopelte Sacc., Annls mycol. 11: 315. 1913.



Classification: Dothideomycetes, Diaporthomycetidae, Diaporthales, Tubakiaceae.



Type species: Tubakia japonica (Sacc.) B. Sutton, basionym: Actinopelte japonica Sacc. Epitype and ex-epitype strains designated by Braun et al. (2018): NBRC H-11611, NBRC 9268 = MUCC2296 = ATCC 22472.



DNA barcodes (genus): ITS, LSU, rpb2.



DNA barcodes (species): ITS, tef1, tub2. Table 21.



Table 21.

DNA barcodes of accepted Tubakia spp.

Species	Isolates1	GenBank accession number2				References
		ITS	rpb2	tef1	tub2
Tubakia americana	CBS 129014	MG591873	MG976449	MG592058	MG592152	Braun et al. (2018)
T. braunii	CBS 115011T	MG591912	MG976488	MG592101	MG592193	Braun et al. (2018)
T. californica	CBS 143670T	MG591835	MG976451	MG592023	MG592117	Braun et al. (2018)
T. dryina	CBS 112097ET	MG591851	MG976455	MG592039	MG592133	Braun et al. (2018)
T. dryinoides	NBRC 9267T	MG591878	MG976461	MG592063	MG592157	Braun et al. (2018)
T. hallii	CBS 129013T	MG591880	MG976462	MG592065	MG592159	Braun et al. (2018)
T. iowensis	CBS 129012T	MG591879	–	MG592064	MG592158	Braun et al. (2018)
T. japonica	NBRC 9268ET	MG591886	MG976465	MG592071	MG592165	Braun et al. (2018)
T. liquidambaris	CBS 139744	MG605068	–	MG603578	–	Harrington & McNew (2018)
T. macnabbii	CBS 137349T	MG605069	–	MG603579	–	Harrington & McNew (2018)
T. melnikiana	CPC 32255T	MG591893	MG976472	MG592080	MG592174	Braun et al. (2018)
T. oblongispora	NBRC 9885T	MG591897	MG976474	MG592084	MG592178	Braun et al. (2018)
T. paradryinoides	NBRC 9884T	MG591898	MG976475	MG592085	MG592179	Braun et al. (2018)
T. seoraksanensis	CBS 127492IsoT	MG591908	MG976485	MG592096	MG592188	Braun et al. (2018)
T. sierrafriensis	CPC 33020T	MG591910	MG976486	MG592099	MG592191	Braun et al. (2018)
T. suttoniana	CBS 639.93IsoT	MG591921	MG976493	MG592110	MG592202	Braun et al. (2018)
T. tiffanyae	CBS 137345T	MG605081	–	–	–	Harrington & McNew (2018)

¹CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; CPC: Culture collection of Pedro Crous, housed at the Westerdijk Fungal Biodiversity Institute; NBRC: Biological Resource Center, NITE, Chiba, Japan. ^{T, ET} and ^IsoT indicate ex-type, ex-epitype and ex-isotype strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene.

Ascomata perithecial, pigmented, dark, on fallen overwintered leaves, rostrate, beak short, usually lateral-eccentric, slightly protuberant, with periphysate ostiolate; ascomatal wall variable in thickness, paler than stromatic layers, polyascal. Paraphyses lacking. Asci unitunicate, 8-spored, oblong-ellipsoid, stalk short to oblong, ascal apex with two refractive conoid structures, asci deliquescing at maturity. Ascospores more or less uniseriate, becoming irregularly biseriate, one-celled, hyaline, ellipsoid to fusiform, often inequilateral or slightly curved, wall finely ornamented, content granular-guttulate. Conidiomata pycnothyrial, usually circular or subcircular when viewed from above, superficial, easily removable, scutellate, fixed to the leaf by a central columella; scutellum composed of loose to dense hyphal strands, mostly branched, thick-walled, pigmented, margin compact or outer portions of the radiating hyphal strands looser to free, tips rounded, truncate or pointed, margin usually not recurved. Conidiophores reduced to conidiogenous cells. Conidiogenous cells phialidic, usually subcylindrical-conical, lageniform, hyaline to pale brown, arising from small, colourless fertile cells around the upper part of the central pycnothyrial columella, percurrently proliferating, sometimes forming indistinct periclinal thickenings or annellations (collarettes). Conidia formed singly, globose to broad ellipsoid-obovoid, sometimes subcylindrical or somewhat irregular, wall thin to somewhat thickened, smooth to faintly rough, hyaline to pigmented, apex rounded, base rounded to attenuated, sometimes with distinct frill or peg-like basal hilum (adapted from Braun et al. 2018).



