Coelomycetous Dothideomycetes with emphasis on the families Cucurbitariaceae and Didymellaceae

Abstract

The taxonomy of the coelomycetes has undergone dramatic changes in recent years, but remains controversial due to the high number of taxa involved, their poor morphological differentiation, the rare occurrence of the sexual morphs, and rapid loss of fertility in vitro. In the present study, we revisited the families Cucurbitariaceae and Didymellaceae (Pleosporales, Dothideomycetes), which include numerous plant pathogens, endophytic species associated with a wide host range, and saprobes. The taxonomy of two of the most relevant genera, i.e. Phoma and Pyrenochaeta, remains ambiguous after several phylogenetic studies, and needs further revision. We have studied a total of 143 strains of coelomycetes from clinical or environmental origin, by combining the LSU, ITS, tub2 and rpb2 sequences for a multi-locus analysis and a detailed morphological comparison. The resulting phylogenetic tree revealed that some fungi previously considered as members of Cucurbitariaceae represented five different families, and four of them, Neopyrenochaetaceae, Parapyrenochaetaceae, Pseudopyrenochaetaceae and Pyrenochaetopsidaceae, are proposed here as new. Furthermore, 13 new genera, 28 new species, and 20 new combinations are proposed within the Pleosporineae. Moreover, four new typifications are introduced to stabilise the taxonomy of these fungi.

Introduction

The Pleosporales is the largest order of the class Dothideomycetes (phylum Ascomycota), encompassing more than 4 700 species distributed over 332 genera, and 53 families (Kirk et al., 2008, Zhang et al., 2009, Zhang et al., 2012, Ariyawansa et al., 2013, Hyde et al., 2013, Amaradasa et al., 2014, Trakunyingcharoen et al., 2014, Wijayawardene et al., 2014, Crous et al., 2015a, Sharma et al., 2015, Tanaka et al., 2015, Jaklitsch et al., 2016, Jaklitsch and Voglmayr, 2016, Wanasinghe et al., 2016, Crous and Groenewald, 2017, Hashimoto et al., 2017, Hernández-Restrepo et al., 2017). These fungi are characterised by the production of pseudothecial ascomata (mostly globose and usually papillate) consisting of a peridial wall composed by several layers of cells, within which the fissitunicate (bitunicate) asci are produced amidst a persistent hamathecium (the vegetative structures inside an ascoma) (Jaklitsch and Voglmayr, 2016, Jaklitsch et al., 2017, Zhang et al., 2009, Zhang et al., 2012) and ascospores, which are mostly septate but variable in shape and pigmentation. The asexual morphs of the Pleosporales are characterised by conidia produced within discrete sporocarps (conidiomata), and sometimes conidia are generated on conidiophores produced on mycelium. Phoma and its relatives are the most common pleosporalean asexual morphs and are characterised by the presence of pycnidia (globose to pyriform conidiomata from which the conidia arise throughout an apical opening) (De Gruyter et al., 2009, De Gruyter et al., 2010, Aveskamp et al., 2010, Chen et al., 2015). Pleosporales are mainly saprobic on plant debris, epiphytic, endophytic or parasitic of living plants, fungi and insects, or mycobionts in lichens (Kruys et al., 2006, Aveskamp et al., 2008, Aveskamp et al., 2010, De Gruyter et al., 2009, Zhang et al., 2009, Zhang et al., 2012, Lawrey et al., 2012, Kocakaya et al., 2015). These fungi can also infect humans (Punithalingam, 1979, Ahmed et al., 2014, Ahmed et al., 2015, Ahmed et al., 2017, Borman et al., 2016, Valenzuela-Lopez et al., 2016).

Modern phylogenetic studies support the division of the Pleosporales into the suborders Pleosporineae and Massarineae (Zhang et al., 2009, Zhang et al., 2012, Hyde et al., 2013, Tanaka et al., 2015). The former includes nine families, i.e. Coniothyriaceae, Cucurbitariaceae, Didymellaceae, Dothidotthiaceae, Halojulellaceae, Leptosphaeriaceae, Neophaeosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae and Shiraiaceae (Zhang et al., 2012, De Gruyter et al., 2013, Ariyawansa et al., 2013, Ariyawansa et al., 2015b, Liu et al., 2013), which encompass plant pathogens of economic importance including the well-known genera such as Alternaria, Ascochyta, Bipolaris, Didymella and Leptosphaeria (Zhang et al., 2012, Ariyawansa et al., 2013, De Gruyter et al., 2013, Liu et al., 2013, Woudenberg et al., 2013). Recently, Tanaka et al. (2015) revised the suborder Massarineae and accepted 12 families; however, more studies are needed for a better understanding of their phylogenetic relationships. Numerous species of Pleosporales are relatively common in clinical samples, most of which belong to the families Cucurbitariaceae and Didymellaceae (Valenzuela-Lopez et al. 2016). Cucurbitariaceae is still a poorly known family, which was erected by Winter (1885) with Cucurbitaria as the type genus, and characterised by ostiolate ascomata aggregated on a basal pseudostromatic structure, hamathecium composed of wide persistent filaments, fissitunicate, cylindrical to cylindrical-clavate asci and dark, phragmosporous or muriform ascospores. In the last revision of Cucurbitariaceae, four sexual genera (Cucurbitaria, Curreya, Rhytidiella and Syncarpella) and two asexual genera (Pyrenochaeta and Pyrenochaetopsis) were accepted (Doilom et al. 2013). The latter two genera are characterised by phoma-like, setose pycnidia, and hyaline, aseptate conidia (De Gruyter et al., 2010, De Gruyter et al., 2013). Recently, Jaklitsch & Voglmayr (2017) demonstrated that some species of Cucurbitaria, such as C. obducens, C. piceae (both producing muriform ascospores) and C. rhododendri (with phragmospores), belong to three different genera of Melanommataceae. Wanasinghe et al. (2017b) proposed Neocucurbitaria, characterised by solitary ascomata, the presence of periphyses and muriform ascospores, as a new genus of Cucurbitariaceae. However, the current members of this family need to be re-evaluated, including their asexual morphs.

The family Didymellaceae also includes economically important plant pathogens, such as the causal agents of blackleg and ascochyta blight (Rouxel and Balesdent, 2005, McDonald and Peck, 2009, Salam et al., 2011, De Gruyter et al., 2013), but also diverse endophytic, fungicolous and lichenicolous taxa belong to this fungal group (Aveskamp et al. 2010), whereas a few members are known as pathogens of humans (de Hoog et al. 2011). This family was established by de Gruyter et al. (2009) and embraces the species traditionally classified in the genera Ascochyta, Didymella and Phoma. However, Phoma is one of the largest and most polyphyletic fungal genera (with more than 3 000 names recorded) with species occurring in more than 25 families (http://www.indexfungorum.org).

Zhang et al. (2009), included Didymellaceae in their study and accepted the sexual genera Didymella, Leptosphaerulina, Macroventuria, Monascostroma and Platychora. In general, these genera are characterised by dark pseudothecial ascomata, filamentous pseudoparaphyses, 8-spored, fissitunicate, clavate to saccate asci, and hyaline, 1-septate, fusiform to biconical ascospores; with the only exception being Leptosphaerulina, which has hyaline to brown, ellipsoid, cylindrical or oblong, phragmosporous or muriformly septate ascospores, which also lack pseudoparaphyses. Several studies have tried to resolve the taxonomy of the asexual morphs of the Didymellaceae, especially Phoma and its relatives, with more or less success. Subsequently, de Gruyter et al. (2010) transferred several species of Phoma to Pyrenochaetopsis (Cucurbitariaceae), Neosetophoma and Setophoma (Phaeosphaeriaceae), and resurrected the genus Paraphoma (Phaeosphaeriaceae). The study by Aveskamp et al. (2010), based on the sequences of four loci, revealed that the subdivision of Phoma in sections (Boerema et al. 2004) was phylogenetically inconsistent, and they thus proposed Boeremia to accommodate species morphologically close to Phoma exigua, while species of Phoma section Sclerophomella were transferred to Epicoccum and Peyronellaea. Furthermore, de Gruyter et al. (2013) transferred some species of Phoma sections Plenodomus and Heterospora to the Leptosphaeriaceae and some from Phoma section Pilosa and Ascochyta to Pleosporaceae. Recently, Chen et al. (2015) proposed nine genera (Allophoma, Calophoma, Heterophoma, Neoascochyta, Neodidymelliopsis, Nothophoma, Paraboeremia, Phomatodes and Xenodidymella) in Didymellaceae, transferred Microsphaeropsis (Didymellaceae) to the family Microsphaeropsidaceae, and restricted Phoma to Phoma herbarum (Chen et al. 2017). Other authors have added the genera Briansuttonomyces, Didymellocamarosporium, Heracleicola, Neodidymella, Neomicrosphaeropsis and Pseudoascochyta to Didymellaceae (Ariyawansa et al., 2015a, Crous and Groenewald, 2016, Crous et al., 2016a, Thambugala et al., 2016, Wijayawardene et al., 2016). However, the genera Didymellocamarosporium, Heracleicola and Neodidymella were studied by Chen et al. (2017) and revealed as probable synonyms of older genera within Didymellaceae.

To resolve the taxonomy of the Cucurbitariaceae and the Didymellaceae we have tried to delineate the phylogenetic relationships within these families performing a multi-locus analysis including ex-type and reference strains of most of the phoma-like and pyrenochaeta-like taxa available in the culture collection of Westerdijk Fungal Biodiversity Institute (Utrecht, The Netherlands; formerly CBS-KNAW), and numerous isolates of clinical origin from the USA.

Materials and methods

Isolates and reference fungal strains

This study comprised 70 clinical isolates previously identified as belonging to the Pleosporales (Valenzuela-Lopez et al. 2016), provided by the Fungus Testing Laboratory of the University of Texas Health Science Center at San Antonio (UTHSC; San Antonio, Texas, USA), two environmental strains from Spain (CBS 141688) and New Zealand (CBS 141689) respectively, and 71 reference and ex-type strains belonging to the Cucurbitariaceae and Didymellaceae provided by the CBS culture collection (Table 1).

Table 1.

Isolates used in this study and their GenBank accession numbers. Numbers of new taxa, combinations and sequences generated are indicated in bold.