Culture characteristics: Colonies on MEA flat, with dense or fluffy, sparse to moderate aerial mycelium, margins regular or scalloped; surface ivory white, dingy white to pale yellow, straw, cream to light grey, smoke grey, white with center green olive and brown hyphal stripes, creamy white with or without concentric rings of olivaceous mycelium, or white to grey with wet conidial masses olive green to black; reverse pale grey, greyish white with olivaceous margins, smoke grey with olivaceous grey margins, golden yellow to slightly darker, yellowish grey with concentric rings, yellow with dark grey concentric rings, straw with dark brown concentric rings, or middle dark grey and yellow to medium brown towards the rim.



Optimal media and cultivation conditions: MEA, OA, PDA and PNA at 25 °C under near-ultraviolet light.



Distribution: North America, Asia, Australia and Europe.



Hosts: Castanea spp., Chrysolepis chrysophylla, Lithocarpus densiflorus and Quercus spp (Fagaceae), Liquidambar styraciflua (Hamamelidaceae), Lindera glauca (Lauraceae), and Pinus tabuliformis (Pinaceae). Reported from other hosts not verified such as Acer spp. (Aceraceae), Carya spp. (Juglandaceae) and Fraxinus spp. (Oleaceae).



Disease symptoms: Leaf spots, necrosis and death. Tubakia iowensis also causes petiole necrosis and death of whole leaves on bur oak (bur oak blight).



Notes: Tubakia was recently revised by Braun et al. (2018), resulting in the introduction of five new genera to accommodate species previously placed in Tubakia, i.e. Apiognomonioides, Involutiscutellula, Oblongisporothyrium, Paratubakia and Saprothyrium. All these genera together with Racheliella and Sphaerosporithyrium, both genera also described during the revision of the genus Tubakia, were accommodated in the new family Tubakiaceae (Braun et al. 2018). Presently, 16 species are accepted in the genus based on molecular data (ITS, tef1 and tub2 sequences). These species may form different types of asexual morphs, being the punctiform conidiomata (pycnothyria) composed of convex scutella with radiating threads of cells fixed to the substratum by a central columella the most common and characteristic structure formed. Other asexual morphs include sporodochial conidiomata and crustose or pustulate pycnidioid conidiomata. The conidia are globose to broad ellipsoid-obovoid, sometimes subcylindrical or somewhat irregular, aseptate, hyaline, subhyaline to pigmented. Tubakia suttoniana is the only species that produces sexual morph characterised by ostiolate ascomata, unitunicate asci with two refractive conoid structures in the ascal apex, and one-celled, hyaline ascospores.

 Species of Tubakia are endophytes and/or pathogens in leaves and twigs of many tree species, causing distinct leaf lesions in different hosts including oak (Quercus spp.), chestnut (Castanea spp.) and other hardwood species. Moreover, T. iowensis is also capable of causing petiole necrosis and death of whole leaves on bur oak (Q. macrocarpa), sometimes killing nearly every leaf on a susceptible tree. This disease is known as bur oak blight and is most common in Iowa and Minnesota, but it has been noted in western and southern Wisconsin, northern Illinois, northeast Kansas, eastern Nebraska, and eastern South Dakota, with isolated groups of affected trees in counties of Illinois and Missouri that border Iowa (Harrington & McNew 2016).



References: Harrington et al. 2012 (morphology and pathogenicity), Harrington & McNew 2016 (pathogenicity, bur oak blight), Harrington & McNew 2018 (morphology and phylogeny), Braun et al. 2018 (morphology, pathogenicity and phylogeny).



Authors: Y. Marin-Felix & P.W. Crous



Zasmidium Fr., Summa veg. Scand., Sectio Post. (Stockholm): 407. 1849. Fig. 83.

Fig. 83.

RAxML phylogram obtained from the combined ITS (534 bp), LSU (741 bp) and rpb2 (739 bp) sequence alignment of all accepted species of Zasmidium. The tree was rooted to Anellosympodiella juniperi CBS 137992 and Neopenidiella nectandrae CBS 734.78. The novelties proposed in this study are indicated in bold. RAxML bootstrap support (BS) values above 70 % and Bayesian posterior probability scores above 0.95 are shown at the nodes. GenBank accession numbers are listed in Table 22 and Videiraet al. (2017). ^{T, ET, HT} and ^NT indicate ex-type, ex-epitype, holotype and ex-neootype strains, respectively. TreeBASE: S23834.

Synonyms: Periconiella Sacc., Atti Ist. Veneto Sci. Lett. Arti 3: 727. 1885.

Biharia Thirum. & Mishra, Sydowia 7: 79. 1953.

Stenellopsis B. Huguenin, Bull. Trimestriel Soc. Mycol. France 81: 695. 1966.

Verrucispora D.E. Shaw & Alcorn, Proc. Linn. Soc. New South Wales 92: 171. 1967. (nom. illegit., Art. 53.1).

Verrucisporota D.E. Shaw & Alcorn, Austral. Syst. Bot. 6: 273. 1993.



Classification: Dothideomycetes, Dothideomycetidae, Capnodiales, Mycosphaerellaceae.



Type species: Zasmidium cellare (Pers.) Fr., basionym: Racodium cellare Pers. Neotype designated by Videira et al. (2017): CBS 146.36 (duplicate cultures ATCC 36951 = IFO 4862 = IMI 044943 = LCP 52.402 = LSHB BB274 = MUCL 10089).



DNA barcode (genus): LSU.



DNA barcodes (species): ITS, rpb2, act, tef1, tub2. Table 22. Fig. 84.



Table 22.

DNA barcodes of accepted Zasmidium spp.

Species	Isolates1	GenBank accession numbers2						References
		ITS	LSU	rpb2	act	tef1	tub2
Zasmidium angulare	CBS 132094T	JQ622088	JQ622096	MF951690	–	JQ622113	–	Li et al. (2012), Videira et al. (2017)
Z. anthuriicola	CBS 118742T	FJ839626	FJ839662	MF951691	–	KF253229	KF252763	Crous et al., 2009a, Quaedvlieg et al., 2013, Videira et al., 2017
Z. aporosae	MFLU 12-2206HT	KC677912	–	–	–	–	–	Phengsintham et al. (2013)
Z. arcuatum	CBS 113477T	EU041779	EU041836	MF951692	–	–	–	Arzanlou et al., 2007, Videira et al., 2017
Z. aucklandicum	CPC 13569	MF951409	MF951280	MF951733	–	–	–	Videira et al. (2017)
Z. biverticillatum	CBS 335.36	EU041796	EU041853	–	–	–	–	Arzanlou et al. (2007)
Z. cellare	CBS 146.36NT	EU041821	EU041878	MF951693	–	–	–	Arzanlou et al., 2007, Videira et al., 2017
Z. cerophillum	CBS 103.59T	EU041798	GU214485	MF951694	–	–	–	Arzanlou et al., 2007, Crous et al., 2009b, Videira et al., 2017
Z. citri-griseum	CBS 139467ET	KF901796	KF902155	KF902518	–	KF903385	KF903079	Quaedvlieg et al. (2014)
Z. commune	CBS 142530T	KY979765	KY979820	–	KY979860	–	–	Crous et al. (2017a)
Z. cyatheae	CPC 24725T	KT037530	KT037571	–	KT037629	KT037490	–	Guatimosim et al. (2016)
Z. dasypogonis	CBS 143397T	MG386048	MG386101	–	–	–	–	Crous et al. (2017b)
Z. daviesiae	CBS 116002	FJ839633	FJ839669	MF951698	KF903477	KF903373	KF903069	Crous et al., 2009a, Quaedvlieg et al., 2014, Videira et al., 2017
Z. ducassei	BRIP 53367T	HQ149687	–	–	–	–	–	Shivas et al. (2011)
	CPC 32929	MK539971	MK540041	–	MK540233	MK540167	-	Present study
Z. elaeocarpi	CBS 142187T	MF951398	MF951263	MF951699	–	–	–	Videira et al. (2017)
Z. eucalypticola	CBS 142186T	MF951400	MF951265	MF951701	–	–	–	Videira et al. (2017)
Z. eucalyptigenum	CBS 138860T	KP004458	KP004486	–	KT037630	–	–	Crous et al., 2014c, Guatimosim et al., 2016
Z. eucalyptorum	CBS 118500T	KF901652	MF951266	MF951702	KF903495	KF903101	–	Quaedvlieg et al., 2014, Videira et al., 2017
Z. fructicola	CBS 139625T	KP896052	KP895922	MF951703	KP896003	KP896099	–	Huang et al., 2015, Videira et al., 2017
Z. fructigenum	CBS 139626T	KP896056	KP895926	MF951704	KP896007	KP896103	KP896149	Huang et al., 2015, Videira et al., 2017