Species	Old name	CBS strain1 no.	Other strain1 no.	Status2	Host, substrate	Country	GenBank accession numbers3
							LSU	ITS	TUB	RPB2
Allocucurbitaria botulispora	Pyrenochaeta sp.	CBS 142452	UTHSC:DI16-273; FMR 13764	T	Human superficial tissue	USA	LN907416	LT592932	LT593001	LT593070
Allophoma cylindrispora	Phoma sp.	CBS 142453	UTHSC:DI16-233; FMR 13723	T	Human superficial tissue	USA	LN907376	LT592920	LT592989	LT593058
A.labilis		CBS 124.93			Solanum lycopersicum	The Netherlands	GU238091	GU237765	GU237619	KT389552
A.minor		CBS 325.82	FMR 14905	T	Syzygium aromaticum	Indonesia	GU238107	GU237831	GU237632	KT389553
A.nicaraguensis		CBS 506.91	FMR 14904	T	Coffea arabica	Nicaragua	GU238058	GU237876	GU237596	KT389551
A.oligotrophica	Phoma costarricencis	CBS 497.91	FMR 14902		Coffea arabica	Unknown	GU238059	GU237870	GU237597	LT623247
			CGMCC 3.18114	T	Air sample	China	KY742194	KY742040	KY742282	KY742128
A.piperis		CBS 268.93		T	Peperomia pereskiifolia	Netherlands	GU238129	GU237816	GU237644	KT389554
A.tropica		CBS 436.75	FMR 14903	T	Saintpaulia ionantha	Germany	GU238149	GU237864	GU237663	KT389556
A.zantedeschiae		CBS 131.93			Calla sp.	The Netherlands	GU238159	FJ427084	FJ427188	KT389557
		CBS 229.32			Cicer arietinum	Romania	KT389690	KT389473	KT389558	KT389767
Alternariaster bidentis		CBS 134021	CPC 19479	T	Bidens sulphurea	Brazil	KC609341	KC609333	–	KC609347
A.helianthi		CBS 327.69	IFO 9089		Helianthus annuus	Unknown	KC584369	KC609335	–	KC584494
Ascochyta herbicola		CBS 629.97			Water	USA	GU238083	GU237898	GU237614	KP330421
A.pisi		CBS 126.54	AFTOL-ID 1583		Pisum sativum	The Netherlands	DQ678070	GU237772	GU237531	DQ677967
A.rabiei		CBS 206.30			Unknown	Unknown	KT389695	KT389478	KT389772	KT389559
A.versabilis		CBS 876.97			Silene sp.	The Netherlands	GU238152	GU237909	GU237664	KT389561
A.viciae		CBS 451.68			Vicia sepium	The Netherlands	KT389701	KT389484	KT389778	KT389562
Boeremia exigua		CBS 118.38			Cheiranthus cheiri	Denmark	KT389706	KT389489	KT389783	KT389582
		CBS 119.38			Nicotiana tabacum	Unknown	KT389707	KT389490	KT389784	KT389583
B.lycopersici		CBS 378.67			Solanum lycopersicum	The Netherlands	GU237950	GU237848	GU237512	KT389580
Briansuttonomyces eucalypti		CBS 114879	CPC 362	T	Eucalyptus sp.	South Africa	KU728519	KU728479	KU728595	–
		CBS 114887	CPC 363		Eucalyptus sp.	South Africa	KU728520	KU728480	KU728596	–
Calophoma aquilegiicola		CBS 107.96			Aconitum pyramidale	The Netherlands	GU238041	GU237735	GU237581	KT389586
		CBS 108.96			Aquilegia sp.	The Netherlands	GU238042	GU237736	GU237582	–
C.clematidina		CBS 102.66			Clematis sp.	UK	FJ515630	FJ426988	FJ427099	KT389587
		CBS 108.79		T	Clematis sp.	The Netherlands	FJ515632	FJ426989	FJ427100	KT389588
C.clematidis-rectae		CBS 507.63		T	Clematis sp.	The Netherlands	FJ515647	FJ515606	FJ515624	KT389589
C.rosae			CGMCC 3.18347	T	Rosa sp.	China	KY742203	KY742049	KY742291	KY742135
			LC 8119		Rosa sp.	China	KY742204	KY742050	KY742292	KY742136
Camarosporidiella aborescentis	Camarosporium aborescentis		MFLUCC 14-0604	T	Colutea arborescens	Russia	KP711378	KP711377	–	–
	Camarosporium arezzoensis		MFLUCC 14-0238	T	Cytisus sp.	Italy	KP120927	KP120926	–	–
C.aureum	Camarosporium aureum		MFLUCC 14-0620	T	Cotinus coggygria	Russia	KP744478	KP744436	–	–
C.clematidis	Camarosporium clematidis		MFLUCC 13-0336	T	Clematis vitalba	Italy	KJ562188	KJ562213	–	–
C.elongata	Cucurbitaria elongata		MFLUCC 14-0260		Cytisus scoparius	Italy	KJ724249	–	–	–
	Cucurbitaria elongata	CBS 171.55	AFTOL-ID 1568		Cytisus sessilifolius	France	DQ678061	–	–	DQ677957
C.robiniicola	Camarosporium robiniicola		MFLUCC 13-0527		Robinia pseudacacia	Italy	KJ589412	KJ562214	–	–
C.spartii	Camarosporium spartii		MFLUCC 13-0548		Cytisus sp.	Italy	KJ589413	KJ562215	–	–
Camarosporium quaternatum		CBS 142617	CPC 23216		Daphne mezereum	Germany	KY929170	KY929135	–	–
		CBS 142616	CPC 31081	T	Lycium barbarum	Hungary	KY929136	KY929171	–	–
			CPC 31518		Lycium barbarum	Hungary	KY929172	KY929137	–	–
Camarosporomyces flavigenus		CBS 314.80		T	Water	Romania	GU238076	KY929138	–	–
Coniothyrium palmarum		CBS 758.73	CMW 5283		Phoenix dactylifera	Israel	JX681085	–	–	–
		CBS 400.71			Chamaerops humilis	Italy	EU754153	AY720708	KT389792	KT389592
C.telephii		CBS 188.71			Air sample	Finland	GQ387599	JF740188	KT389793	KT389593
		CBS 856.97			Mineral wool	Finland	GQ387600	JF740189
Cucurbitaria berberidis			MFLUCC 11-0387		Berberis vulgaris	Austria	KC506796	–	–	–
		CBS 130007	FMR 15751; MFLUCC 11-0384; CB1	T	Berberis vulgaris	Austria	KC506793	LT717673	LT717676	LT854936
Cumuliphoma indica	Phoma omnivirens	CBS 654.77	FMR 15341	T	Unknown	India	GU238122	FJ427043	FJ427153	LT623261
	Phoma omnivirens	CBS 991.95	FMR 15331		Soil	Papua New Guinea	GU238121	FJ427044	FJ427154	LT623262
C.omnivirens	Phoma omnivirens	CBS 341.86	FMR 14915	T	Phaseolus vulgaris	Belgium	LT623214	FJ427042	FJ427152	LT623260
C.pneumoniae	Phoma sp.	CBS 142454	UTHSC:DI16-249; FMR 13739	T	Human respiratory tract	USA	LN907392	LT592925	LT592994	LT593063
Cucurbidothis pityophila		CBS 149.32	FMR 15744		Unknown	The Netherlands	JX681087	GQ203756	LT854934	LT854935
Didymella aeria			LC 8120		Air sample	China	KY742206	KY742052	KY742294	KY742138
			CGMCC 3.18353	T	Air sample	China	KY742205	KY742051	KY742137	KY742293
D.aliena		CBS 379.93			Berberis sp.	The Netherlands	GU238037	GU237851	GU237578	KP330416
D.americana		CBS 185.85			Zea mays	USA	GU237990	FJ426972	FJ427088	KT389594
D.anserina		CBS 253.80			Unknown	Germany	KT389715	KT389498	KT389795	KT389595
	Peyronellaea sp.		UTHSC:DI16-255; FMR 13745		Human respiratory tract	USA	LN907398	LT592926	LT592995	LT593064
D.aquatica			CGMCC 3.18349	T	Water	China	KY742209	KY742055	KY742297	KY742140
			LC 5555		Water	China	KY742210	KY742056	KY742298	KY742141
D.arachidicola		CBS 333.75		T	Arachis hypogaea	South Africa	GU237996	GU237833	GU237554	KT389598
D.aurea		CBS 269.93		T	Medicago polymorpha	New Zealand	GU237999	GU237818	GU237557	KT389599
D.bellidis		CBS 714.85			Bellis perennis	The Netherlands	GU238046	GU237904	GU237586	KP330417
D.boeremae		CBS 109942		T	Medicago littoralis cv. Harbinger	Australia	GU238048	FJ426982	FJ427097	KT389600
D.brunneospora	Didymella sp.	CBS 115.58	FMR 15745	T	Chrysanthemum roseum	Germany	KT389723	KT389505	KT389802	KT389625
D.chenopodii		CBS 128.93			Chenopodium quinoa cv. Sajana	Peru	GU238055	GU237775	GU237591	KT389602
D.chloroguttulata			CGMCC 3.18351	T	Air sample	China	KY742211	KY742057	KY742299	KY742142
			LC 8122		Air sample	China	KY742212	KY742058	KY742300	KY742143
D.coffeae-arabicae		CBS 123380	PD 84/1013	T	Coffea arabica	Ethiopia	GU238005	FJ426993	FJ427104	KT389603
D.curtisii			PD 92/1460		Sprekelia sp.	The Netherlands	GU238012	FJ427041	FJ427151	KT389604
D.ellipsoidea			CGMCC 3.18350	T	Air sample	China	KY742214	KY742060	KY742302	KY742145
			LC 8123		Air sample	China	KY742215	KY742061	KY742303	KY742146
D.eucalyptica		CBS 377.91			Eucalyptus sp.	Australia	GU238007	GU237846	GU237562	KT389605
D.exigua		CBS 183.55		T	Rumex arifolius	France	EU754155	GU237794	GU237525	EU874850
D.gardeniae		CBS 626.68	IMI 108771; FMR 14901	T	Gardenia jasminoides	India	GQ387595	FJ427003	FJ427114	KT389606
	Peyronellaea sp.		UTHSC:DI16-211; FMR 13701		Human superficial tissue	USA	LN907354	LT592908	LT592977	LT593046
	Peyronellaea calorpreferens		UTHSC:DI16-226; FMR 13716		Human superficial tissue	USA	LN907369	LT592913	LT592982	LT593051
	Peyronellaea sp.		UTHSC:DI16-274; FMR 13765		Human superficial tissue	USA	LN907417	LT592933	LT593002	LT593071
	Peyronellaea sp.		UTHSC:DI16-295; FMR 13788		Human superficial tissue	USA	LN907438	LT592944	LT593013	LT593083
D.glomerata		CBS 528.66		T	Chrysanthemum sp.	The Netherlands	JX681105	FJ427013	FJ427124	GU371781
	Peyronellaea glomerata		UTHSC:DI16-205; FMR 13695		Human superficial tissue	USA	LN907348	LT592905	LT592974	LT593043
D.heteroderae		CBS 109.92	PD 73/1405	T	Undefined food material	The Netherlands	GU238002	FJ426983	FJ427098	KT389601
	Peyronellaea calorpreferens		UTHSC:DI16-190; FMR 13680		Human superficial tissue	USA	LN907333	LT592896	LT592965	LT593034
	Peyronellaea calorpreferens		UTHSC:DI16-224; FMR 13714		Human superficial tissue	USA	LN907367	LT592911	LT592980	LT593049
	Peyronellaea calorpreferens		UTHSC:DI16-227; FMR 13717		Human superficial tissue	USA	LN907370	LT592914	LT592983	LT593052
	Peyronellaea calorpreferens		UTHSC:DI16-231; FMR 13721		Human superficial tissue	USA	LN907374	LT592918	LT592987	LT593056
	Peyronellaea calorpreferens		UTHSC:DI16-232; FMR 13722		Human deep tissue/fluids	USA	LN907375	LT592919	LT592988	LT593057
	Peyronellaea calorpreferens		UTHSC:DI16-234; FMR 13724		Human superficial tissue	USA	LN907377	LT592921	LT592990	LT593059
	Peyronellaea calorpreferens		UTHSC:DI16-235; FMR 13725		Human superficial tissue	USA	LN907378	LT592922	LT592991	LT593060
	Peyronellaea calorpreferens		UTHSC:DI16-305; FMR 13798		Human respiratory tract	USA	LN907448	LT592951	LT593020	LT593090
D.ilicicola			CGMCC 3.18355	T	Ilex chinensis	Italy	KY742219	KY742065	KY742307	KY742150
			LC 8127		Ilex chinensis	Italy	KY742220	KY742066	KY742308	KY742151
D.infuscatispora			CGMCC 3.18356	T	Chrysanthemum indicum	China	KY742221	KY742067	KY742309	KY742152
			LC 8129		Chrysanthemum indicum	China	KY742222	KY742068	KY742310	–
D.keratinophila	Peyronellaea sp.	CBS 143032	UTHSC:DI16-200; FMR 13690	T	Human superficial tissue	USA	LN907343	LT592901	LT592970	LT593039
	Peyronellaea sp.		UTHSC:DI16-228; FMR 13718		Human superficial tissue	USA	LN907371	LT592915	LT592984	LT593053
	Phoma sp.		UTHSC:DI16-282; FMR 13774		Human superficial tissue	USA	LN907425	LT592938	LT593007	LT593077
D.lethalis		CBS 103.25			Unknown	Unknown	GU238010	GU237729	GU237564	KT389607
D.macrophylla			CGMCC 3.18357	T	Hydrangea macrophylla	Italy	KY742224	KY742070	KY742312	KY742154
			LC 8132		Hydrangea macrophylla	Italy	KY742225	KY742071	KY742313	KY742155
D.macrostoma		CBS 223.69			Acer pseudoplatanus	Switzerland	GU238096	GU237801	GU237623	KT389608
D.maydis		CBS 588.69		T	Zea mays	USA	EU754192	FJ427086	FJ427190	GU371782
D.microchlamydospora		CBS 105.95		T	Eucalyptus sp.	UK	GU238104	FJ427028	FJ427138	KP330424
	Phoma sp.		UTHSC:DI16-199; FMR 13689		Human superficial tissue	USA	LN907342	LT592900	LT592969	LT593038
	Peyronellaea sp.		UTHSC:DI16-365; FMR 13858		Human superficial tissue	USA	LN907508	LT592964	LT593033	LT593103
D.molleriana		CBS 229.79			Digitalis purpurea	New Zealand	GU238067	GU237802	GU237605	KP330418
D.musae	Phoma sp.		UTHSC:DI16-230; FMR 13720		Human superficial tissue	USA	LN907373	LT592917	LT592986	LT593055
		CBS 463.69	FMR 15339		Mangifera indica	India	GU238011	FJ427026	FJ427136	LT623248
D.negriana		CBS 358.71			Vitis vinifera	Germany	GU238116	GU237838	GU237635	KT389610
			ICMP 10845; LC 5249		Vitis vinifera	former Yugoslavia	KY742227	KY742073	KY742315	–
D.nigricans		CBS 444.81	PD 77/919		Actinidea chinensis	New Zealand	GU238001	GU237915	GU237559	KT389611
D.ocimicola			CGMCC 3.18358	T	Ocimum sp.	China	KY742232	KY742078	KY742320	–
			LC 8138		Ocimum sp.	China	KY742233	KY742079	KY742321	–
D.pedeiae		CBS 124517		T	Schefflera elegantissima	The Netherlands	GU238127	GU237770	GU237642	KT389612
D.pinodella		CBS 531.66			Trifolium pretense	USA	GU238017	FJ427052	FJ427162	KT389613
D.pinodes		CBS 525.77		T	Pisum sativum	Belgium	GU238023	GU237883	GU237572	KT389614
		CBS 374.84	FMR 15345		Pisum sativum	The Netherlands	EU754135	JF810523	LT623229	LT623249
D.pomorum		CBS 285.76		T	Heracleum dissectum	Russia	GU238025	FJ427053	FJ427163	KT389615
D.protuberans		CBS 381.96	FMR 14899	T	Lycium halifolium	The Netherlands	GU238029	GU237853	GU237574	KT389620
	Peyronellaea sp.		UTHSC:DI16-302; FMR 13795		Environmental	USA	LN907445	LT592949	LT593018	LT593088
D.pteridis		CBS 379.96	FMR 15750		Pteris sp.	The Netherlands	KT389722	KT389504	KT389801	KT389624
D.rhei		CBS 109177			Rheum rhaponticum	New Zealand	GU238139	GU237743	GU237653	KP330428
D.rumicicola	Didymella acetosellae	CBS 179.97			Rumex hydrolapathum	The Netherlands	GU238034	GU237793	GU237575	KP330415
		CBS 683.79		T	Rumex obtusifolius	New Zealand	KT389721	KT389503	KT389800	KT389622
D.sancta		CBS 281.83		T	Ailanthus altissima	South Africa	GU238030	FJ427063	FJ427170	KT389623
		CBS 644.97	FMR 15351		Opuntia ficus-indica	Argentina	LT623211	FJ427064	FJ427171	LT623250
D.segeticola			CGMCC 3.17489	T	Cirsium segetum	China	KP330455	KP330443	KP330399	KP330414
			CGMCC 3.17498		Cirsium segetum	China	KP330454	KP330442	KP330398	KP330413
D.sinensis			LC 8142		Dendrobium officinale	China	KY742241	KY742087	KY742329	KY742166
			LC 8143		Dendrobium officinale	China	KY742242	KY742088	KY742330	KY742167
Didymella sp.	Didymella segeticola		LC 8141		Camellia sasanqua	Japan	KY742238	KY742084	KY742326	KY742164
D.subglomerata		CBS 110.92			Triticum sp.	USA	GU238032	FJ427080	FJ427186	KT389626
D.suiyangensis			CGMCC 3.18352	T	Air sample	China	KY742243	KY742089	KY742330	KY742168
			LC 8144		Air sample	China	KY742244	KY742090	KY742332	KY742169
D.viburnicola		CBS 523.73			Viburnum cassioides	The Netherlands	GU238155	GU237879	GU237667	KP330430
Dothidotthia aspera		CBS 119688	CPC 12932		Acer negundo	USA	EU673275	–	–	–
D.symphoricarpi		CBS 119687	CPC 12929	T	Symphoricarpos rotundifolius	USA	EU673273	–	–	–
Ectophoma multirostrata	Phoma multirostrata	CBS 110.79	FMR 15342		Cucumis sativus	The Netherlands	GU238110	FJ427030	FJ427140	LT623264
	Phoma multirostrata	CBS 274.60	FMR 15335	T	Soil	Maharashtra	GU238111	FJ427031	FJ427141	LT623265
	Phoma multirostrata	CBS 368.65	FMR 15336		Unknown	India	GU238112	FJ427033	FJ427143	LT623266
E.pomi	Phoma pereupyrena	CBS 267.92	FMR 15346	T	Coffea arabica	India	GU238128	GU237814	GU237643	LT623263
Epicoccum brasiliense		CBS 120105	FMR 14907	T	Amaranthus sp.	Brazil	GU238049	GU237760	GU237588	KT389627
E.camelliae			CGMCC 3.18343	T	Camellia sinensis	China	KY742245	KY742091	KY742333	KY742170
	Epicoccum sorghinum		UTHSC:DI16-201; FMR 13691		Human respiratory tract	USA	LN907344	LT592902	LT592971	LT593040
	Epicoccum sorghinum		UTHSC:DI16-202; FMR 13692		Human superficial tissue	USA	LN907345	LT592903	LT592972	LT593041
	Epicoccum sorghinum		UTHSC:DI16-206; FMR 13696		Human superficial tissue	USA	LN907349	LT592906	LT592975	LT593044
	Epicoccum sorghinum		UTHSC:DI16-280; FMR 13772		Human superficial tissue	USA	LN907423	LT592937	LT593006	LT593076
	Epicoccum sorghinum		UTHSC:DI16-338; FMR 13831		Human superficial tissue	USA	LN907481	LT592959	LT593028	LT593098
	Epicoccum sorghinum		UTHSC:DI16-345; FMR 13838		Human subcutaneous tissue	USA	LN907488	LT592961	LT593030	LT593100
			LC 4862		Camellia sinensis	China	KY742246	KY742092	KY742334	KY742171
E.catenisporum	Epicoccum sorghinum	CBS 181.80	FMR 14911	T	Oryza sativa	Guinea-Bissau	LT623213	FJ427069	FJ427175	LT623253
E.dendrobii			CGMCC 3.18359	T	Dendrobium fimbriatum	China	KY742247	KY742093	KY742335	–
			LC 8146		Dendrobium fimbriatum	China	KY742248	KY74209	KY742336	-
E.draconis		CBS 186.83	FMR 14908		Dracaena sp.	Rwanda	GU238070	GU237795	GU237607	KT389628
E.duchesneae			LC 8147		Duchesnea indica	China	KY742250	KY742096	KY742338	–
			CGMCC 3.18345	T	Duchesnea indica	China	KY742249	KY742095	KY742337	–
E.henningsii		CBS 104.80			Acacia mearnsii	Kenya	GU238081	GU237731	GU237612	KT389629
E.hordei			CGMCC 3.18360	T	Hordeum vulgare	Australia	KY742251	KY742097	KY742339	–
			LC 8149		Hordeum vulgare	Australia	KY742252	KY742098	KY742340	–
E.huancayense		CBS 105.80		T	Solanum sp.	Peru	GU238084	GU237732	GU237615	KT389630
E.italicum			CGMCC 3.18361	T	Acca sellowiana	Italy	KY742253	KY742099	KY742341	KY742172
			LC 8151		Acca sellowiana	Italy	KY74225	KY742100	KY742342	KY742173
E.keratinophilum	Phoma sp.		UTHSC:DI16-244; FMR 13734		Human superficial tissue	USA	LN907387	LT592924	LT592993	LT593062
	Phoma sp.		UTHSC:DI16-258; FMR 13748		Human respiratory tract	USA	LN907401	LT592928	LT592997	LT593066
	Phoma sp.	CBS 142455	UTHSC:DI16-271; FMR 13762	T	Human superficial tissue	USA	LN907414	LT592930	LT592999	LT593068
	Phoma sp.		UTHSC:DI16-272; FMR 13763		Human superficial tissue	USA	LN907415	LT592931	LT593000	LT593069
	Phoma sp.		UTHSC:DI16-299; FMR 13792		Human deep tissue/fluids	USA	LN907442	LT592947	LT593016	LT593086
E.latusicollum	Epicoccum sorghinum		UTHSC:DI16-197; FMR 13687		Human superficial tissue	USA	LN907340	LT592898	LT592967	LT593036
			CGMCC 3.18346	T	Sorghum bicolor	China	KY742255	KY742101	KY742343	KY742174
			LC 4859		Camellia sinensis	China	KY742256	KY742102	KY742344	KY742175
E.layuense			CGMCC 3.18362	T	Perilla sp.	China	KY742261	KY742107	KY742349	–
			LC 8156		Perilla sp.	China	KY742262	KY742108	KY742350	–
E.nigrum		CBS 125.82			Human toe nail	The Netherlands	GU237974	FJ426995	FJ427106	KT389631
		CBS 173.73		T	Dactylis glomerata	USA	GU237975	FJ426996	FJ427107	KT389632
E.ovisporum	Epicoccum sorghinum	CBS 180.80	FMR 14910	T	Zea mays	South Africa	LT623212	FJ427068	FJ427174	LT623252
E.pimprinum			PD 77/1028		Soil	India	GU237977	FJ427050	FJ427160	KT389633
E.plurivorum		CBS 558.81	FMR 14909	T	Setaria sp.	New Zealand	GU238132	GU237888	GU237647	KT389634
E.pneumoniae	Epicoccum sorghinum		UTHSC:DI16-257; FMR 13747	T	Human respiratory tract	USA	LN907400	LT592927	LT592996	LT593065
E.poae			LC 8161		Poa annua	USA	KY742268	KY742114	KY742356	KY742183
			CGMCC 3.18363	T	Poa annua	USA	KY742267	KY742113	KY742355	KY742182
			LC 8162		Poa annua	USA	KY742269	KY742115	KY742357	KY742184
E.proteae	Phoma proteae	CBS 114179	CPC 1854; FMR 15332	T	Protea cv. carnival	South Africa	JQ044452	JQ044433	LT623230	LT623251
E.sorghinum		CBS 179.80			Sorghum vulgare	Puerto Rico	GU237978	FJ427067	FJ427173	KT389635
		CBS 627.68			Citrus sp.	France	GU237979	FJ427072	FJ427178	KT389636
			UTHSC:DI16-288; FMR 13780		Human superficial tissue	USA	LN907431	LT592940	LT593009	LT593079
			UTHSC:DI16-301; FMR 13794		Human respiratory tract	USA	LN907444	LT592948	LT593017	LT593087
E.viticis			BRIP 29294; LC 5257		Andropogon gayanus	Australia	KY742271	KY742117	KY742359	–
			CGMCC 3.18344	T	Vitex negundo	China	KY742272	KY742118	KY742360	KY742186
Foliophoma fallens		CBS 161.78			Olea europaea	New Zealand	GU238074	KY929147	–	KC584502
		CBS 284.70			Nerium oleander	Italy	GU238078	KY929148	–	–
Halojulella avicenniae			BCC 18422		Mangrove wood	Thailand	GU371823	–	–	GU371787
			BCC 20173		Mangrove wood	Thailand	GU371822	–	–	GU371786
Heterophoma adonidis		CBS 114309			Adonis vernalis	Sweden	KT389724	KT389506	KT389803	KT389637
H.nobilis		CBS 507.91			Dictamnus albus	The Netherlands	GU238065	GU237877	GU237603	KT389638
H.verbascicola			CGMCC 3.18364	T	Verbascum thapsus	China	KY742273	KY742119	KY742361	KY742187
			LC 8164		Verbascum thapsus	China	KY742274	KY742120	KY742362	KY742188
Juxtiphoma eupyrena	Phoma eupyrena	CBS 374.91	FMR 15329		Solanum tuberosum	The Netherlands	GU238072	FJ426999	FJ427110	LT623268
	Phoma eupyrena	CBS 527.66	FMR 15337		Wheat field soil	Germany	GU238073	FJ427000	FJ427111	LT623269
Leptosphaeria conoidea		CBS 616.75			Lunaria annua	The Netherlands	JF740279	JF740201	KT389804	KT389639
L.doliolum		CBS 505.75		T	Urtica dioica	The Netherlands	GQ387576	JF740205	JF740144	KT389640
Leptosphaerulina americana		CBS 213.55			Trifolium pratense	USA	GU237981	GU237799	GU237539	KT389641
L.australis		CBS 317.83			Eugenia aromatica	Indonesia	EU754166	GU237829	GU237540	GU371790
Libertasomyces myopori		CBS 141302	CPC 27354	T	Myoporum serratum	South Africa	KX228332	NR_145200	–	–
L.platani		CBS 142112	CPC 29609	T	Platanus sp.	New Zealand	KY173507	KY173416	KY173604	KY173585
L.quercus		CBS 134.97	INIFAT C96/108	T	Quercus ilex	Spain	DQ377883	–	–	–
Macroventuria anomochaeta		CBS 525.71		T	Decayed canvas	South Africa	GU237984	GU237881	GU237544	GU456346
M.wentii		CBS 526.71		T	Plant litter	USA	GU237986	GU237884	GU237546	KT389642
Microsphaeriopsis olivacea		CBS 233.77			Pinus laricio	France	GU237988	GU237803	GU237549	KT389643
M.proteae		CBS 111319	CPC 1425		Protea nitida	South Africa	JN712563	JN712497	–	JN712650
Neoascochyta argentina		CBS 112524		T	Triticum aestivum	Argentina	KT389742	KT389524	KT389822	–
N.cylindrispora	Ascochyta sp.		UTHSC:DI16-352; FMR 13845		Human superficial tissue	USA	LN907495	LT592962	LT593031	LT593101
	Ascochyta sp.	CBS 142456	UTHSC:DI16-359; FMR 13852	T	Human superficial tissue	USA	LN907502	LT592963	LT593032	LT593102
N.desmazieri		CBS 297.69		T	Lolium perenne	Germany	KT389726	KT389508	KT389807	KT389644
	Ascochyta sp.		UTHSC:DI16-207; FMR 13697		Human respiratory tract	USA	LN907350	LT592907	LT592976	LT593045
	Ascochyta sp.		UTHSC:DI16-320; FMR 13813		Unknown	USA	LN907463	LT592956	LT593025	LT593095
	Ascochyta sp.		UTHSC:DI16-332; FMR 13825		Human superficial tissue	USA	LN907475	LT592958	LT593027	LT593097
	Ascochyta sp.		UTHSC:DI16-341; FMR 13834		Human superficial tissue	USA	LN907484	LT592960	LT593029	LT593099
N.europaea		CBS 820.84		T	Hordeum vulgare	Germany	KT389729	KT389511	KT389809	KT389646
N.exitialis		CBS 118.40			Unknown	Unknown	KT389732	KT389514	KT389812	KT389647
		CBS 389.86			Triticum aestivum	Switzerland	KT389733	KT389515	KT389813	KT389648
N.graminicola		CBS 301.69			Lolium multiflorum	Germany	KT389737	KT389519	KT389817	KT389650
N.graminicola		CBS 816.84			Hordeum vulgare	Germany	KT389741	KT389523	KT389821	KT389651
N.paspali		CBS 560.81		T	Paspalum dilatatum	New Zealand	GU238124	FJ427048	FJ427158	KP330426
N.soli			LC 8166		Soil	China	KY742276	KY742122	KY742364	–
			CGMCC 3.18365	T	Soil	China	KY742275	KY742121	KY742363	–
N.tardicrescens	Neoascochyta sp.	CBS 689.97	FMR 15352	T	Hay	Norway	KT389744	KT389526	KT389824	KT389654
	Ascochyta sp.		UTHSC:DI16-291; FMR 13783		Human superficial tissue	USA	LN907434	LT592942	LT593011	LT593081
N.triticicola		CBS 544.74		T	Triticum aestivum	South Africa	EU754134	GU237887	GU237488	KT389652
Neocamarosporium betae		CBS 109410	PD 77/113		Beta vulgaris	Unknown	EU754178	KY940790	–	GU371774
		CBS 523.66	IHEM 3915; PD 66/270		Beta vulgaris	The Netherlands	EU754179	FJ426981	KT389842	KT389670
N.calvescens		CBS 246.79	PD 77/655		Atriplex hastata	Germany	EU754131	KY940774	–	KC584500
N.goegapense		CBS 138008	CPC 23676	T	Mesembryanthemum sp.	South Africa	KJ869220	KJ869163	–	–
Neocucurbitaria aquatica	Pyrenochaeta quercina	CBS 297.74	FMR 14867	T	Sea water	Montenegro	EU754177	LT623221	LT623238	LT623278
N.cava	Pyrenochaeta cava	CBS 115979	FMR 15333		Unknown	The Netherlands	EU754198	AY853248	LT623234	LT623273
	Pyrenochaeta cava	CBS 257.68	FMR 15747; IMI 331911	T	Wheat-field soil	Germany	EU754199	JF740260	KT389844	LT717681
N.hakeae	Pyrenochaeta hakeae	CBS 142109	CPC 28920	T	Hakea sp.	Australia	KY173526	KY173436	KY173613	KY173593
N.irregularis	Pyrenochaeta unguis-hominis	CBS 142791	UTHSC:DI16-229; FMR 13719	T	Human subcutaneous tissue	USA	LN907372	LT592916	LT592985	LT593054
N.keratinophila	Pyrenochaeta keratinophila	CBS 121759	FMR 9444	T	Man corneal scrapings	Spain	LT623215	EU885415	LT623236	LT623275
N.quercina	Pyrenochaeta quercina	CBS 115095	FMR 14868	T	Quercus robur	Italy	GQ387619	LT623220	LT623237	LT623277
N.unguis-hominis	Pyrenochaeta unguis-hominis		UTHSC:DI16-213; FMR 13703		Unknown	USA	LN907356	LT592910	LT592979	LT593048
	Pyrenochaeta unguis-hominis	CBS 111112	FMR 14866		Agapornis sp. Lung	The Netherlands	GQ387623	LT623222	LT623239	LT623279
	Pyrenochaeta unguis-hominis	CBS 112.79	FMR 15748		Air sample	Wales	GQ387622	LT717672	LT717675	LT717682
Neodidymelliopsis achlydis		CBS 256 77		T	Achlys triphylla	Canada	KT389749	KT389531	KT389829	–
N.cannabis		CBS 234.37			Cannabis sativa	Unknown	GU237961	GU237804	GU237523	KP330403
N.longicolla	Phoma sp.		UTHSC:DI16-322; FMR 13815		Human respiratory tract	USA	LN907465	LT592957	LT593026	LT593096
		CBS 382 96		T	Soil in desert	Israel	KT389750	KT389532	KT389830	–
N.polemonii		CBS 109181		T	Polemonium caeruleum	The Netherlands	GU238133	GU237746	KT389828	KP330427
N.xanthina		CBS 383.68		T	Delphinium sp.	The Netherlands	GU238157	GU237855	KT389831	KP330431
Neomicrosphaeriopsis italica			MFLUCC 15-0485	T	Tamarix sp.	Italy	KU729854	KU900318	–	KU674820
			MFLUCC 15-0484		Tamarix sp.	Italy	KU729853	KU900319	KX453298	KU695539
Neophaeosphaeria agaves		CBS 136429	CPC 21264	T	Agave tequilana var. azul	Mexico	KF777227	NR_137833	–	–
N.filamentosa		CBS 102202			Yucca rostrata	Mexico	GQ387577	JF740259	–	GU371773
Neoplatysporoides aloicola		CBS 139901	CPC 24435	T	Aloe sp.	Tanzania	KR476754	KR476719	–	–
Neopyrenochaeta acicola	Pyrenochaeta acicola	CBS 812.95	FMR 14872	T	Waterpipe	The Netherlands	GQ387602	LT623218	LT623232	LT623271
N.fragariae	Pyrenochaeta acicola	CBS 101634	FMR 14871	T	Fragaria ananassa	The Netherlands	GQ387603	LT623217	LT623231	LT623270
N.inflorescentiae	Pyrenochaeta inflorescentiae	CBS 119222	FMR 15334	T	Protea neriifolia	South Africa	EU552153	EU552153	LT623233	LT623272
N.telephoni	Pyrenochaeta telephoni	CBS 139022	FMR 15754	T	Screen of a mobile phone	India	KM516290	KM516291	LT717678	LT717685
Neopyrenochaetopsis hominis	Pyrenochaeta sp.	CBS 143033	UTHSC:DI16-238; FMR 13728	T	Human superficial tissue	USA	LN907381	LT592923	LT592992	LT593061
Nothophoma anigozanthi		CBS 381.91	FMR 14914	T	Anigozanthus maugleisii	The Netherlands	GU238039	GU237852	GU237580	KT389655
N.arachidis-hypogaeae		CBS 125.93			Arachis hypogaea	India	GU238043	GU237771	GU237583	KT389656
N.gossypiicola		CBS 377.67	FMR 14912		Gossypium sp.	USA	GU238079	GU237845	GU237611	KT389658
	Phoma sp.		UTHSC:DI16-294; FMR 13787		Human deep tissue/fluids	USA	LN907437	LT592943	LT593012	LT593082
N.infossa		CBS 123395		T	Fraxinus pennsylvanica	Argentina	GU238089	FJ427025	FJ427135	KT389659
N.macrospora		CBS 140674	UTHSC:DI16-276; FMR 13767	T	Human respiratory tract	USA	LN880537	LN880536	LN880539	LT593073
N.quercina		CBS 633.92	FMR 14913		Quercus sp.	Ukraine	EU754127	GU237900	GU237609	KT389657
	Leptosphaerulina sp.		UTHSC:DI16-270; FMR 13761		Human superficial tissue	USA	LN907413	LT592929	LT592998	LT593067
N.variabilis	Phoma sp.	CBS 142457	UTHSC:DI16-285; FMR 13777	T	Human respiratory tract	USA	LN907428	LT592939	LT593008	LT593078
Ochrocladosporium elatum		CBS 146.33	IMI 049629; ATCC 11280		Wood pulp	Sweden	EU040233	EU040233	–	–
O.frigidarii		CBS 103.81		T	Cooled room	Germany	EU040234	EU040234	–	–
Ophiosphaerella herpotricha		CBS 620.86	AFTOL-ID 1569		Bromus erectus	Switzerland	DQ678062	KF498728	–	DQ677958
Paraboeremia adianticola		CBS 187.83	FMR 15344		Polystichum adiantiforme	USA	GU238035	GU237796	GU237576	KP330401
P.camelliae			CGMCC 3.18106	T	Camellia sp.	China	KX829042	KX829034	KX829058	KX829050
			CGMCC 3.18107		Camellia sp.	China	KX829043	KX829035	KX829059	KX829051
			CGMCC 3.18108		Camellia sp.	China	KX829044	KX829036	KX829060	KX829052
P.litseae			CGMCC 3.18109	T	Litsea sp.	China	KX829037	KX829029	KX829053	KX829045
			CGMCC 3.18110		Litsea sp.	China	KX829038	KX829030	KX829054	KX829046
P.oligotrophica			CGMCC 3.18111	T	Limestone	China	KX829039	KX829031	KX829055	KX829047
			CGMCC 3.18112		Limestone	China	KX829040	KX829032	KX829056	KX829048
P.putaminum		CBS 130.69	FMR 15338		Malus sylvestris	Denmark	GU238138	GU237777	GU237652	LT623254
P.selaginellae		CBS 122.93	FMR 15348	T	Selaginella sp.	The Netherlands	GU238142	GU237762	GU237656	LT623255
Paraconiothyrium estuarinum		CBS 109850	FMR 14887	T	Sediment from estuarine	Brazil	JX496129	JX496016	JX496355	LT854937
Paracucurbitaria italica	Pyrenochaeta corni	CBS 234.92	FMR 14869	T	Olea europaea	Italy	EU754176	LT623219	LT623235	LT623274
P.corni	Pyrenochaeta corni	CBS 248.79	FMR 16593		Fraxinus excelsior	The Netherlands	GQ387608	LT903672	LT900365	LT903673
Paraepicoccum amazonense			MFLUCC 15-0493		Tamarix sp.	Italy	KU900294	KU752190	–	KU820871
			MFLUCC 15-0491		Tamarix sp.	Italy	KU900295	KU752191	–	KU820872
Paraleptosphaeria dryadis		CBS 643.86	ETH 9446		Dryas octopetala	Switzerland	GU301828	JF740213	–	GU371733
Parapyrenochaeta acaciae	Pyrenochaeta acaciae	CBS 141291	FMR 15755; CPC 25527	T	Acacia sp.	Australia	KX228316	KX228265	LT717679	LT717686
P.protearum	Pyrenochaeta protearum	CBS 131315	FMR 15752; CPC 18322	T	Protea mundii	South Africa	JQ044453	JQ044434	LT717677	LT717683
	Pyrenochaeta pinicola	CBS 137997	FMR 15753; CPC 23455		Pinus sp.	France	KJ869209	KJ869152	KJ869249	LT717684
Phaeomycocentrospora cantuariensis		CBS 132014	CPC 11694		Humulus scandens	South Korea	GU253716	GU269668	–	–
			CPC 10157		Humulus scandens	South Korea	GU253712	GU269664	–	–
Phaeosphaeria oryzae		CBS 110110		T	Oryza sativa	Korea	KF251689	KF251186	KF252680	–
Phoma herbarum		CBS 502.91			Nerium sp.	The Netherlands	GU238082	GU237874	GU237613	KP330419
		CBS 615.75	FMR 15340		Rosa multiflora cv. Cathayensis	The Netherlands	KF251715	FJ427022	KF252703	KP330420
		CBS 377.92			Human leg	UK	KT389756	KT389536	KT389837	KT389663
			UTHSC:DI16-319; FMR 13812		Human superficial tissue	USA	LN907462	LT592955	LT593024	LT593024
			UTHSC:DI16-204; FMR 13694		Human deep tissue/fluids	USA	LN907347	LT592904	LT592973	LT593042
			UTHSC:DI16-212; FMR 13702		Human respiratory tract	USA	LN907355	LT592909	LT592978	LT593047
			UTHSC:DI16-306; FMR 13799		Human respiratory tract	USA	LN907449	LT592952	LT593021	LT593091
			UTHSC:DI16-307; FMR 13800		Human respiratory tract	USA	LN907450	LT592953	LT593022	LT593092
Phomatodes aubrietiae		CBS 627.97		T	Aubrietia sp.	The Netherlands	GU238045	GU237895	GU237585	KT389665
P.nebulosa		CBS 100191			Thlaspi arvense	Poland	KP330446	KP330434	KP330390	KT389666
		CBS 740.96			Armoracia rusticana	The Netherlands	KT389758	KT389540	KT389839	KT389667
Pleiochaeta ghindensis		CBS 552.92			Acacia mellifera	Namibia	EU167561	EU167561	–	–
P.setosa		CBS 496.63	MUCL 8091		Cytisus racemosus	Germany	EU167563	EU167563	–	–
Pleospora herbarum		CBS 191.86		T	Medicago sativa	Uttar Pradesh	JX681120	NR_111243	–	KC584471
P.typhicola		CBS 132.69			Typha angustifolia	The Netherlands	JF740325	–	KT389843	KC584505
Preussia terricola			AFTOL-ID 282; DAOM 230091		Unknown	Unknown	AY544686	KT225529	–	DQ470895
Pseudoascochyta novae-zelandiea		CBS 141689	FMR 15110; ICMP 10493	T	Cordyline australis	New Zealand	LT592893	LT592892	LT592894	LT592895
P.pratensis		CBS 141688	FMR 14524	T	Soil	Spain	LT223131	LT223130	LT223132	LT223133
Pseudopyrenochaeta lycopersici	Pyrenochaeta lycopersici	CBS 306.65	FMR 15746	T	Lycopersicon esculentum	Germany	EU754205	NR_103581	LT717674	LT717680
P.terretris	Pyrenochaeta lycopersici	CBS 282.72	FMR 15327	T	Soil	The Netherlands	LT623216	LT623228	LT623246	LT623287
Pyrenochaeta nobilis		CBS 407.76	FMR 14870	T	Laurus nobilis	Italy	EU754206	EU930011	KT389845	LT623276
Pyrenochaetopsis americana	Pyrenochaetopsis sp.		UTHSC:DI16-225; FMR 13715		Unknown	USA	LN907368	LT592912	LT592981	LT593050
P.botulispora	Pyrenochaetopsis sp.		UTHSC:DI16-289; FMR 13781		Human respiratory tract	USA	LN907432	LT592941	LT593010	LT593080
	Pyrenochaetopsis sp.		UTHSC:DI16-297; FMR 13790		Human superficial tissue	USA	LN907440	LT592945	LT593014	LT593084
	Pyrenochaetopsis sp.	CBS 142458	UTHSC:DI16-298; FMR 13791	T	Human respiratory tract	USA	LN907441	LT592946	LT593015	LT593085
P.confluens	Pyrenochaetopsis sp.	CBS 142459	UTHSC:DI16-303; FMR 13796	T	Human deep tissue/fluids	USA	LN907446	LT592950	LT593019	LT593089
P.decipiens		CBS 343.85	FMR 14880	T	Globodera pallida	The Netherlands	GQ387624	LT623223	LT623240	LT623280
P.globosa	Pyrenochaetopsis sp.	CBS 143034	UTHSC:DI16-275; FMR 13766	T	Human superficial tissue	USA	LN907418	LT592934	LT593003	LT593072
P.indica		CBS 124454	FMR 14879	T	Saccharum officinarum	India	GQ387626	LT623224	LT623241	LT623281
P.leptospora		CBS 101635	FMR 14877	T	Secale cereale	Unknow	GQ387627	JF740262	LT623242	LT623282
	Coniothyrium cereale	CBS 122787	FMR 14873		Unknown	Germany	EU754151	LT623225	LT623243	LT623283
P.microspora	Pyrenochaetopsis sp.		UTHSC:DI16-198; FMR 13688		Human superficial tissue	USA	LN907341	LT592899	LT592968	LT593037
		CBS 102876	FMR 14874	T	Water	Montenegro	GQ387631	LT623226	LT623244	LT623284
P.paucisetosa	Pyrenochaetopsis sp.	CBS 142460	UTHSC:DI16-193; FMR 13683	T	Human superficial tissue	USA	LN907336	LT592897	LT592966	LT593035
P.poae		CBS 136769	FMR 14876	T	Poa sp.	The Netherlands	KJ869175	KJ869117	KJ869243	LT623286
P.setosissima	Pyrenochaetopsis microspora	CBS 119739	FMR 14875	T	Coffea arabica	Brazil	GQ387632	LT623227	LT623245	LT623285
P.tabarestanensis		CBS 139506	IBRC-M 30051	T	Soil	Iran	KF803343	KF730241	KX789523	–
P.uberiformis	Pyrenochaetopsis sp.	CBS 142461	UTHSC:DI16-277; FMR 13769	T	Human superficial tissue	USA	LN907420	LT592935	LT593004	LT593074
Querciphoma carteri		CBS 105.91			Quercus robur	Germany	KF251712	JF740181	KF252700	KT389591
Remotididymella anthropophila	Phoma sp.	CBS 142462	UTHSC:DI16-278; FMR 13770	T	Human respiratory tract	USA	LN907421	LT592936	LT593005	LT593075
R.destructiva	Phoma destructiva var. destructiva	CBS 133.93	FMR 15349		Solanum lycopersicon	Guadeloupe	GU238064	GU237779	GU237602	LT623257
	Phoma destructiva var. destructiva	CBS 378.73	FMR 15328	T	Lycopersicon esculentum	Tonga	GU238063	GU237849	GU237601	LT623258
	Phoma destructiva var. diversispora	CBS 162.78	FMR 14906		Lycopersicon esculentum	The Netherlands	GU238062	GU237788	GU237600	LT623259
Shiraia bambusicola			NBRC 30754		Phyllostachys sp.	Japan	AB354969	AB354988	AB355003	–
			NBRC 30771		Phyllostachys sp.	Japan	AB354971	AB354990	AB355005	–
			NBRC 30753		Phyllostachys sp.	Japan	AB354968	AB354987	AB355002	–
			NBRC 30772		Phyllostachys sp.	Japan	AB354972	AB354991	AB355006	–
Similiphoma crystallifera	Phoma crystallifera	CBS 193.82	FMR 15343	T	Chamaespartium sagittale	Austria	GU238060	GU237797	GU237598	LT623267
Sporormiella minima		CBS 524.50	AFTOL-ID 1256		Dung of goat	Panama	DQ678056	KT389543	–	DQ677950
Stagonosporopsis dorenboschii		CBS 426.90		T	Physostegia virginiana	The Netherlands	GU238185	GU237862	GU237690	KT389678
S.hortensis		CBS 572.85			Phaseolus vulgaris	The Netherlands	GU238199	GU237893	GU237704	KT389681
Staurosphaeria aloes	Hazslinszkyomyces aloes	CBS 136437	CPC 21572	T	Aloe dichotoma	South Africa	KF777198	NR_137821	–	–
S.aptrootii	Hazslinszkyomyces aptrootii	CBS 483.95		T	Lycium sp.	The Netherlands	GU301806	KY929149	–	–
S.lyciicola	Hazslinszkyomyces lycii	CBS 142619	CPC 30998	T	Lycium barbarum	Hungary	KY929180	KY929150	–	–
	Hazslinszkyomyces lycii		CPC 31014		Lycium barbarum	Hungary	KY929181	KY929151	–	–
Vacuiphoma bulgarica	Phoma bulgarica	CBS 357.84	FMR 14917	T	Trachystemon orientale	Bulgaria	GU238050	GU237837	GU237589	LT623256
V.oculihominis	Phoma sp.		UTHSC:DI16-308; FMR 13801	T	Human superficial tissue	USA	LN907451	LT592954	LT593023	LT593093
Xenodidymella applanata		CBS 205.63			Rubus idaeus	The Netherlands	GU237998	GU237798	GU237556	KP330402
		CBS 115577			Rubus idaeus	Sweden	KT389762	KT389546	KT389850	KT389688
X.asphodeli		CBS 375.62		T	Asphodelus albus	France	KT389765	KT389549	KT389853	KT389689
X.catariae		CBS 102635			Nepeta catenaria	The Netherlands	GU237962	GU237727	GU237524	KP330404
X.humicola		CBS 220.85			Franseria sp.	USA	GU238086	GU237800	GU237617	KP330422
X.saxea	Phoma saxea	CBS 419.92	FMR 15347	T	Corroded mediterranean marble	Unknown	GU238141	GU237860	GU237655	KP330429
Xenopyrenochaetopsis pratorum	Pyrenochaetopsis pratorum	CBS 445.81	FMR 14878	T	Lolium perenne	New Zealand	GU238136	JF740263	KT389846	KT389671

¹AFTOL: Assembling the Fungal Tree of Life; ATCC: American Type Culture Collection, Virginia, USA; BCC: Biotec Culture Collection, Pathum Thani, Thailand; BCCM/IHEM: Biomedical Fungi and Yeasts Collection, Louvain-la-Neuve, Belgium; BCCM/MUCL: Mycothèque de l'Université catholique de Louvain, Louvain-la-Neuve, Belgium; BRIP: Plant Pathology Herbarium, Department of Employment, Economic, Development and Innovation, Queensland, Australia; CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; CGMCC: China General Microbiological Culture Collection, Beijing, China; CMW: Collection of the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa; CPC: Culture collection of Pedro Crous, housed at CBS; DAOM: Canadian Collection of Fungal Cultures, Ottawa, Canada; ETH: Herbaria of the department of Environmental Systems Science. Institute of Integrative Biology, Zürich, Switzerland; FMR, Facultat de Medicina, Universitat Rovira i Virgili, Reus, Spain; IBRC: Iranian Biological Resources Center, Tehran, Iran; ICMP: International Collection of Microorganisms from Plants, Auckland, New Zealand; IFO: Institute for Fermentation, Osaka, Japan, now NBRC; IMI: International Mycological Institute, CABI-Bioscience, Egham, Bakeham Lane, U.K.; INIFAT: Instituto de Investigaciones Fundamentales en Agricultura Tropical “Alejandro de Humboldt”, Santiago de las Vegas, Cuba; LC: Corresponding author's personal collection deposited in laboratory, housed at CAS, China; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Rai, Thailand; NBRC: Biological Resource Center, National Institute of Technology and Evaluation, Chiba, Japan; PD: Plant Protection Service, Wageningen, the Netherlands; UTHSC, Fungus Testing Laboratory at the University of Texas Health Science Center, San Antonio, Texas, USA.