Z. gahniicola	CBS 143422T	MG386050	MG386103	–	–	–	–	Crous et al. (2017b)
Z. grevilleae	CBS 124107T	FJ839634	FJ839670	MF951705	–	–	–	Crous et al., 2009a, Videira et al., 2017
Z. gupoyu	CBS 122099	MF951401	MF951267	MF951706	–	–	–	Videira et al. (2017)
Z. hakeae	CBS 142185T	MF951402	MF951268	MF951707	–	–	–	Videira et al. (2017)
Z. indonesianum	CBS 139627T	KF901739	KF902086	MF951710	–	KF903377	–	Quaedvlieg et al., 2014, Videira et al., 2017
Z. iteae	CBS 113094T	MF951405	MF951271	MF951711	–	–	–	Videira et al. (2017)
Z. lonicericola	CBS 125008ET	KF251283	KF251787	MF951712	–	KF253231	KF252765	Quaedvlieg et al., 2013, Videira et al., 2017
Z. macluricola	BRIP 52143T	GU108499	–	–	–	–	–	Shivas et al. (2009)
Z. musae	CBS 122477T	EU514291	–	–	EU514346	–	–	Arzanlou et al. (2008)
Z. musae-banksii	CBS 121710T	EU041795	EU041852	MF951716	–	–	–	Arzanlou et al., 2007, Videira et al., 2017
Z. musicola	CBS 122479T	EU514294	MF951275	MF951717	–	–	–	Arzanlou et al., 2008, Videira et al., 2017
Z. musigenum	CBS 365.36T	EU041801	EU041858	–	–	–	–	Arzanlou et al. (2007)
Z. nocoxi	CBS 125009T	KF251284	KF251788	MF951719	–	KF253232	KF252766	Quaedvlieg et al., 2013, Videira et al., 2017
Z. pitospori	CBS 122274	MF951406	MF951276	MF951720	–	–	–	Videira et al. (2017)
Z. podocarpi	CBS 142529T	KY979766	KY979821	–	KY979861	–	KY979930	Crous et al. (2017a)
Z. proteacearum	CBS 116003	FJ839635	FJ839671	MF951721	KF903478	–	KF903070	Crous et al., 2009a, Quaedvlieg et al., 2014, Videira et al., 2017
Z. pseudoparkii	CBS 110999T	DQ303023	JF700965	MF951723	KF903419	KF903273	KF902977	Crous et al., 2006, Quaedvlieg et al., 2011, Quaedvlieg et al., 2013, Videira et al., 2017
Z. pseudotsugae	rapssd	EF114687	EF114704	–	–	–	–	Winton et al. (2007)
Z. pseudovespa	CBS 121159T	MF951407	KF901836	MF951724			KF902812	Quaedvlieg et al., 2013, Quaedvlieg et al., 2014, Videira et al., 2017
Z. queenslandicum	CBS 122475T	EU514295	MF951277	MF951725	–	–	–	Arzanlou et al., 2008, Videira et al., 2017
Z. rothmanniae	CBS 137983T	KJ869135	MH878613	–	–	–	–	Crous et al., 2014c, Vu et al., 2019
Z. scaevolicola	CBS 127009T	KF251285	KF251789	MF951726	–	KF253233	KF252767	Quaedvlieg et al., 2013, Videira et al., 2017
Z. schini	CBS 142188T	MF951408	MF951278	MF951727	–	–	–	Videira et al. (2017)
Z. strelitziae	CBS 121711T	EU041803	EU041860	MF951729	–	–	–	Arzanlou et al., 2007, Videira et al., 2017
Z. suregadae	MFLU 12-2212HT	KC677914	KC677939	–	–	–	–	Phengsintham et al. (2013)
Z. syzygii	CBS 133580T	KC005777	KC005798	MF951730	–	–	–	Crous et al., 2012, Videira et al., 2017
Z. thailandicum	CBS 145027T	MK539970	MK540040	–	–	–	–	Present study
Z. tsugae	ratstk	EF114688	EF114705	–	–	–	–	Winton et al. (2007)
Z. velutinum	CBS 101948ET	EU041781	EU041838	MF951731	–	–	–	Arzanlou et al., 2007, Videira et al., 2017
Z. xenoparkii	CBS 111185T	DQ303028	JF700966	MF951732	KF903438	KF903274	KF902978	Crous et al., 2006, Quaedvlieg et al., 2011, Quaedvlieg et al., 2014, Videira et al., 2017