²T: ex-type strain

³ITS: internal transcibed spacer regions 1 & 2 including 5.8S nrDNA gene; LSU: 28S large subunit of the nrRNA gene; RPB2: RNA polymerase II second subunit; TUB: ß-tubulin.

Phenotypic study

For cultural characterisation, isolates were grown on oatmeal agar (OA; 30 g of filtered oat flakes, 15 g of agar-agar, 1 L tap water) and malt extract agar (MEA; 40 g of malt extract, 15 g of agar-agar, 1 L distilled water), at 25 ± 1 °C for 14 d in darkness (recipes according to Boerema et al. 2004 and Crous et al. 2009). Some of the cultures were incubated under near-ultraviolet (UV) light (12 h light, 12 h dark) or on carnation leaf agar (CLA) to induce sporulation if necessary (Fisher et al., 1982, Su et al., 2012). Colony diameters were measured after 7 d at 25 ± 1 °C, and colony characterisation was performed 14 d after inoculation on the culture media. Colours were according to Kornerup & Wanscher (1978). The ability of the isolates to grow at cardinal temperatures were determined on potato dextrose agar (PDA; Pronadisa, Madrid, Spain) after 7 d in darkness, ranging from 5 to 35 °C at 5 °C intervals, and including 37 °C.

Micromorphological characterisation was performed by examining at least 30 individuals of each structure (Aveskamp et al., 2010, Chen et al., 2015). Wet mounts (in Shear's mounting medium and in water) of structures were examined by using an Olympus CH2 compound microscope (Olympus Corporation, Tokyo, Japan). Photo micrographs were captured using a Zeiss Axio-Imager M1 microscope (Oberkochen, Germany) with a DeltaPix Infinity X digital camera using Nomarski differential interference contrast. The production of metabolite E+ (NaOH spot test) was carried out by the application of a droplet of 1N NaOH on a colony grown on MEA (Dorenbosch, 1970, Noordeloos et al., 1993).

DNA isolation, PCR amplification and sequencing

The total genomic DNA was extracted from colonies grown on PDA after 7 d incubation at 20 ± 1 °C, using the FastDNA kit protocol (Bio101, Vista, CA), with a FastPrep FP120 instrument (Thermo Savant, Holbrook, NY) according to the manufacturer's protocol. DNA was quantified by using Nanodrop 2000 (Thermo Scientific, Madrid, Spain). The following loci were amplified and sequenced: a fragment of the 28S nrRNA gene (LSU) with the primer pair LR0R (Rehner & Samuels 1994) and LR5 (Vilgalys & Hester 1990), internal transcribed spacer region (ITS1-5.8S-ITS2) with the primer pair ITS5 and ITS4 (White et al. 1990), a fragment of the beta-tubulin gene (tub2) with the primers TUB2Fw and TUB4Rd (Woudenberg et al. 2009) and a fragment of the RNA polymerase II subunit 2 gene (rpb2) with RPB2-5F2 (Sung et al. 2007) and fRPB2-7cR primers (Liu et al. 1999). The PCR amplifications were performed in a total volume of 25 μL containing 5 μL 10× PCR Buffer (Invitrogen, California, USA), 0.2 mM dNTPs, 0.5 μM of each primer, 1 U Taq DNA polymerase and 1–10 ng genomic DNA. PCR conditions for LSU, ITS and tub2 were set as follows: an initial denaturation at 95 °C for 5 min, followed by 35 cycles of denaturation, annealing and extension, and a final extension step at 72 °C for 10 min. For the LSU and ITS amplification, the 35 cycles consisted of 45 s at 95 °C, 45 s at 53 °C and 2 min at 72 °C; and for the tub2 region 30 s at 94 °C, 45 s at 56 °C and 1 min at 72 °C. The PCR program for rpb2 amplification consisted of 5 cycles of 45 s at 94 °C, 45 s at 60 °C and 2 min at 72 °C, then 5 cycles with a 58 °C annealing temperature and 30 cycles with a 54 °C annealing temperature (Woudenberg et al. 2013). Sequencing of the amplicons was made in both directions with the same primer pair used for amplification at Macrogen Europe (Macrogen Inc., Amsterdam, The Netherlands). The consensus sequences were obtained using the SeqMan software v. 7 (DNAStar Lasergene, Madison, WI, USA).

Phylogenetic analyses

Sequences of related species described in previous studies were obtained from GenBank (Aveskamp et al., 2009, Aveskamp et al., 2010, De Gruyter et al., 2010, De Gruyter et al., 2013, Wijayawardene et al., 2014, Chen et al., 2015, Chen et al., 2017, Thambugala et al., 2016), and listed in Table 1. For the phylogenetic study, the alignments of the sequences were performed using MEGA v. 6.06 (Tamura et al. 2013), using the ClustalW application (Thompson et al. 1994), refined with MUSCLE (Edgar 2004) and manually adjusted using the same software platform. The ambiguous regions were excluded from the analyses. Phylogenetic reconstructions were made by maximum-likelihood (ML) and Bayesian inference (BI) with RAxML v. 8.2.10 (Stamatakis 2014) and MrBayes v. 3.2.6 (Ronquist et al. 2012), respectively. The best substitution model for each gene matrix correspond to GTR+I+G, and was estimated using MrModelTest v. 2.3 (Nylander 2004). For ML analyses, nearest-neighbour interchange was used as the heuristic method for tree inference. Support for internal branches was assessed by 1 000 ML bootstrapped pseudoreplicates. Bootstrap support (BS) ≥70 was considered significant. For BI analyses, Markov chain Monte Carlo (MCMC) sampling was performed with 46 M generations, with samples taken every 1 000 generations. The 50 % majority rule consensus trees and posterior probability values (PP) were calculated after removing the first 25 % of the resulting trees for burn-in. A PP value ≥0.95 was considered as significant. Both ML and BS analyses were run in CIPRES (Miller et al. 2012). Preussia terricola (AFTOL-ID 282) and Sporormiella minima (CBS 524.50) served as outgroup taxa. Sequences generated in this study were deposited in GenBank (see Table 1), the final matrices used for phylogenetic analyses in TreeBASE (www.treebase.org; accession number: S21115) and the novel taxonomic descriptions and nomenclature in MycoBank (www.mycobank.org; Crous et al. 2004).

Results

Phylogenetic analyses

The final concatenated dataset obtained with both ML and Bayesian analysis contained 357 ingroup strains with a total of 1 888 characters including gaps (519 for LSU, 336 for ITS, 434 for tub2 and 599 for rpb2), of which 742 are parsimony informative (132 for LSU, 111 for ITS, 149 for tub2 and 350 for rpb2). The sequence datasets did not show conflict in the tree topologies for the 70 % reciprocal bootstrap trees, which allowed to combine the four genes for the multi-locus analysis.

The ML analysis showed similar tree topology and was congruent with that obtained in the Bayesian analysis. For the BI multi-locus analysis, a total of 34 677 trees were sampled after the burn-in with a stop value of 0.01. The support values were slightly different with the two analysis methods; with BI, posterior probabilities being higher than the ML bootstrap support values (Fig. 1).

Fig. 1.

Phylogenetic tree inferred from a Maximum likelihood analysis based on a concatenated alignment of LSU, ITS, tub2 and rpb2 sequences of 357 strains representing species in Cucurbitariaceae, Didymellaceae and allied families within Pleosporales. The Bayesian posterior probabilities (PP) above 0.95 and the RAxML bootstrap support values (BS) above 70 % are given at the nodes (PP/BS). Fully supported branched (1 PP/100 BS) are indicated in bold. Some branches were shortened to fit them to the page, these are indicated by two diagonal lines with the number of times a branch was shortened. Newly proposed taxa are given in bold. Type strains are indicated by a superscript T. The tree was rooted with Preussia terricola (AFTOL-ID 828) and Sporormiella minima (CBS 524.50).

The phylogenetic tree distinguished two main supported clades corresponding to the suborders Massarineae (1 PP / 100 % BS), with only the family Didymosphaeriaceae (clade T) here included, and Pleosporineae (1 PP / 74 % BS), emcompassing over 19 families (clades A–S), respectively. Four of the families of the latter suborder are proposed here as new, i.e., Pseudopyrenochaetaceae (clade D), Neopyrenochaetaceae (clade E), Pyrenochaetopsidaceae (clade F) and Parapyrenochaetaceae (clade N). The main clade of the Pleosporineae corresponded to the Didymellaceae (clade A) showing 25 well-supported terminal clades with the only exception being Epicoccum (A2). Twenty terminal clades corresponded to known genera and six are proposed here as new: Ectophoma (A7), Remotididymella (A8), Similiphoma (A9), Cumuliphoma (A12), Juxtiphoma (A13) and Vacuiphoma (A14). The genus Didymella (A1; 1 PP / 90 % BS), comprised 48 species and one undescribed, including two proposed here as new: D. keratinophila sp. nov. (the type strain CBS 143032, UTHSC DI16-228 and UTHSC DI16-282), which is phylogenetically close to D. sancta and D. coffeae-arabicae, and D. brunneospora sp. nov. (CBS 115.58). Several of the clinical strains included in Didymella were distributed among seven known species, i.e., D. heteroderae (nine strains), D. gardeniae (four strains), D. microchlamydospora (two strains), and D. anserina, D. glomerata, D. musae and D. protuberans with only one strain for each. Epicoccum (A2; unsupported) was represented by 17 previously described species (including the type species E. nigrum), the new species E. catenisporum sp. nov., E. ovisporum sp. nov., E. pneumoniae sp. nov. (phylogenetically related with E. camelliae, E. latusicollum, E. sorghinum and E. viticis), and E. keratinophilum sp. nov. (phylogenetically related with E. brasiliense and E. draconis). Finally, E. proteae (basionym Phoma proteae), which clustered with E. huancayense, is here combined in Epicoccum. Allophoma (clade A3; 1 PP / 96 % BS) is enlarged with A. cylindrispora sp. nov., previously identified as Phoma sp. (Valenzuela-Lopez et al. 2016), clustering with A. minor and A. piperis. The clades from A4 to A6 encompassed three genera i.e. Heterophoma (A4; 1 PP / 98 % BS), Stagonosporopsis (A5; 1 PP / 75 % BS) and Boeremia (A6; 1 PP / 100 % BS). The new genus Ectophoma (clade A7; 1 PP / 100 % BS) comprise two new combinations previously included in Phoma, i.e. the generic type E. multirostrata (syn. P. multirostrata) and E. pomi (syn. P. pereupyrena). The new genus Remotididymella (A8; 0.97 PP / 91 % BS) comprised R. destructiva comb. nov. (basionym Phoma destructiva), the type species, and the new species R. anthropophila. For Phoma crystallifera the new monotypic genus Similiphoma (clade A9) and the new combination S. crystallifera are proposed. The clade corresponding to the genus Paraboeremia (clade A10; 1 PP / 99 % BS) included the six accepted species. Macroventuria formed a well-supported clade (A11; 1 PP / 100 % BS) and included the ex-type strains of M. anomochaeta and M. wentii. Cumuliphoma gen. nov. (clade A12; 1 PP / 94 % BS) included C. omnivirens comb. nov. (syn. Phoma omnivirens), C. indica sp. nov. (with two strains previously identified as P. omnivirens) and C. pneumoniae sp. nov., the latter represented by a clinical strain. The proposed new monotypic genus Juxtiphoma (clade A13; 1 PP / 100 % BS), includes two strains of J. eupyrena comb. nov. (basionym Phoma eupryrena). The new genus Vacuiphoma (clade A14; 1 PP / 100 % BS), included the type species V. bulgarica comb. nov. (basionym Phoma bulgarica) and the new species V. oculihominis described from a sterile clinical strain (UTHSC DI16-308). The genus Nothophoma (clade A15; 1 PP / 95 % BS) comprised seven species, including the generic type, N. infossa, and N. variabilis sp. nov., which is based on a clinical strain phylogenetically related with the ex-type strain of N. anigozanthi. The clade corresponding to Ascochyta (clade A16; 1 PP / 92 % BS), grouped five species, including the type species A. pisi. Clade A17 (1 PP / 100 % BS) included the type species of Phomatodes (P. aubrietiae) and two strains of P. nebulosa, the other species of the genus. The Briansuttonomyces clade (A18, 1 PP / 100 % BS), included two strains of the only species of the genus, B. eucalypti. The clade A19 (1 PP / 100 % BS) encompassed the ex-type strains of the two species of Pseudoascochyta, P. novae-zelandiae and P. pratensis. The Neomicrosphaeropsis clade (A20; 1 PP / 100 % BS), contained the type species of the genus, N. italica. In Phoma (A21; 1 PP / 100 % BS) eight strains were grouped, all of them identified as P. herbarum (five from clinical origin and three reference strains). The genus Calophoma (A22; 1 PP / 93 % BS) comprised four species: C. aquilegiicola, C. clematidis-rectae, C. clematidina (type species of the genus) and C. rosae. The clade corresponding to Leptosphaerulina (A23; 1 PP / 100 % BS) contained the two known species, L. americana and L. australis. Xenodidymella (A24; - PP / 74 % BS), grouped the four species of this genus and the new combination Xenodidymella saxea (basionym Phoma saxea), which forms a basal clade with a strain of X. humicola. The clade A25 (1 PP / 100 % BS) included five species of Neodidymelliopsis. Neoascochyta (A26; 1 PP / 98 % BS) represented a basal clade of the Didymellaceae, very distant from the other genera of that family, and grouped 10 species, two of which are here proposed as new: Neoascochyta cylindrispora sp. nov. and Neoascochyta tardicrescens sp. nov.

In the family Cucurbitariaceae (clade C; 1 PP / 98 % BS) analyses resulted in four clades, which we recognise as genera. Neocucurbitaria (C1; 1 PP / 94 % BS), which included two new species, N. irregularis (CBS 142791) and N. aquatica (CBS 297.74), and the three new combinations, N. cava (syn. Pyrenochaeta cava), N. hakeae (basionym Pyrenochaeta hakeae) and N. keratinophila (basionym Pyrenochaeta keratinophila); the new genus Paracucurbitaria (C2; 1 PP / 100 % BS), with two species P. corni comb. nov. (syn. Pyrenochaeta corni) and P. italica sp. nov.; the new genus Allocucurbitaria (clade C3), with the type species A. botulispora sp. nov. Finally, the genus Cucurbitaria (clade C4; 1 PP / 100 % BS) including only the type species, C. berberidis.

Pseudopyrenochaetaceae fam. nov. (clade D; 1 PP / 99 % BS) is introduced to accommodate Pyrenochaeta lycopersici and P. terrestris in the new genus Pseudopyrenochaeta.

The generic type of Pyrenochaeta, Pyrenochaeta nobilis, was phylogenetically distant from the Cucurbitariaceae in our phylogeny, and therefore we consider this species as incertae sedis.

The proposed new family Neopyrenochaetaceae (clade E; 1 PP / 100 % BS) encompassed several taxa previously included in Pyrenochaeta. However, since they were located outside from Cucurbitariaceae s. str. we propose the new genus Neopyrenochaeta, with the new combinations: N. acicola (syn. Pyrenochaeta acicola), N. inflorescentiae (basionym. Pyrenochaeta inflorescentiae) and N. telephoni (basionym Pyrenochaeta telephoni), and the new species N. fragariae.

The new family Pyrenochaetopsidaceae (clade F; 0.98 PP / 75 % BS) grouped three clades, which correspond to the genera Pyrenochaetopsis, the type genus (type species, P. leptospora) (F1; 1 PP / 100 % BS), Xenopyrenochaetopsis (type species, X. pratorum comb. nov.) (F2) and Neopyrenochaetopsis (type species, N. hominis sp. nov.) (F3). Pyrenochaetopsis encompassed seven new species: P. americana, P. botulispora, P. confluens, P. globosa, P. pauciseptata, P. setosissima and P. uberiformis.

The Clade N (1 PP / 100 % BS), which consists of several isolates previously recognised in Pyrenochaeta, is proposed as the new family Parapyrenochaetaceae. Accordingly, the new genus Parapyrenochaeta is proposed for P. acaciae comb. nov. (basionym Pyrenochaeta acaciae), and the type species Parapyrenochaeta protearum comb. nov. (basionym Pyrenochaeta protearum). The strain CBS 137997, previously identified as Pyrenochaeta pinicola, was re-identified as Parapyrenochaeta protearum.

The monospecific genus Paraepicoccum was introduced by Matsushima (1993), later epitypified as Paraepicoccum amazonense by Thambugala et al. (2016) and considered as incertae sedis in Pleosporineae, which is supported by our phylogenetic results.

Taxonomy

After multi-locus sequence analysis of 357 strains distributed among several families within Pleosporineae and the morphological study of 143 strains, in the present paper we propose: four new families, 13 new genera, 28 new species, 20 new combinations, and four typifications. Novel taxa are described and illustrated. Six species proved to be sterile in culture, and therefore are described based on DNA sequence data, following the approach of Chen et al. (2017). Clades and genera are given as they appear in the phylogenetic tree, and species are listed in alphabetical order.



Clade A: Didymellaceae Gruyter et al., Mycol. Res. 113: 516. 2009.



Type genus: Didymella Sacc.



Clade A1: Didymella



Didymella Sacc. ex Sacc., Syll. Fung. 1: 545. 1882. emend. Chen et al., Stud. Mycol. 82: 173. 2015.

Synonym: Peyronellaea Goid. ex Togliani, Ann. Sperim. Agrar. II 6: 93. 1952.



Type species: Didymella exigua (Niessl) Sacc.



Didymella anserina (Marchal) Q. Chen & L. Cai, Stud. Mycol. 82: 173. 2015.

Basionym: Phoma anserina Marchal, Champignon Copr. 11: 1891.

Synonyms: Peyronellaea anserina (Marchal) Aveskamp et al., Stud. Mycol. 65: 31. 2010.

Phoma radicis-callunae R.W. Rayner, Bot. Gaz. 73: 231. 1922.

Phoma suecica J.F.H. Beyma, Antonie van Leeuwenhoek 8: 110. 1942.



Description: de Gruyter & Noordeloos (1992).



Materials examined: Germany, Giessen, Dec. 1979, R. Hadlok, living culture CBS 253.80. USA, from human sputum sample, 2008, D.A. Sutton, living cultures UTHSC DI16-255 = FMR 13745.



Notes: Didymella anserina is a ubiquitous soil fungus that has been found in Africa, Europe and North America. Although frequently present on herbaceous or woody plants, it has been recorded from many other substrates. Our strain UTHSC DI16-255 is the first report from a human clinical specimen, and it is morphologically similar to the reference strain of D. anserina (CBS 253.80).



Didymella brunneospora Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, sp. nov. MycoBank MB820815. Fig. 2.



Fig. 2.

Didymella brunneospora (CBS 115.58). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Etymology: From Latin brunneus-, brown, and -spora, spore, because of the conidial pigmentation.



Description: Hyphae hyaline to pale brown, smooth- and thin-walled, septate, 2–5 μm wide. Conidiomata pycnidial, pale brown to dark brown, mostly solitary, occasionally confluent, superficial on OA, glabrous, globose, 140–250 μm diam, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–5 layered, 25–70 μm thick, composed of pale brown to brown, flattened polygonal cells of 8–15 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 7–10 × 6.5–8 μm. Conidia aseptate, hyaline to pale brown, smooth- and thin-walled, obovoid to cylindrical, 4.5–7 × 3–3.5 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 26 mm diam after 7 d at 25 ± 1 °C, flattened, with abundant production of pycnidia, olive brown (M. 4E6); reverse yellowish brown (M. 5E4). Colonies on MEA reaching 28 mm diam after 7 d at 25 ± 1 °C, flattened, orange melon (M. 5A6) to orange-white (M. 5A2); reverse orange melon (M. 5A6) to orange white (M. 5A2). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.

Material examined: Germany, isolated from flower-stalk of Chrysanthemum roseum, R. Schneider (holotype CBS H-23199, ex-holotype living cultures IMB 8675 = DSM 62044 = CBS 115.58 = FMR 15745).



Notes: Ascochyta pyrethri (Brunaud 1887), reported on decaying stems of Pyrethri sinensis in Saintes (France), was originally described (very briefly and lacking of measurements of their reproductive structures) in French, but later Latinised by Saccardo (Saccardo 1892), changing the order of the authors. The description of that fungus by Saccardo was based on the original diagnosis: pycnidia conical-globose, sparse to arrange in linear series, erumpent, black; conidia numerous, ovoid, ellipsoidal or long ellipsoidal, somewhat obtuse at both ends, straight or slightly curved, subhyaline. However, Saccardo described the conidia as not being constricted at the septum, which was not mentioned in the original description. Moreover, the protologue lacks illustrations and references to herbarium material, which makes this taxon doubtful. The strain CBS 115.58, previously identified as Ascochyta pyrethri; clusters distant from Ascochyta and produces pale brown, aseptate conidia, features not seen in that genus, and thus being considered herein as a new species of the genus Didymella.



Didymella gardeniae (S. Chandra & Tandon) Q. Chen & L. Cai, Stud. Mycol. 82: 176. 2015.

Basionym: Pyrenochaeta gardeniae S. Chandra & Tandon, Mycopathol. Mycol. Appl. 29: 274. 1966.

Synonyms: Phoma gardeniae (S. Chandra & Tandon) Boerema, Verslagen Meded. Plantenziektenk. Dienst Wageningen 156: 27. 1980.

Peyronellaea gardeniae (S. Chandra & Tandon) Aveskamp et al., Stud. Mycol. 65: 32. 2010.



Description: de Gruyter & Boerema (2002).



Materials examined: India, Allahabad, from the leaf of Gardenia jasminoides, 1966, S. Chandra & R.N. Tandon (isotype CBS H-7605, ex-isotype living cultures CBS 626.68 = IMI 108771 = FMR 14901). USA, from human nail distrophy, 2006, D.A. Sutton, living cultures UTHSC DI16-211 = FMR 13701; from human toe nail, 2007, D.A. Sutton, living cultures UTHSC DI16-226 = FMR 13716; from human toe nails, 2009, D.A. Sutton, living cultures UTHSC DI16-274 = FMR 13765; from human wound neck, 2010, D.A. Sutton, living cultures UTHSC DI16-295 = FMR 13788.



Notes: Didymella gardeniae was first isolated from a leaf of Gardenia jasminoides in India (Chandra & Tandon, 1966), and it seems to be a common soil- and air-borne fungus recovered also from Netherlands Antilles. Here, it is for first time associated with human clinical specimens from North America. Morphologically our strains resemble D. gardeniae, but have setose pycnidia, which are more characteristic of Pyrenochaeta than phoma-like taxa. Also remarkable is the fact that our strains are capable of growing at 37 °C.



Didymella glomerata (Corda) Q. Chen & L. Cai, Stud. Mycol. 82: 176. 2015. Fig. 3.

Fig. 3.

Didymella glomerata (UTHSC DI16-205). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Alternaroid chlamydospores. H. Conidiogenous cells. I. Conidia. Scale bars: F = 100 μm. G–I = 10 μm.

Basionym: Coniothyrium glomeratum Corda, Icon. Fung. (Prague) 4: 39. 1840.

Synonyms: Phoma glomerata (Corda) Wollenw. & Hochapfel, Z. Parasitenk. 3: 592. 1936.

Peyronellaea glomerata (Corda) Goid. ex Togliani, Ann. Sperim. Agrar. III 6: 93. 1952.



Description: Boerema et al. (2004).



Materials examined: Lectotype designated here (MBT 377971): plate 8, fig. 108, in Corda, AKJ. 1840. Icones fungorum hucusque cognitorum. Tomus IV, Praga (http://bibdigital.rjb.csic.es/ing/Libro.php?Libro=1812). The Netherlands, from Chrysanthemum sp., 1963 (epitype designated here CBS H-16351, MBT377905, ex-epitype living cultures CBS 528.66 = PD 63/590). USA, from human superficial tissue sample, 2006, D.A. Sutton, living culture UTHSC DI16-205 = FMR 13695.



Notes: Coniothyrium glomeratum was introduced by Corda (1840). The description of this fungus is brief, and the illustrations are not very detailed. The natural source has been mentioned as dry greyed wood chips, but without any geographic location. No original material of the basionym exists. Therefore, we designate the illustration by Corda here as lectotype and CBS H-16351 as epitype of Coniothyrium glomeratum. Other authors placed this fungus in other genera, such as Aphosphaeria, Ascochyta, Peyronella and Phoma, but also in Alternaria, because the production of alternarioid chains of chlamydospores in vitro. For a complete discussion about synonymies of this fungus see Boerema et al. (1965), who gave an exhaustive morphological description in vitro of this fungus. Didymella glomerata is characterised by the production of subhyaline to carbonaceous, small to large, glabrous pycnidia bearing one (to two or three) ostioles, aseptate, hyaline to dark-coloured, ovoid to ellipsoidal conidia measuring mostly 6–7.5 × 3–3.5 μm, and alternaroid chlamydospores in chains. The fungus is distributed worldwide, and has been recovered from soil, different kinds of living and dead plants, and inorganic materials, and it can also infect humans (Punithalingam 1979, de Hoog et al. 2011). The strain UTHSC DI16-205, that phylogenetically clusters with the reference strain CBS 528.66 of Didymella glomerata, is morphologically indistinguishable from it.



Didymella heteroderae (Sen. Y. Chen et al.) Q. Chen & L. Cai, Stud. Mycol. 82: 176. 2015.

Basionym: Phoma heteroderae Sen Y. Chen et al., Mycologia 88: 885. 1996 (1997).

Synonyms: Peyronellaea heteroderae (Sen Y. Chen et al.) Crous, Persoonia 32: 223. 2014.

Phoma pomorum var. calorpreferens Boerema et al., Persoonia 15: 207. 1993.

Phoma calorpreferens (Boerema et al.) Aveskamp et al., Mycologia 101: 370. 2009.

Peyronellaea calorpreferens (Boerema et al.) Aveskamp et al., Stud. Mycol. 65: 31. 2010.



Description: Boerema (1993).



Materials examined: The Netherlands, from undefined food material, 1973, G.H. Boerema (holotype L 990.290.418, ex-holotype living cultures CBS 109.92 = PD 73/1405). USA, from human left plantar foot, 2005, D.A. Sutton, living cultures UTHSC DI16-190 = FMR 13680; from human nail, 2007, D.A. Sutton, living cultures UTHSC DI16-224 = FMR 13714; from human nail, 2007, D.A. Sutton, living cultures UTHSC DI16-227 = FMR 13717; from human fingernail, 2007, D.A. Sutton, living cultures UTHSC DI16-231 = FMR 13721; from human urine, 2007, D.A. Sutton, living cultures UTHSC DI16-232 = FMR 13722; from human nail, 2007, D.A. Sutton, living cultures UTHSC DI16-234 = FMR 13724; from human scalp, 2007, D.A. Sutton, living cultures UTHSC DI16-235 = FMR 13725; from human sputum sample, 2011, D.A. Sutton, living culturse UTHSC DI16-305 = FMR 13798.



Notes: Our strains are morphologically similar to the ex-type strain of D. heteroderae, and also show an identical DNA nucleotide sequence dataset. However, we proved that our strains are able to grow and sporulate at 37 °C (Valenzuela-Lopez et al. 2016), a higher temperature than that given in the original species description (Boerema et al. 2004).



Didymella keratinophila Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB820813. Fig. 4.



Fig. 4.

Didymella keratinophila (CBS 143032). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Section of pycnidium. H. Conidiogenous cells. I. Conidia. Scale bars: F, G = 100 μm. H, I = 10 μm.

Etymology: From Greg κɛρατινων-, keratin, and – φίλος, friend of, because the source from which the fungus was isolated.



Description: Hyphae pale brown, smooth- and thin-walled, septate, 2.5–8 μm wide. Conidiomata pycnidial, brown, solitary, superficial on OA, glabrous, broadly ellipsoidal, 250–270 × 200–230 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–5 layered, 15–35 μm thick, composed of brown, flattened polygonal cells of 5–10 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform or globose, 4.5–6 × 3–4.5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, guttulate, ovoid to cylindrical, 4–6 × 2.5–3 μm. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 54 mm diam after 7 d at 25 ± 1 °C, flattened, greyish brown (M. 5F3); reverse greyish brown (M. 5F3). Colonies on MEA reaching 57–67 mm after 7 d at 25 ± 1 °C, flattened, brownish orange (M. 5C3); reverse brownish grey (M. 5C2). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 37 °C.



Materials examined: USA, from human finger-hand lesion, 2006, D.A. Sutton (holotype CBS H-23200, ex-type living cultures CBS 143032 = UTHSC DI16-200 = FMR 13690); from human toe nail, 2007, D.A. Sutton, living cultures UTHSC DI16-228 = FMR 13718; from human nail, 2009, D.A. Sutton, living cultures UTHSC DI16-282 = FMR 13774.



Notes: Didymella keratinophila was recovered from a human superficial tissue specimen in the USA, and forms a well-supported sister clade with D. sancta. Didymella keratinophila differs phenotypically from D. sancta (and related species, such as D. glomerata, D. musae and D. pomorum) by the absence of chlamydospores in vitro (brown, alternarioid, phragmosporous and dyctiosporous, singly and terminally produced in D. sancta), smaller conidia (4–6 × 2.5–3 μm vs. 5–7 (–7.5) × 2.5–4 (–4.5) μm in D. sancta) and a negative NaOH spot test.



Didymella microchlamydospora (Aveskamp & Verkley) Q. Chen & L. Cai, Stud. Mycol. 82: 178. 2015.

Basionym: Phoma microchlamydospora Aveskamp & Verkley, Mycologia 101: 374. 2009.



Description: Aveskamp et al. (2009).

Materials examined: UK, from leaves of Eucalyptus sp., 1994, A.M. Ainsworth (holotype CBS H-20147, ex-holotype living culture CBS 105.95). USA, from human skin leg, 2006, D.A. Sutton, living cultures UTHSC DI16-199 = FMR 13689; from human corneal lesion, 2014, D.A. Sutton, living cultures UTHSC DI16-365 = FMR 13858.



Notes: Phoma microchlamydospora was described as a new species by Aveskamp et al. (2009) from leaves of Eucalyptus sp. in Great Britain, being subsequently transferred to the genus Didymella by Chen et al. (2015) after a phylogenetic study. Our two strains of this species differ in the geographic origin (USA) and in substrate (isolated from human clinical specimens), but they are morphologically and genetically similar to the ex-type living culture of D. microchlamydospora, being characterised by the production of abundant micropycnidia, globose pycnidia with 1–3 papillate ostioles, frequently on a neck, hyaline, one-celled, globose to ellipsoidal conidia, and relatively small, one-celled to multi-celled chlamydospores arranged in chains.



Didymella musae (P. Joly) Q. Chen & L. Cai, Stud. Mycol. 82: 178. 2015. Fig. 5.

Fig. 5.

Didymella musae (CBS 463.69). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Basionym: Peyronellaea musae P. Joly, Rev. Mycol. 26: 97. 1961.

Synonym: Phoma jolyana Piroz. & Morgan-Jones, Trans. Brit. Mycol. Soc. 51: 200. 1968.



Description: Boerema (1993).



Materials examined: India, from fruit of Mangifera indica, May 1969, living cultures CBS 463.69 = FMR 15339. USA, from human cornea lesion, 2007, D.A. Sutton, living cultures UTHSC DI16-230 = FMR 13720.



Notes: The strain UTHSC DI16-230, which is morphologically similar to the reference strain CBS 463.69, only differs genetically in a few nucleotides of the tub2 gene.



Didymella protuberans (Lév.) Q. Chen & L. Cai, Stud. Mycol. 82: 180. 2015.

Basionym: Phoma protuberans Lév., Ann. Sci. Nat. Bot. III 5: 281. 1846.

Synonyms: Peyronellaea protuberans (Lév.) Aveskamp et al., Stud. Mycol. 65: 33. 2010.

Didymella alectorolophi Rehm, Hedwigia 64: 294. 1923.

Peyronellaea alectorolophi (Rehm.) Aveskamp et al., Stud. Mycol. 65: 31. 2010.

Phoma alecotorolophi Boerema et al., Persoonia 16: 366. 1997.

Phoma obtusa Fuckel, Jahrb. Nassauischen Vereins Naturk. 23–24: 378. 1870.