¹BRIP: Queensland Plant Pathology Herbarium, Brisbane, Australia; CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; CPC: Culture collection of Pedro Crous, housed at the Westerdijk Fungal Biodiversity Institute; MFLU: Mae Fah Luang University herbarium, Chiang Rai, Thailand; rapssd and ratstk were not specified in the original publications. ^{T, ET, HT} and ^NT indicate ex-type, ex-epitype, holotype and ex-neotype strains, respectively.

²ITS: internal transcribed spacers and intervening 5.8S nrDNA; LSU: partial large subunit (28S) nrRNA gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; act: partial actin gene; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene.

Fig. 84.

Zasmidium spp. A–C. Disease symptoms caused by Zasmidium cyatheae (ex-type CPC 24725). A, B. Frond spots on Cyathea delgadii. C. Erumpent subcuticular ascomata, fruiting epiphyllous. D–F. Sexual morph of Zasmidium cyatheae (ex-type CPC 24725). D. Ascoma. E. Asci. F. Ascospores. G–R. Asexual morph. G–L. Conidiophores. G. Zasmidium biverticillatum (CBS 335.36). H. Zasmidium citri-griseum (ex-epitype CBS 139467). I. Zasmidium fructigenum (ex-type CBS 139626). J. Zasmidium indonesianum (ex-type CBS 139627). K. Zasmidium musigenum (ex-type CBS 365.36). L. Zasmidium strelitziae (ex-type CBS 121711). M–Q. Conidiophores. M. Zasmidium biverticillatum (CBS 335.36). N. Zasmidium biverticillatum (CBS 335.36). O. Zasmidium citri-griseum (ex-epitype CBS 139467). P. Zasmidium fructicola (ex-type CBS 139625). Q. Zasmidium musigenum (ex-type CBS 365.36). R. Primary and secondary conidia of Zasmidium cellare (ex-neotype CBS 146.36). Scale bars: 10 μm. Pictures A–F taken from Guatimosim et al. (2016); G, K–N, Q, R from Arzanlou et al. (2007); H–J, O, P from Huang et al. (2015).

Ascomata pseudothecial, amphigenous or epiphyllous, dark brown or black, globose, single to aggregated; necks rarely perceptible, usually a paler coloured circular area, composed of convergent yellow hyphae; ascomatal wall composed of 2–3 layers of cells of textura angularis. Asci bitunicate, fasciculate, subsessile, obpyriform, obovoid to ellipsoidal, obclavate to fusoid-ellipsoidal, saccate or clavate to cylindrical, aparaphysate, 8-spored. Ascospores 2–3-seriate to multiseriate, hyaline, smooth-walled, guttulate, without sheath, fusoid to ellipsoidal with obtuse ends, straight to slightly curved, uniseptate, constricted or not at the septum, widest in the middle of apical cell. In plant pathogenic species, mycelium mostly immersed as well as superficial, rarely only immersed; hyphae branched, septate, hyaline or almost so to pigmented, pale olivaceous to brown, wall thin to somewhat thickened, immersed hyphae smooth-walled or almost so to faintly rough, external hyphae distinctly verruculose to verrucose (in culture immersed hyphae usually smooth-walled or almost so, aerial hyphae verruculose). Stromata lacking to well-developed, pigmented. Conidiophores solitary, arising from superficial hyphae, lateral, occasionally terminal, in vivo (in plant pathogenic taxa) sometimes also fasciculate, arising from internal hyphae or stromata, semimacronematous to macronematous, in culture occasionally micronematous, cylindrical, filiform, subuliform, straight to strongly geniculate-sinuous, mostly unbranched, aseptate, i.e. reduced to conidiogenous cells, to pluriseptate, subhyaline to pigmented, pale olivaceous to medium dark brown, wall thin to somewhat thickened, smooth to verruculose. Conidiogenous cells integrated, terminal, occasionally intercalary, rarely pleurogenous, or conidiophores reduced to conidiogenous cells, mostly polyblastic, sympodial, with conspicuous, somewhat thickened and darkened-refractive, planate loci. Conidia solitary or catenate, in simple or branched acropetal chains, shape and size variable, ranging from amero- to scolecosporous, aseptate to transversely plurieuseptate, subhyaline to pigmented, pale olivaceous to brown, wall thin to somewhat thickened, smooth or almost so to usually distinctly verruculose (in plant pathogenic species without superficial mycelium always verruculose); hila somewhat thickened and darkened-refractive, planate, conidial secession schizolytic (asexual morph description adapted from Braun et al. 2013).