Peyronellaea obtusa (Fuckel) Aveskamp et al., Stud. Mycol. 65: 33. 2010.



Description: Chen et al. (2015).



Materials examined: The Netherlands, from a leaf of Lycium halimifolium, 1971 (neotype HMAS 246694, ex-neotype living cultures CBS 381.96 = PD 71/706). USA, from chocolate, 2011, D.A. Sutton, living cultures UTHSC DI16-302 = FMR 13795.



Notes: The strain UTHSC DI16-302 isolated from the USA clusters with the ex-neotype strain of Didymella protuberans, being morphologically similar.



Didymella rumicicola (Boerema & Loer.) Q. Chen & L. Cai, Stud. Mycol. 82: 181. 2015.

Basionym: Phoma rumicicola Boerema & Loer., New Zealand J. Bot. 18: 473. 1980.



Description: Chen et al. (2015).



Materials examined: New Zealand, Levin, from Rumex obtusifolius, Jun. 1979, G.F. Laundon (holotype PDD 50667, isotype CBS H-7627, ex-isotype living cultures CBS 683.79 = LEV 15094). The Netherlands, Baarn, from a stem of Rumex hydrolapathum, Mar. 1996, H.A. van der Aa, living culture CBS 179.97.



Notes: The strain CBS 179.97 was initially identified as Didymella acetosellae; this strain is genetically identical to the ex-type strain of D. rumicicola (CBS 683.79), and the host pertains to the same genus of plants (Rumex). Consequently, we assigned this strain to D. rumicicola.



Didymella sp.



Material examined: Japan, from Camellia sasanqua, living culture LC 8141.



Notes: This strain was considered by Chen et al. (2017) as a reference strain of Didymella segeticola. However, in our phylogenetic study, this strain is distinct from the ex-type strain of Didymella segeticola, with strain LC 8141 differing in 7 bp in rpb2. It was also isolated from a different host and country, and therefore we maintain this strain as Didymella sp.



Clade A2: Epicoccum



Epicoccum Link, Mag. Neuesten Entdeck. Gesammten Naturk. Ges. Naturf. Freunde Berlin 7: 32. 1815, emend. Q. Chen & L. Cai, Stud. Mycol. 82: 171. 2015.



Type species: Epicoccum nigrum Link.



Epicoccum camelliae Q. Chen et al., Stud. Mycol. 87: 140. 2017.



Description: Chen et al. (2017).



Materials examined: China, Jiangxi, Ganzhou, leaves of Camellia sinensis, 7 Sep. 2013, Y. Zhang (holotype HMAS 247159, ex-holotype culture CGMCC 3.18343 = LC 4858); ibid. LC4862. USA, from human respiratory tract, 2006, D.A. Sutton, living cultures UTHSC DI16-201 = FMR 13691; from human nail, 2006, D.A. Sutton, living cultures UTHSC DI16-202 = FMR 13692; from human toe nail, 2006, D.A. Sutton, living cultures UTHSC DI16-206 = FMR 13696; from human toe nail, 2009, D.A. Sutton, living cultures UTHSC DI16-280 = FMR 13772; from human nail, 2011, D.A. Sutton, living cultures UTHSC DI16-338 = FMR 13831; from human abscess, 2012, D.A. Sutton, living cultures UTHSC DI16-345 = FMR 13838.



Notes: A total of six isolates molecularly identified as E. camelliae clustered together with E. viticis forming a low-supported clade. Our isolates, as well as those of Chen et al. (2017), remained sterile. Consequently, further studies will be needed to fully characterise this species.



Epicoccum catenisporum Valenzuela-Lopez, Stchigel, Crous, Guarro & Cano, sp. nov., MycoBank MB819762. Fig. 6.



Fig. 6.

Epicoccum catenisporum (CBS 181.80). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Chlamydospores in chains. H. Conidiogenous cells. I. Conidia. Scale bars: F = 100 μm. G–I = 10 μm.

Etymology: From Latin catena-, chain, and -spora, spore, because of the disposition of the chlamydospores in chains.



Description: Hyphae pale brown, smooth- and thin-walled, septate, 2.5–5 μm wide. Conidiomata pycnidial, brown to dark brown, solitary, superficial and immersed (OA), glabrous, subglobose, 170–190 × 140–160 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–5 layered, 15–50 μm thick, composed of brown to dark brown, flattened polygonal cells of 5–10 μm diam, Conidiogenous cells phialidic, hyaline, smooth-walled, doliiform or ampulliform, 4–6 × 2–4 μm. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid or ellipsoidal, 4–5 × 2–3 μm, guttulate. Chlamydospores aseptate, dark brown, smooth- and thick-walled, in chains or singly, then intercalary disposed, ellipsoidal to ovoid, 9.5–12 × 4.5–8.5 μm.



Culture characteristics: Colonies on OA reaching 53 mm diam after 7 d at 25 ± 1 °C, flattened, powdery due to the production of abundant pycnidia, orange grey (M. 5B1) to yellowish brown (M. 5F5); reverse pale brown (M. 5D4) to brownish grey (M. 5F2). Colonies on MEA reaching 36 mm after 7 d at 25 ± 1 °C, flattened to floccose, white (M. 5A1) to orange white (M. 5A2); reverse white (M. 5A1) to pale orange (M. 5A4). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 15 °C; maximum temperature of growth 35 °C.



Material examined: Guinea-Bissau, Gacheu, from a leaf spot of Oryza sativa, Oct. 1978, deposited by G.H. Boerema (holotype CBS H-23203, ex-holotype living cultures CBS 181.80 = PD 78/974 = FMR 14911).



Notes: The strain CBS 181.80 was previously identified as Phoma sorghina (currently E. sorghinum) by Aveskamp et al. (2009). However, it is phylogenetically different from that species. Epicoccum catenisporum is morphologically characterised by the production of pycnidia as observed in several other members of Epicoccum.



Epicoccum keratinophilum Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov., MycoBank MB819758. Fig. 7.



Fig. 7.

Epicoccum keratinophilum (CBS 142455). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cell. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: From Greek κɛράτινη-, keratin, and -φίλος, friend, linked to the origin of the fungus.



Description: Hyphae pale brown, smooth- and thin-walled, septate, 2.5–5 μm wide. Conidiomata pycnidial, brown, solitary, superficial or immersed (OA), glabrous, subglobose, 200–300 × 180–240 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–4 layered, 15–45 μm thick, composed of brown to dark brown, flattened polygonal cells of 5–20 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform to globose, 4–5 μm diam. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical, 4–6 × 1.5–2 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 30–35 mm diam after 7 d at 25 ± 1 °C, flattened, entire edge, yellowish brown (M. 5E7) to brownish grey (M. 5F2); reverse brownish grey (M.5F2). Colonies on MEA reaching 30–37 mm diam after 7 d at 25 ± 1 °C, flattened, entire edge, white (M. 2A1) to yellowish white (M. 3A2); reverse dull yellow (M. 3B3). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Materials examined: USA, Texas, from animal skin lesion, 2009, D.A. Sutton (holotype CBS H-23032, ex-holotype living cultures CBS 142455 = UTHSC DI16-271 = FMR 13762); Texas, from human superficial tissue, 2007, D.A. Sutton, living cultures UTHSC DI16-244 = FMR 13734; from human bronchial wash sample, 2008, D.A. Sutton, living cultures UTHSC DI16-258 = FMR 13748; from human toe nail, 2009, D.A. Sutton, living cultures UTHSC DI16-272 = FMR 13763; from human biopsy tissue, 2011, D.A. Sutton, living culture UTHSC DI16-299 = FMR 13792.



Notes: In our phylogenetic tree E. keratinophilum forms a well-supported clade distant from its morphological relatives E. brasiliense and E. draconis. All E. keratinophilum strains have been recovered from clinical samples, and morphologically differ from E. brasiliense in producing smaller pycnidia and conidia, and from both E. brasiliense and E. draconis by a negative NaOH spot test reaction.



Epicoccum latusicollum Q. Chen et al., Stud. Mycol. 87: 144. 2017.



Description: Chen et al. (2017).



Materials examined: China, Jiangxi, Ganzhou, endophyte of Camellia sinensis, 7 Sep. 2013, Y. Zhang, living culture LC 4859; Shandong, Jining, on leaves of Sorghum bicolor, 3 Aug. 2013, N. Zhou (holotype HMAS 247164, ex-holotype living culture CGMCC 3.18346 = LC 5158). USA, from human eye, 2005, D.A. Sutton, living cultures UTHSC DI16-197 = FMR 13687.



Notes: The strain UTHSC DI16-197 that was isolated from a human eye sample clustered with the ex-type strain of E. latusicollum that was recently introduced by Chen et al. (2017), being characterised by the production of pycnidial conidiomata. Unfortunately, our strain was sterile, and morphological comparison was not possible, but genetically it is identical to the latter species.



Epicoccum ovisporum Valenzuela-Lopez, Stchigel, Crous, Guarro & Cano, sp. nov., MycoBank MB819761. Fig. 8.



Fig. 8.

Epicoccum ovisporum (CBS 180.80). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G, H. Conidiogenous cells. I. Conidia. Scale bars: F = 100 μm. G–I = 10 μm.

Etymology: From Latin ovum-, egg, and -spora, spore, due to the shape of the conidia.



Description: Hyphae hyaline to pale brown, smooth- and thin-walled, septate, 2.5–5 μm wide. Conidiomata pycnidial, brown, solitary, mostly superficial on OA and immersed into MEA, glabrous, subglobose to globose, 100–190 × 85–180 μm, with short papillate ostiolar neck; pycnidial wall of textura angularis, 3–4 layered, 12.5–35 μm thick, composed of brown, flattened polygonal cells of 5–20 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, doliiform to ampulliform, 5–6 × 2–3 μm. Conidia aseptate, hyaline, smooth- and thin-walled, guttulate, ovoid, ellipsoidal to cylindrical, 5–7 × 2–3 μm. Chlamydospores multi-celled, brown to dark brown, smooth-walled, disposed in chains or singly, then intercalary and terminally, globose to subglobose, 10–22.5 × 10–20 μm.



Culture characteristics: Colonies on OA reaching 36 mm diam after 7 d at 25 ± 1 °C, flattened, with abundant production of pycnidia, greenish grey (M. 29B2); reverse orange grey (M.5B2). Colonies on MEA reaching 38 mm after 7 d at 25 ± 1 °C, floccose, orange grey (M. 5B2) to grey (M. 5C1), producing a hyaline exudate; reverse yellowish brown (M. 5D8). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 15 °C; maximum temperature of growth 30 °C.



Material examined: South Africa, Potchefstroom, from a leaf of Zea mays, Nov. 1978, isolated by W.J. Jooste, deposited by G.H. Boerema (holotype CBS H-23204, ex-holotype living cultures CBS 180.80 = PD 78/1100 = FMR 14910).



Notes: The strain CBS 180.80 was previously assigned to E. sorghinum (Aveskamp et al., 2009, Aveskamp et al., 2010); however, in our phylogenetic tree it represents a new species, forming a basal clade together with E. catenisporum and E. sorghinum, being distant from the rest of the species of the genus. The above-mentioned species are morphologically similar to E. ovisporum by producing pycnidia instead of sporodochia.



Epicoccum pneumoniae Valenzuela-Lopez, Stchigel, Guarro & Cano, sp. nov. MycoBank MB822112.



Etymology: The species name refers to the infection associated with this specimen.



Culture sterile. Epicoccum pneumoniae differs from its closest phylogenetic species Epicoccum latusicollum based on alignment of the concatenated four loci deposited in TreeBASE (S21115): LSU deletion in position: 382; ITS positions: 587 (C); tub2 positions: 1075 (T), 1102 (T), 1152 (T), 1159 (T), 1161 (G), 1207 (G), 1209 (T), 1210 (A), 1212 (G), 1213 (T), 1254 (T), 1260 (C), 1284 (C); rpb2 positions: 1312 (A), 1336 (A), 1339 (G), 1351 (C), 1354 (T), 1384 (C), 1453 (T), 1456 (C), 1495 (T), 1553 (C), 1609 (T), 1757 (T), 1769 (C), 1813 (C), 1816 (C), 1843 (C), 1873 (C), 1897 (C).



Culture characteristics: Colonies on OA reaching 29 mm diam after 7 d at 25 ± 1 °C, flattened, reddish grey (M. 9B2) to white (M. 9A1); reverse white (M. 9A1). Colonies on MEA reaching 31 mm after 7 d at 25 ± 1 °C, flattened to floccose, pinkish white (M. 9A2) to white (M. 9A1); reverse white (M. 9A1). NaOH spot test negative. Crystals absent.



Material examined: USA, from human sputum sample, 2008, D.A. Sutton (holotype FMR H-13747, ex-holotype living cultures UTHSC DI16-257 = FMR 13747).



Notes: The strain UTHSC DI16-257, which remained sterile, forms a basal clade with E. latusicollum; however, this strain clearly differs phylogenetically from the latter species mainly in the loci tub2 and rpb2. Therefore it is proposed here as a new species, Epicoccum pneumoniae.



Epicoccum proteae (Crous) Valenzuela-Lopez, Stchigel, Crous, Guarro & Cano, comb. nov. MycoBank MB820830.

Basionym: Phoma proteae Crous, Persoonia 27: 151. 2011.



Description: Crous et al. (2011).



Material examined: South Africa, Western Cape Province, Somerset West, Karibia Farm, from leaves of Protea cv. Carnival (P. compacta × P. neriifolia), 21 July 1998, J.E. Taylor & S. Denman (holotype CBS H-20771, ex-holotype living cultures CPC 1854 = CBS 114179 = FMR 15332).



Notes: This species was first proposed by Crous et al. (2011) within Phoma, which is characterised by producing brown, globose pycnidia and hyaline, aseptate conidia. However, our phylogenetic study showed that the ex-type strain of this species clustered in Epicoccum. Therefore, we propose a new combination for this species.



Epicoccum sorghinum (Sacc.) Aveskamp et al., Stud. Mycol. 65: 36. 2010.

Basionym: Phyllosticta sorghina Sacc., Michelia 1: 140. 1878.

Synonym: Phoma sorghina (Sacc.) Boerema et al., Persoonia 7: 134. 1973.



Description: Boerema et al. (2004).



Materials examined: France, Antibes, from a twig of Citrus sp., 1966, living cultures CBS 627.68 = PD 66/926. Puerto Rico, Mayaguez, from Sorghum vulgare, Apr. 1976, R. Alconera, living cultures CBS 179.80 = PD 76/1018; USA, from human foot, 2010, D.A. Sutton, living cultures UTHSC DI16-288 = FMR 13692; from human bronchial wash sample, 2011, D.A. Sutton, living cultures UTHSC DI16-301 = FMR 13794.



Notes: Two strains (UTHSC DI16-288 and UTHSC DI16-301) isolated from human clinical specimens in the USA clustered with the reference strains CBS 179.80 and CBS 627.68 of E. sorghinum. The latter species had been reported from several different substrates mainly from vegetal materials and it seems to be a widely distributed fungus, also having been associated with human infections (Punithalingam, 1985, Rai, 1989). Morphologically E. sorghinum was described producing mainly pycnidial conidiomata. Unfortunately, our strains were sterile, and further studies are needed to resolve the taxonomy of this species.



Clade A3: Allophoma



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



Type species: Allophoma tropica (R. Schneid. & Boerema) Q. Chen & L. Cai, Stud. Mycol. 82: 162. 2015.



Allophoma cylindrispora Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB819625. Fig. 9.



Fig. 9.

Allophoma cylindrispora (CBS 142453). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidium. F. Conidiogenous cells. G. Conidia. Scale bars: E = 100 μm. F, G = 10 μm.

Etymology: From Latin cylindricus-, of cylindrical shape, and -spora, spore.



Description: Hyphae brown, septate, smooth- and thin-walled, 2.5–5 μm wide. Conidiomata pycnidial, brown to dark brown, confluent, superficial and immersed (OA), glabrous, ovoid, 120–210 × 90–140 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–4-layered, 15–30 μm thick, composed of brown to dark brown, flattened polygonal cells of 5–12.5 μm diam,. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 3.5–4 × 4.5–5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical, 3–4 × 2 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 36 mm diam after 7 d at 25 ± 1 °C, flattened, beige (M. 4C3) to olive brown (M. 4F3); reverse blond (M. 4C4) to olive brown (M. 4F3). Colonies on MEA reaching 25–27 mm after 7 d at 25 ± 1 °C, flattened, white (M. 4A1); reverse pale yellow (M. 4A4) to yellowish orange (M. 4B7). NaOH spot test negative. Crystals absent. Optimal temperature of growth and of sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: USA, from a human eye lesion, 2007, D.A. Sutton (holotype CBS H-23030, ex-holotype living cultures CBS 142453 = UTHSC DI16-233 = FMR 13723).



Notes: This species forms a clade which is distinct from the closest relatives, A. minor and A. piperis. Unfortunately, the morphological distinction between these three species is difficult. Although these species differ in geography and substrate, molecular data is required for species identification. Allophoma cylindrispora sporulates poorly in culture.



Clade A7: Ectophoma



Ectophoma Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, gen. nov. MycoBank MB819952.



Etymology: From the Greek ɛκτοs, outside, because it is phylogenetically far from Phoma.



Conidiomata pycnidial, brown to dark brown, solitary or confluent, pycnidial wall of textura angularis, glabrous, globose to subglobose or irregular, ostiolate, with one or more short necks. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform to globose. Conidia aseptate, hyaline, smooth- and thin-walled, oblong to ellipsoidal, guttulate.



Type species: Ectophoma multirostrata (P.N. Mathur et al.) Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel.



Ectophoma multirostrata (P.N. Mathur et al.) Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, comb. nov., MycoBank MB819953. Fig. 10.

Fig. 10.

Ectophoma multirostrata (CBS 274.60). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Basionym: Sphaeronaema multirostratum P.N. Mathur et al., Sydowia 13: 146. 1959.

Synonym: Phoma multirostrata (P.N. Mathur et al.) Dorenb. & Boerema, Mycopathol. Mycol. Appl. 50: 256. 1973.

Description: Boerema et al. (2004).



Materials examined: India, Maharashtra, Poona, Talegaon, from poultry farm soil, Mar. 1959, M. J. Thirumalachar (isotype CBS H-7616, ex-isotype living cultures CBS 274.60 = IMI 081598 = FMR 15335); Maharashtra, Poona, Talegaon, from soil, Mar. 1959, M.J. Thirumalachar, living cultures CBS 368.65 = PD 92/1757 = FMR 15336. The Netherlands, Hoorn, greenhouse, from the stem of Cucumis sativus, Aug. 1967, G.H. Boerema, living cultures CBS 110.79 = PD 65/8875 = FMR 15342.