Culture characteristics: Colonies slow growing, with sparse to moderate aerial mycelium, rarely with aerial mycelium absent, sometimes with mucoid exudate, margins smooth and regular, lobate or feathery. On MEA olivaceous, olivaceous green with margins whitish, brown olivaceous, olivaceous grey, iron mouse grey, grey, cream, yellowish brown, vinaceous buff to olivaceous buff, dark brown, or dark brown with margins grey; reverse pale or dark grey olivaceous, olivaceous black, mouse grey, iron-grey, greenish black, pale orange, isabelline, buff, dark brown, or brown vinaceous. On PDA pale white with margins pale olivaceous grey, pale mouse grey, olivaceous grey, iron-grey, iron-grey with patches orange, or brown olivaceous; reverse olivaceous grey, iron-grey, iron-grey with patches orange, or isabelline. On OA mouse grey, olivaceous grey, smoke grey with margins olivaceous grey, iron-grey, or iron-grey with broad margins of orange; reverse olivaceous, olivaceous grey, dark mouse grey, or iron-grey.



Optimal media and cultivation conditions: MEA, OA, PDA and SNA at 25 °C under near-ultraviolet light.



Distribution: Worldwide.



Hosts: Wide range of hosts belonging to 25 different families, including Alocasia odora and Anthurium sp. (Araceae), Aporosa villosa (Euphorbiaceae), Brabejum stellatifolium, Grevillea spp. and Hakea undulata (Proteaceae), Citrus spp. (Rutaceae), Cyathea delgadii (Cyatheaceae), Dasypogon sp. (Dasypogonaceae), Daviesia latifolia (Fabaceae), Elaeocarpus kirtonii (Elaeocarpaceae), Eucalyptus spp. (Myrtaceae), Gahnia sieberiana (Cyperaceae), Geniostoma rupestre (Loganiaceae), Itea parvifolia (Escalloniaceae), Lonicera japonica (Caprifoliaceae), Maclura cochinchinensis (Moraceae), Malus spp. (Rosaceae), Pittosporum tenuifolium (Pittosporaceae), Podocarpus sp. (Podocarpaceae), Pseudotsuga menziesii and Tsuga heterophylla (Pinaceae), Restio subverticillatus (Restionaceae), Rothmannia engleriana (Rubiaceae), Sasa sp. (Poaceae), Scaevola taccada (Goodeniaceae), Schinus terebinthifolius (Anacardiaceae), Strelitzia sp. (Strelitziaceae), and Syzygium cordatum (Myrtaceae).



Disease symptoms: Causing various lesions, ranging from yellowish discolorations to distinct leaf spots. Also associated with sooty blotch and flyspeck diseases. Also isolated from wall in wine cellar.



Notes: The genus Zasmidium is morphologically similar to Stenella, producing thickened and darkened conidiogenous loci and hila (Braun et al. 2013). However, these genera differ in the conidial hila and scars, being flat in Stenella and planate and somewhat thickened, darkened in Zasmidium. Moreover, Stenella belongs to Teratosphaeriaceae while Zasmidium is located within Mycosphaerellaceae (Arzanlou et al., 2007, Quaedvlieg et al., 2013, Videira et al., 2017).

 A recent phylogenetic analysis based on LSU, ITS and rpb2 showed that species belonging to other genera, i.e. Mycosphaerella, Parastenella, Periconiella, Ramichloridium, Rasutoria, Stenella and Verrucisporota, were located in the monophyletic clade representing the genus Zasmidium (Videira et al. 2017). Therefore, 12 new combinations were introduced, and the genera Periconiella and Verrucisporota reduced to synonymy with Zasmidium. Based on our phylogenetic analysis, 48 species are accepted in the genus together with one new species described here, and a new combination based on Ramichloridium ducassei.