Notes: Aveskamp et al. (2009) transferred this species from Sphaeronaema to Phoma. In our study, P. multirostrata forms a distinct clade, separated from all genera previously described in the Didymellaceae. Therefore, we propose a new genus to accommodate this species.



Ectophoma pomi (A.S. Horne) Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, comb. nov. MycoBank MB819954. Fig. 11.

Fig. 11.

Ectophoma pomi (CBS 267.92). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Chlamydospores. H. Arrow indicate the conidiogenous cell. I. Conidia. Scale bars: F = 50 μm. G–I = 10 μm.

Basionym: Polyopeus pomi A.S. Horne, J. Bot., Lond. 58: 240. 1920.

Synonym: Phoma pereupyrena Gruyter et al., Persoonia 15: 398. 1993.



Description: Boerema et al. (2004).



Material examined: India, from a leaf spot of Coffea arabica, 1976, deposited by J. de Gruyter (neotype designated here CBS H-23202, MBT377913, ex-neotype living cultures CBS 267.92 = PD 76/1014 = FMR 15346).



Notes: Polyopeus pomi, introduced by Horne (1920) was validly described growing on potato mush agar, and was isolated from the fruits of Malus domestica “Cox's Orange Pippin”, in the UK, where it produced dark spots. No illustration is available, and no type material is mentioned in the publication. Therefore, based on the original description, we propose CBS H-23202 as neotype. The fungus produces black, subglobose to irregularly shaped pycnidia with a blackish neck, and hyaline, ellipsoidal conidia, 5−9 × 2−3 μm.



Clade A8: Remotididymella



Remotididymella Valenzuela-Lopez, Crous, Cano, Guarro & Stchigel, gen. nov. MycoBank MB819990.



Etymology: From Latin remotus-, distant, because it is phylogenetic far removed from the similar genus Didymella.



Conidiomata pycnidial, brown to dark brown, mostly confluent; pycnidial wall of textura angularis, mostly glabrous, globose or irregularly-shaped, with a single ostiole. Conidiogenous cells phialidic, hyaline, smooth-walled, globose or ampulliform. Conidia aseptate, hyaline, smooth- and thin-walled, allantoid or cylindrical, guttulate.



Type species: Remotididymella destructiva (Plowr.) Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel.



Remotididymella anthropophila Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB819991. Fig. 12.



Fig. 12.

Remotididymella anthropophila (CBS 142462). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: From Greek ανθρώπος-, human, and –φίλος, friend, because that fungus has been isolated from a human sample.



Description: Hyphae brown, smooth- and thin-walled, septate, 2.5–8 μm wide. Conidiomata pycnidial, apricot to pale brown, translucent, solitary or confluent, superficial (OA), glabrous, globose to subglobose, 300–400 × 250–400 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–5 layered, 30–40 μm thick, composed of subhyaline to pale brown flattened polygonal cells of 5–20 μm diam,. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform to globose, 5–6 μm diam. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical, 5.5–7.5 × 1.5–2.5 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 60 mm diam after 7 d at 25 ± 1 °C, flattened, yellowish brown (M. 5E3) to greyish brown (M. 5F3); reverse greyish brown (M. 5F3). Colonies on MEA reaching 35–36 mm diam after 7 d at 25 ± 1 °C, flattened, greyishorange (M. 5B3) to pale brown (M. 5D6); reverse orange white (M. 5A2) to brownish yellow (M. 5C7). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 35 °C.



Material examined: USA, Texas, from human bronchial secretion, D.A. Sutton (holotype CBS H-23039, ex-holotype living cultures CBS 142462 = UTHSC DI16-278 = FMR 13770).



Notes: The new species Remotididymella anthropophila is genetically distinct from its nearest neighbour R. destructiva. Morphologically it is the only species of the genus that produces pale-brown pycnidia, which is unusual in phoma-like species, and it differs in substrate and location with the latter species.



Remotididymella destructiva (Plowr.) Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, comb. nov. MycoBank MB819992. Fig. 13.

Fig. 13.

Remotididymella destructiva (CBS 378.73). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Basionym: Phoma destructiva Plowr., Gard. Chron. II 16: 621. 1881.

Synonyms: Diplodina destructiva (Plowr.) Petr., Annls mycol. 19(1/2): 19. 1921.

Phoma destructiva var. diversispora Gruyter et al., Persoonia 18: 28. 2002.



Description from ex-epitype (CBS 378.73): Hyphae brown, smooth- and thin-walled, septate, 2.5–6 μm wide. Conidiomata pycnidial, dark brown, mostly confluent, rarely solitary, superficial or immersed (OA), glabrous, ovoid to irregularly-shaped, 120–250 × 90–180 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–4 layered, 12.5–50 μm thick, composed of brown, flattened polygonal cells of 5–10 μm diam,. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 10–12 × 5–6 μm. Conidia aseptate, hyaline, smooth- and thin-walled, variable in shape, mostly allantoid to cylindrical, 3.5–8 × 2–2.5 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 21 mm diam after 7 d at 25 ± 1 °C, flattened, front and reverse dark grey (M. 4F1). Colonies on MEA reaching 10 mm diam after 7 d at 25 ± 1 °C, flattened, front and reverse olive brown to dark grey (M. 5F2). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 15 °C; maximum temperature of growth 30 °C.



Materials examined: Lectotype designated here (MBT378116): fig. 123, in Plowright. 1881. The Gardeners' chronicle: a weekly illustrated journal of horticulture and allied subjects (http://www.biodiversitylibrary.org/item/84372#page/639/mode/1up). Guadeloupe, from fruit of Lycopersicon esculentum, 1987, living cultures CBS 133.93 = PD 88/961 = IMI 173142. The Netherlands, Berkel en Rodenrijs, from a leaf of Lycopersicon esculentum, Oct. 1977, G.H. Boerema, living culture CBS 162.78 = PD 77/725. Tonga, Friendly Islands, from decaying fruit of Lycopersicon esculentum, 1967, G.F. Laundon (epitype designated here CBS H-16200, MBT377914, ex-epitype living cultures CBS 378.73 = FMR 15328 = CECT 2877).



Notes: Phoma destructiva was originally described by Plowright (1881), infecting fruits of Lycopersicon esculentum in King’s Lynn, UK. Later, many representative specimens were collected from the similar hosts in other countries of Europe, and in North and South America (De Gruyter et al., 2002, Boerema et al., 2004). Phoma destructiva is characterised by the production of olivaceous black, globose, glabrous pycnidia with up to three papillate ostioles, hyaline, aseptate, subglobose to ellipsoidal conidia of σ = 5.8 × 2.2 μm, scarce and larger 1-septate conidia, and by the absence of chlamydospores. De Gruyter et al. (2002), based on morphological differences of the conidia, recognized two varieties, destructiva and diversispora. However, the isolates CBS 378.73 and CBS 133.93, representative strains of “Phoma destructiva var. destructiva”, and CBS 162.78, representative of “Phoma destructiva var. diversispora”, were phylogenetically and morphologically very similar in our study. Therefore, we did not accept these varieties, and propose CBS H-16200 as the epitype of Remotididymella destructiva.



Clade A9: Similiphoma



Similiphoma Valenzuela-Lopez, Crous, Cano, Guarro & Stchigel, gen. nov., MycoBank MB820847.



Etymology: From Latin similis-, similar to, due to the morphological similarity with Phoma.



Conidiomata pycnidial, brown, confluent or solitary; pycnidium wall of textura angularis, glabrous or with short hyphal outgrowths, globose to subglobose, with one or two papillate ostioles. Conidiogenous cells phialidic, hyaline, smooth-walled, globose or ampulliform. Conidia aseptate, hyaline, smooth- and thin-walled, ellipsoidal to cylindrical, guttulate.



Type species: Similiphoma crystallifera (de Gruyter et al.) Valenzuela-Lopez, Crous, Cano, Guarro & Stchigel.



Similiphoma crystallifera (Gruyter et al.) Valenzuela-Lopez, Crous, Cano, Guarro & Stchigel, comb. nov. MycoBank MB820848. Fig. 14.

Fig. 14.

Similiphoma crystallifera (CBS 193.82). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Basionym: Phoma crystallifera Gruyter et al., Persoonia 15: 393. 1993.



Description: Boerema et al. (2004).



Material examined: Austria, Kärnten, Wallersberg near Völkermarkt, from Chamaespartium sagittale, 1982, H.A. van der Aa (holotype L 992.177-456, ex-holotype living cultures CBS 193.82 = FMR 15343).



Notes: Similiphoma crystallifera CBS 193.82 clustered phylogenetically distant from the closest morphologically related genera Ectophoma, Epicoccum and Phoma. Consequently, we designated this strain as the type species of the new genus Similiphoma.



Clade A10: Paraboeremia



Paraboeremia Q. Chen & L. Cai, Stud. Mycol. 82: 183. 2015.



Type species: Paraboeremia selaginellae (Sacc.) Q. Chen & L. Cai.



Paraboeremia putaminum (Speg.) Q. Chen & L. Cai, Stud. Mycol. 82: 184. 2015. Fig. 15.

Fig. 15.

Paraboeremia putaminum (CBS 130.69). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Basionym: Phoma putaminum Speg., Atti Soc. Crittog. Ital. 3: 66. 1881.



Description: de Gruyter & Noordeloos (1992).



Material examined: Denmark, from the rhizosphere of Malus sylvestris, Mar. 1968, E. Sønderhousen, living cultures CBS 130.69 = CECT 20054 = IMI 331916 = FMR 15338.



Notes: This species was introduced by Spegazzini in 1881, isolated from pine wood in Sweden, and in the last study of this species by Chen et al. (2015) from two reference strains (CBS 130.69 and CBS 372.91) was placed within the genus Paraboeremia. However, without an illustration and rpb2 sequences, in our study, the rpb2 sequence and the illustration were provided of the reference strain CBS 130.69, which it resembles morphologically (de Gruyter & Noordeloos 1992), but further studies are needed to clarify its typification.



Paraboeremia selaginellae (Sacc.) Q. Chen & L. Cai, Stud. Mycol. 82: 184. 2015.

Basionym: Phyllosticta selaginellae Sacc., Malpighia 11: 304. 1897.

Synonym: Phoma selaginellicola Gruyter et al., Persoonia 15: 399. 1993.



Description: Chen et al. (2015).



Material examined: The Netherlands, from a leaf of Selaginella sp., 1977, G.H. Boerema (neotype HMAS 246693, MBT202501, ex-neotype living cultures CBS 122.93 = PD 77/1049 = FMR 15348).



Notes: This species was already typified by Chen et al. (2015) providing DNA sequence data and illustrations. However, the rpb2 sequence was not given, and therefore in the present study the rpb2 sequence of the ex-type strain CBS 122.93 is added.



Clade A12: Cumuliphoma



Cumuliphoma Valenzuela-Lopez, Stchigel, Crous, Guarro & Cano, gen. nov. MycoBank MB819878.



Etymology: From Latin cumulus-, heap or pile, in reference to the aggregated pycnidia.



Conidiomata pycnidial, brown, mostly confluent, pycnidial wall of textura angularis, mostly glabrous, globose or nearly so, with a single ostiole. Conidiogenous cells phialidic, hyaline, smooth-walled, globose to ampulliform. Conidia aseptate, hyaline, smooth- and thin-walled, ellipsoidal to cylindrical, guttulate. Chlamydospores mostly absent.



Type species: Cumuliphoma omnivirens (Aveskamp et al.) Valenzuela-Lopez, Stchigel, Crous, Guarro & Cano.



Cumuliphoma indica Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, sp. nov. MycoBank MB819880. Fig. 16.



Fig. 16.

Cumuliphoma indica (CBS 654.77). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: The name refers to the geographic origin of the fungus, India.



Description: Hyphae pale brown to brown, smooth- and thin-walled, septate, 2.5–8 μm wide. Conidiomata pycnidial, brown to dark brown, mostly confluent, rarely solitary, immersed (OA and MEA), glabrous, ovoid to irregularly-shaped, 150–180(–520) × 140–150(–490) μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 3–5-layered, 25–60 μm thick, composed of brown, flattened polygonal cells of 7–23 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, globose to ampulliform, 5–6 × 4–5.5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, ellipsoidal to cylindrical, 4–5.5 × 2–2.5 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 42 mm diam after 7 d at 25 ± 1 °C, flattened, olive brown (M. 4F3); reverse dark grey (M. 4F1). Colonies on MEA reaching 37 mm diam after 7 d at 25 ± 1 °C, flattened, brownish grey (M. 5F2) to pale grey (M. 5C2); reverse brownish grey (M. 5F2). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 15 °C; maximum temperature of growth 30 °C.



Materials examined: India, Jabalpur, from an unknown substrate, 1977, isolated by D.P. Tiwari (holotype CBS H-20152, ex-holotype living cultures CBS 654.77 = FMR 15341). Papua New Guinea, Varirata National Park, from soil, Aug. 1995, A. Aptroot, living cultures CBS 991.95 = FMR 15331.



Notes: The isolates CBS 654.77 and CBS 991.95 were received as “Phoma omnivirens”. However, these isolates were phylogenetically distant from the ex-type strain of C. omnivirens (CBS 341.86), and also both differ morphologically from the latter due to the absence of chlamydospores and micropycnidia.



Cumuliphoma omnivirens (Aveskamp et al.) Valenzuela-Lopez, Stchigel, Crous, Guarro & Cano, comb. nov. MycoBank MB819882.

Basionym: Phoma omnivirens Aveskamp et al., Mycologia 101: 375. 2009.



Description: Aveskamp et al. (2009).



Material examined: Belgium, Gembloux, from Phaseolus vulgaris, 1968, isolated by L. Obando (holotype CBS H-20151, ex-holotype living cultures CBS 341.86 = FMR 14915).



Notes: Cumuliphoma omnivirens is the only species of the genus that produces chlamydospores. Phylogenetically, it is closely related to C. pneumoniae, but is distinct from this species in both rpb2 and tub2 sequences by 9 bp.



Cumuliphoma pneumoniae Valenzuela-Lopez, Stchigel, Crous, Guarro & Cano, sp. nov. MycoBank MB819881. Fig. 17.



Fig. 17.

Cumuliphoma pneumoniae (CBS 142454). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: From Greek πνɛυμονικός-, pulmonary, due to the origin of the ex-type strain.



Description: Hyphae hyaline to brown, smooth- and thin-walled, septate, 2.5–6 μm wide. Conidiomata pycnidial, brown to dark brown, confluent, superficial (OA), glabrous, globose to subglobose, 200–240 × 200 μm, with a short papillate ostiolar neck; pycnidial wall of textura angularis, 3–5 layered, 25–35 μm thick, composed of brown to dark brown, flattened polygonal cells of 5–12 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform to globose, 5–6 × 5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid to cylindrical, 2.5–5 × 2 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 28 mm diam after 7 d at 25 ± 1 °C, flattened, yellowish brown (M. 5F5); reverse brownish grey (M. 5F3). Colonies on MEA reaching 27–29 mm after 7 d at 25 ± 1 °C, flattened, grey (M. 6C1), producing a diffusible greyish orange pigment; reverse dark brown (M. 6F6). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: USA, from human sputum sample, D.A. Sutton (holotype CBS H-23031, ex-holotype living cultures CBS 142454 = UTHSC DI16-249 = FMR 13739).



Notes: Cumuliphoma pneumoniae was isolated from a clinical sample of the respiratory tract. This species is morphologically closely related to C. omnivirens, which is also the phylogenetically nearest species. However, C. pneumoniae does not produce chlamydospores.



Clade A13: Juxtiphoma



Juxtiphoma Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, gen. nov. MycoBank MB821111.



Etymology: From Latin juxta, next to, due to the morphological and phylogenetic similarity with Phoma.



Conidiomata pycnidial, brown, mostly solitary, sometimes confluent, pycnidial wall of textura angularis, glabrous, subglobose to conical, papillate, ostiolate. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid, ellipsoidal or cylindrical, biguttulate. Chlamydospores aseptate, ochraceous-brown, single or in chains, subglobose, barrel-shaped or ellipsoidal.



Type species: Juxtiphoma eupyrena (Sacc.) Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel.



Juxtiphoma eupyrena (Sacc.) Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, comb. nov. MycoBank MB821112.

Basionym: Phoma eupyrena Sacc., Michelia 1: 525. 1879.



Description: Boerema et al. (2004).



Materials examined: Germany, Kiel-Kitzeberg, from wheat field soil, 1966, W. Gams, living cultures CBS 527.66 = FMR 15337 = ATCC 22238. The Netherlands, from the tuber of Solanum tuberosum, 1991, J. de Gruyter, living cultures CBS 374.91 = PD 78/391 = FMR 15329.



Notes: Phoma eupyrena, introduced by Saccardo (1879) and reported on stems of Solanum tuberosum (geographic origin not cited), has been revised by several authors. The description from Saccardo is minimal: blackish, depressed conical, ostiolate pycnidia with hyaline, ovoid conidia, 4 × 1.5 μm. Boerema et al. (2004) characterised this species morphologically and placed it in the section Phoma. Aveskamp et al. (2009) considered it phylogenetically close to “Phoma omnivirens”, and later Aveskamp et al. (2010) regarded P. eupyrena closely related to Microsphaeropsis. However, in our phylogenetic tree this species formed a well-supported monophyletic clade, separate from the other genera of Didymellaceae. Therefore, we propose the new genus Juxtiphoma to accommodate this species.



Clade A14: Vacuiphoma



Vacuiphoma Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, gen. nov. MycoBank MB821451.



Etymology: Based on the occurrence of empty pycnidial structures.



Conidiomata pycnidial, brown to dark brown, solitary, glabrous, subglobose or obpyriform; pycnidial wall of textura angularis, non-papillate.



Type species: Vacuiphoma bulgarica (Aveskamp et al.) Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel.



Vacuiphoma bulgarica (Aveskamp et al.) Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, comb. nov. MycoBank MB821452.

Basionym: Phoma bulgarica Aveskamp et al., Stud. Mycol. 65: 47. 2010.

Description: Aveskamp et al. (2010).



Material examined: Bulgaria, Silkossia, Strandga Mountain, from leafs of Trachystemon orientale, 20 Jun. 1980, S. Vanev (holotype CBS H-20242, ex-holotype living cultures CBS 357.84 = FMR 14917).



Notes: This species was introduced by Aveskamp et al. (2010) within the genus Phoma due to the production of pycnidial conidiomata. However, this species was not able to produce conidia and remains poorly characterised. Genetically this species along with V. oculihominis form a distinct clade within Didymellaceae, thus we treat these species within the new genus Vacuiphoma.



Vacuiphoma oculihominis Valenzuela-Lopez, Stchigel, Guarro & Cano, sp. nov. MycoBank MB822113.



Etymology: The epithet refers to the human eye clinical sample, from which the fungus was isolated.