 The type species of the genus, Z. cellare, has been isolated from wine cellars in Europe and America, while the other species of the genus are associated to plants as saprobic or mostly biotrophic, usually foliicolous, symptomless or causing various lesions, ranging from yellowish discolorations to distinct leaf spots. Zasmidium spp. are pathogens of a wide range of hosts such as Z. biverticillatum and Z. musigenum, which cause tropical speckle disease on members of Musaceae (Stahel, 1937, Jones, 2000), and Z. fructicola and Z. fructigenum, both pathogens of Citrus causing a disease known as citrus greasy spot (Huang et al. 2015).



References: Arzanlou et al., 2007, Videira et al., 2017 (morphology and phylogeny), Braun et al. 2013 (morphology).



Zasmidium ducassei (R.G. Shivas et al.) Y. Marín & Crous, comb. nov. MycoBank MB829646.

Basionym: Ramichloridium ducassei R.G. Shivas et al., Australas. Pl. Path. 40: 63. 2010.



Description and illustration: Shivas et al. (2011).



Typus: Australia, Queensland, Daintree, on leaves of Musa acuminata × balbisiana (Musaceae), 14 Apr. 2010, M. Berridge & K.R.E. Grice (holotype BRIP 53367, culture ex-type BRIP 53367).



Additional material examined: Malaysia, on leaves of Musa sp., 2016, P.W. Crous, CPC 32929.



Notes: This species was initially introduced as R. ducassei to accommodate some isolates associated with a severe leaf speckle disease of Ducasse banana (Musa acuminata × babisiana cv. Pisang awak) in northern Queensland (Shivas et al. 2011). The authors noticed that this species was similar to Zasmidium in having pigmented conidiophores with integrated conidiogenous cells that sympodially proliferate near the apex, with slightly thickened and refractive scars and aseptate, subhyaline conidia also with slightly thickened and refractive hila. However, it was classified in Ramichloridium in preference to Zasmidium because, at the time, Zasmidium was a paraphyletic genus in the Mycosphaerellaceae. In our phylogenetic analysis based on the combined dataset, the ex-type strain of this species was located in the well-supported clade (100 % BS / 1 PP) representing Zasmidium, and therefore a new combination Z. ducassei is proposed. Moreover, additional isolates belonging to this species were obtained from the same host genus, but from different locale, Malaysia.



Zasmidium thailandicum Crous, sp. nov. MycoBank MB829647. Fig. 85.



Fig. 85.

Zasmidium thailandicum (ex-type CBS 145027). A–C. Conidiophores sporulating on SNA. D–F. Conidiogenous cells with apical rachis giving rise to conidia. Scale bars = 10 μm.

Etymology: Named reflects the country from where it was collected, Thailand.



On SNA. Conidiophores solitary, arising from superficial hyphae, subcylindrical, pale brown, 1–3-septate, unbranched or branched below, 20–100 × (1.5–)2 μm. Conidiogenous cells subhyaline, smooth-walled, subcylindrical, apical and intercalary, apical part with well-defined rachis bearing minute (0.5 μm diam) slightly darkened scars, 10–30 × 1.5–2 μm. Ramoconidia fusoid to obclavate, hyaline, smooth-walled, aseptate, guttulate, 8–12(–17) × 2.5–3 μm. Conidia solitary, hyaline, smooth-walled, guttulate, aseptate, ellipsoid, apex obtuse, base protruding, truncate, 0.5–1 μm diam, (3–)4–4.5(–5) × (2–)2.5 μm.



Culture characteristics: Colonies erumpent, spreading, with moderate aerial mycelium and smooth, lobate margins, reaching 20 mm diam after 2 wk at 25 °C. On MEA, PDA and OA surface pale mouse grey, reverse mouse grey.



Typus: Thailand, Rachaburi province, Bangkok, on leaves of Musa sp. (Musaceae), 2010, P.W. Crous, HPC 2158 (holotype CBS H-23850, culture ex-type CBS 145027 = CPC 33960).



Notes: Zasmidium thailandicum is closely related to Z. ducassei. Moreover, both species have been reported from the same host genus, Musa, causing leaf spots on banana leaves. However, these species can be easily distinguished by the length of their conidia [5–10 μm in Z. ducassei vs. (3–)4–4.5(–5) μm in Z. thailandicum].



Authors: P.W. Crous, J.Z. Groenewald, J.J. Luangsa-ard & Y. Marin-Felix