Culture sterile. Vacuiphoma oculihominis differs from its closest phylogenetic species, Vacuiphoma bulgarica, in two bp of the ITS nucleotide sequence, 12 bp of tub2 and 44 bp of rpb2, based on alignment of the concatenated four loci deposited in TreeBASE (S21115).



Culture characteristics: Colonies on OA reaching 30–34 mm diam after 7 d at 25 ± 1 °C, flattened, yellowish grey (M. 2B2) to olive grey (M. 2E2); reverse white (M. 2A1) to olive grey (M. 2E2). Colonies on MEA reaching 33 mm diam after 7 d at 25 ± 1 °C, slightly floccose, white (M. 5A1) to light orange (M. 5A4); reverse light orange (M. 5A4). NaOH spot test negative. Crystals absent. Optimal temperature of growth 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: USA, Illinois, from human eye secretion, 2011, D.A. Sutton (holotype FMR H-13801, ex-holotype living cultures UTHSC DI16-308 = FMR 13801).



Notes: The strain UTHSC DI16-308 was recovered from a human eye clinical specimen, and remained sterile despite being cultured on different types of media. Because this strain is phylogenetically related with V. bulgarica, but distant from that species, it is proposed here as a new taxon.



Clade A15: Nothophoma



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



Type species: Nothophoma infossa (Ellis & Everh.) Q. Chen & L. Cai, Stud. Mycol. 82: 213. 2015.



Nothophoma gossypiicola (Gruyter) Q. Chen & L. Cai, Stud. Mycol. 82: 213. 2015.

Basionym: Phoma gossypiicola Gruyter, Persoonia 18: 96. 2002.



Description: de Gruyter (2002).



Materials examined: USA, Texas, from a leaf of Gossypium sp., 1963, L.S. Bird, living cultures CBS 377.67 = FMR 14912; from human ethmoid sinus lesion, 2010, D.A. Sutton, living cultures UTHSC DI16-294 = FMR 13787.



Notes: This species was recently placed within the genus Nothophoma by Chen et al. (2015). In our study, one isolate from human clinical specimen was identified as N. gossypiicola, which it resembles in both morphology and DNA sequences from the reference strain CBS 377.67, isolated from the same country. This species is morphologically characterised by producing longer conidia (10–12.5 × 2.5–3.5 μm) and chlamydospores arranged in chains. However, further studies are needed to resolve its typification.



Nothophoma macrospora Valenzuela-Lopez et al., Persoonia 36: 431. 2016.



Description: Crous et al. (2016b).



Material examined: USA, Arizona, Phoenix, from human respiratory secretion of a patient with pneumonia, 1 Apr. 2009, D.A. Sutton (holotype CBS H-22377, ex-holotype living cultures CBS 140674 = UTHSC DI16-276 = FMR 13767).



Notes: This species was recently proposed by Valenzuela-Lopez et al. (2016), which is phylogenetically related with N. gossypiicola, but differs morphologically from the latter species in pycnidial shape, conidia (up to 2 vs non-septate) and the absence of chlamydospores (see Crous et al. 2016b). Furthermore, here the sequence of rpb2 is provided and differs in 13 bp from N. gossypiicola, and therefore N. macrospora is also phylogenetically distinct from N. gossypiicola.



Nothophoma quercina (Syd.) Q. Chen & L. Cai, Stud. Mycol. 82: 213. 2015.

Basionym: Cicinobolus quercinus Syd., Ann. Mycol. 13: 42. 1915.

Synonyms: Ampelomyces quercinus (Syd.) Rudakov, Mikol. Fitopatol. 13: 109. 1979.

Phoma fungicola Aveskamp et al., Stud. Mycol. 65: 26. 2010.



Description: Aveskamp et al. (2010).



Materials examined: Ukraine, Crimea, in the vicinity of Feodosiya, on Microsphaera alphitoides from Quercus sp., 1979, O.L. Rudakov living cultures CBS 633.92 = ATCC 36786, VKM MF-325 = FMR 14913. USA, from human superficial foot lesion, 2009, D.A. Sutton, living cultures UTHSC DI16-270 = FMR 13761.



Notes: This species was already accommodated by Chen et al. (2015) within Nothophoma, and is characterised by producing globose to suboblate, glabrous, solitary pycnidia and hyaline, aseptate conidia (see Aveskamp et al. 2010). In our study, one human clinical strain isolated in the USA clustered with the reference strain CBS 633.92 of N. quercina. Morphologically it resembles the latter strain, and only a few differences in bp were genetically noted. However, both strains form a well-supported clade and were identified as the same species.



Nothophoma variabilis Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB819624. Fig. 18.



Fig. 18.

Nothophoma variabilis (CBS 142457). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: From Latin variabilis, due to the variable shape of the conidia.



Description: Hyphae pale brown, septate, smooth- and thin-walled, 2.5–6 μm wide. Conidiomata pycnidial, brown, confluent, superficial (OA), glabrous, subglobose, 150–350 × 130–270 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 3–6-layered, 25–35 μm thick, composed of brown to dark brown, flattened polygonal cells of 5–20 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 6 × 5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, ellipsoidal to cylindrical or irregularly shaped, 4–7 × 3–3.5 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 31 mm diam after 7 d at 25 ± 1 °C, flattened, greyish yellow (M. 4B4) to olive brown (M. 4F3); reverse olive brown (M. 4F3). Colonies on MEA reaching 36 mm after 7 d at 25 ± 1 °C, flattened, olive brown (M. 4F3) to greyish yellow (M. 4C5); reverse olive brown (M. 4F3) to brownish grey (M. 4F2). NaOH spot test negative. Crystals absent. Optimal temperature of growth and of sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 35 °C.



Material examined: USA, from human bronchial wash sample, 2009, D.A. Sutton (holotype CBS H-23034, ex-holotype living cultures CBS 142457 = UTHSC DI16-285 = FMR 13777).



Notes: This species was recovered from a clinical specimen of the respiratory tract, and it is closely related to N. anigozanthi. Both species can be differentiated by the presence of a single pycnidial ostiole (vs. 1–4 in N. anigozanthi), absence of a neck and production of wider conidia (3–3.5 μm vs. 1.5–2.5 μm) in N. variabilis. The NaOH spot test was negative, whereas it produces a dull green to vinaceous black pigmentation in N. anigozanthi.



Clade A21: Phoma



Phoma Sacc., Michelia 2: 4. 1880. emend. Q. Chen & L. Cai, Stud. Mycol. 82: 194. 2015.

Synonym: Atradidymella M.L. Davey & Currah, Amer. J. Bot. 96: 1283. 2009.



Type species: Phoma herbarum Westend.



Phoma herbarum Westend., Bull. Acad. Roy. Sci. Belgique, Cl. Sci. 19: 118. 1852. emend. Chen et al., Stud. Mycol. 82: 195. 2015.

Synonyms: Atradidymella muscivora M.L. Davey & Currah, Amer. J. Bot. 96: 1283. 2009.

Phoma muscivora M.L. Davey & Currah, Amer. J. Bot. 96: 1283. 2009.

Phoma cruris-hominis Punith., Nova Hedwigia 31: 135. 1979.



Description: Chen et al. (2015).



Materials examined: The Netherlands, Emmeloord, from the stem of Rosa multiflora cv. Cathayensis, Apr. 1965, G.H. Boerema, living cultures CBS 615.75 = PD 73/665 = IMI 199779 = FMR 15340; Naaldwijk, from a stem base of Nerium sp., 1986, J. de Gruyter, living cultures CBS 502.91 = PD 82/276. UK, from a leg of woman, Apr. 1977, Y.M. Clayton, holotype of “Phoma cruris-hominis” IMI 213845, living cultures CBS 377.92 = IMI 213845. USA, from human urine catheter, 2006, D.A. Sutton, living cultures UTHSC DI16-204 = FMR 13694; from human bronchial wash sample, 2006, D.A. Sutton, living cultures UTHSC DI16-212 = FMR 13702; from human sputum sample, 2011, D.A. Sutton, living cultures UTHSC DI16-306 = FMR 13799; from human bronchial sample, 2011, D.A. Sutton, living cultures UTHSC DI16-307 = FMR 13800; from human nail, 2010, D.A. Sutton, living cultures UTHSC DI16-319 = FMR 13812.



Notes: In this study five strains from human clinical specimens were identified as Phoma herbarum, all of them corresponding in morphology and genetically with the reference strains CBS 377.92, CBS 502.91 and CBS 615.75. This species was already described as an opportunistic human pathogenic fungus by Punithalingam (1979), and this fact is confirmed in our study.



Clade A24: Xenodidymella



Xenodidymella Q Chen et al., Stud. Mycol. 82: 205. 2015.



Type species: Xenodidymella applanata (Niessl) Q. Chen & L. Cai.



Xenodidymella saxea (Aveskamp et al.) Valenzuela-Lopez, Crous, Cano, Guarro & Stchigel, comb. nov. MycoBank MB820831.

Basionym: Phoma saxea Aveskamp et al., Stud. Mycol. 65: 23. 2010.



Description: Aveskamp et al. (2010).



Material examined: Germany, Oldenburg, from corroded Mediterranean marble, June 1992, J. Kuroczkin (holotype CBS H-20240, ex-holotype cultures CBS 419.92 = FMR 15347).



Notes: This species was introduced by Aveskamp et al. (2010) and placed together with “Phoma humicola” (currently Xenodidymella humicola). In our phylogenetic tree, this species was related to the Xenodidymella clade. Despite that this species could represent another genus based on its low phylogenetic support and morphology, more studies are needed to resolve its taxonomic placement in the Didymellaceae. Thus, a new combination is proposed for this species. Morphologically X. saxea is characterised by producing dimorphic conidia: I) aseptate, hyaline, smooth- and thin-walled, (sub-) globose, (3–)3.5–5.5 μm diam, guttulate; and II) aseptate, hyaline, smooth- and thin-walled, cylindrical to ellipsoidal, (3.5–)4.5–7(–7.5) × 2.5–3.5(–4) μm.



Clade A25: Neodidymelliopsis



Neodidymelliopsis Q. Chen et al., Stud. Mycol. 82: 207. 2015.



Type species: Neodidymelliopsis cannabis (G. Winter) Q. Chen & L. Cai.



Neodidymelliopsis longicolla L.W. Hou et al., Stud. Mycol. 87: 153. 2017.



Description: Chen et al. (2017).



Materials examined: Israel, En Avdat, Negev desert, from soil, Feb. 1996, A. van Iperen (holotype CBS H-23016, ex-holotype living culture CBS 382.96). USA, from human bronchial wash sample, 2011, D.A. Sutton, living cultures UTHSC DI16-322 = FMR 13815.



Notes: This species was recently proposed by Chen et al. (2017), and is characterised by producing globose to flask-shaped, glabrous or pycnidia with hyphal outgrowths. The most characteristic features include its elongated neck, the conidia that are initially hyaline and aseptate, but became pale-brown and septate with age. In our study, the strain UTHSC DI16-322 clustered with the ex-type strain of N. longicolla. However, no morphological comparison was possible because our strain remained sterile.



Clade A26: Neoascochyta



Neoascochyta Q. Chen& L. Cai, Stud. Mycol. 82: 198. 2015.



Type species: Neoascochyta exitialis (Morini) Q. Chen & L. Cai, Stud. Mycol. 82: 199. 2015.



Neoascochyta cylindrispora Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB819691. Fig 19.



Fig. 19.

Neoascochyta cylindrispora (CBS 142456). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: From Latin cylindricus-, of cylindrical shape, and -spora, spore, due to the conidial morphology.



Description: Hyphae pale to dark brown, septate, smooth- and thin- to thick-walled, 4–6 μm wide. Conidiomata pycnidial, brown to dark brown, solitary or confluent, superficial on natural substrate (palm leaf), immersed in culture (OA), glabrous, subglobose, 150–300 × 130–160 μm, bearing a single ostiolar neck; pycnidial wall of textura angularis, composed of brown to dark brown, flattened polygonal cells of 4.5–11.5 μm diam, 2–4 layered, 15–60 μm thick,. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform or globose, 5 × 6 μm wide. Conidia 0–1-septate, hyaline, smooth- and thick-walled, mostly cylindrical or slightly allantoid, 11–11.5 × 3.5–4 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 30–34 mm diam after 7 d at 25 ± 1 °C, flattened, with an entire edge, dark green (M. 28F6); reverse dark green (M. 28F6) to greenish grey (M. 28F2). Colonies on MEA reaching 25–28 mm 7 d at 25 ± 1 °C, flattened, with an entire edge, white (M. 2A1) to olive grey (M. 2E2); reverse white (M. 2A1) to dark green (M. 27F3). NaOH spot test negative. Crystals absent. Optimal temperature for sporulation, 15 °C; optimal temperature of growth 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Materials examined: USA, from human corneal secretion, 2013, D.A. Sutton (holotype CBS H-23033, ex-holotype cultures CBS 142456 = UTHSC DI16-359 = FMR 13852); from human eye secretion, 2012, D.A. Sutton, culture UTHSC DI16-352 = FMR 13845.



Notes: Neoascochyta cylindrispora is phylogenetically distinct from N. desmazieri. It differs from the latter also morphologically by its glabrous pycnidia (covered by hyphal outgrowths in N. desmazieri), its smaller conidiogenous cells (5–6 μm wide vs. 7.5–11 μm wide in N. desmazieri) and shorter conidia (11–11.5 μm vs. 8.5–18 μm in N. desmazieri).



Neoascochyta desmazieri (Cavara) Q. Chen & L. Cai, Stud. Mycol. 82: 198. 2015.

Basionym: Ascochyta desmazieri Cavara, Z. Pflanzenkrankh 3: 21. 1893 (as “desmazieresii”).



Description: Chen et al. (2015).



Materials examined: Germany, Hohenlieth, from Lolium perenne, Apr. 1967, U.G. Schlösser (neotype HMAS 246690, ex-neotype living culture CBS 297.69). USA, from human respiratory tract, 2006, D.A. Sutton, living cultures UTHSC DI16-207 = FMR 13697; from unknow source of clinical sample, 2010, D.A. Sutton, living cultures UTHSC DI16-320 = FMR 13813; from human head superficial tissue sample, 2011, D.A. Sutton, living cultures UTHSC DI16-332 = FMR 13825; from human toe nail, 2011, D.A. Sutton, living cultures UTHSC DI16-341 = FMR 13834.



Notes: In this study four strains from human clinical specimens clustered with the ex-type strain of N. desmazieri, and those strains were morphologically and genetically identical with the type, only differing in location and substrate of isolation.



Neoascochyta tardicrescens Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, sp. nov., MycoBank MB819693. Fig 20.



Fig. 20.

Neoascochyta tardicrescens (CBS 689.97). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G, H. Conidiogenous cells. I. Conidia. Scale bars: F = 100 μm. G–I = 10 μm.

Etymology: From Latin tarde-, slowly, and -crescens, growing, in reference to the slow growing colonies.



Description: Hyphae pale to dark brown, septate, smooth- and thin- to thick-walled, 4–6 μm wide. Conidiomata pycnidial, brown to dark brown, solitary, superficial and immersed (OA), glabrous or covered with hyphal outgrows, globose to subglobose, 100–120 × 100–170 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–4 layered, composed of brown to dark brown, flattened polygonal cells of 12.5–25 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 5–10.5 × 5–8.5 μm. Conidia 1-septate, hyaline, smooth- and thick-walled, cylindrical to allantoid, 10–13.5 × 3–4 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 6 mm diam after 7 d at 25 ± 1 °C, flattened, undulate, dark green (M. 27F3); reverse olive brown (M. 4F3) to brownish grey (M. 4F2). Colonies on MEA reaching 7 mm diam after 7 d at 25 ± 1 °C, flattened, undulate, yellowhish grey (M. 2B2); reverse yellowish-brown (M. 5E8) to greenish grey (M. 28F2). NaOH spot test negative. Crystals absent. Optimal temperature for sporulation 15 °C; optimal temperature of growth 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Materials examined: Norway, Oslo, from hay, Apr. 1997, M. Torp (holotype CBS H-9005, ex-holotype living cultures CBS 689.97 = FMR 15352). USA, from human feet, 2010, D.A. Sutton, living cultures UTHSC DI16-291 = FMR 13783.



Notes: The strains CBS 689.97 and UTHSC DI16-291 grow and sporulate better at lower temperatures (around 15 °C) than at room temperature, and clearly differ morphologically from N. argentina in producing smaller conidiomata (100–120 × 100–170 μm vs. 210–390 × 140–270 ìm), in the presence of necks (absent vs. present), in the number of ostioles (1 vs. 1–3), and in their smaller conidiogenous cells (5–10.5 × 5–8.5 μm vs. 7.5–14.5 × 6–13.5 μm). Nonetheless, these strains formed a sister clade to N. argentina.



Clade C: Cucurbitariaceae G. Winter, Rabenhorst's Kryptogamen-Flora, Pilze-Ascomyceten 1.2: 308. 1885.



Type genus: Cucurbitaria Gray, Nat. Arr. Brit. Pl. (London) 1: 519. 1821.



Clade C1: Neocucurbitaria Wanas., E.B.G. Jones & K.D. Hyde, Mycosphere 8: 408. 2017.



Type species: Neocucurbitaria unguis-hominis (Punith. & M.P. English) Wanas. et al.



Neocucurbitaria aquatica Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, sp. nov. MycoBank MB822114.



Etymology: The species name refers to the habitat from which the fungus was recovered (sea water).



Culture sterile. Neocucurbitaria aquatica differs from its phylogenetically closest species N. unguis-hominis, based on the alignment of the concatenated four loci deposited in TreeBASE (S21115): LSU position, 412 (C); ITS positions, 539 (C), 595 (A); tub2 positions, 1121 (G), 1170 (G), 1257 (T); rpb2 positions, 1351 (A), 1387 (T), 1439 (T), 1801 (C), and 1816 (C).



Culture characteristics: Colonies on OA reaching 21–24 mm diam after 7 d at 25 ± 1 °C, flattened, olive (M. 3F4); reverse olive (M. 3F4) to dark grey (M. 3F1). Colonies on MEA reaching 16–17 mm diam after 7 d at 25 ± 1 °C, flattened, yellowish grey (M. 3B2); reverse grey (M. 3B1). NaOH spot test negative. Crystals absent. Optimal temperature of growth 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 35 °C.



Material examined: Montenegro, Kotor bay, from sea water, Oct. 1973, M. Muntañola-Cvetkovic, (holotype CBS H-16102, ex-holotype living culture CBS 297.74 = FMR 14867).



Notes: Neocucurbitaria aquatica was previously identified as “Pyrenochaeta quercina” based on LSU and SSU loci sequencing (de Gruyter et al. 2010). However, in our phylogenetic analysis using four loci, N. aquatica was closely related to Neocucurbitaria unguis-hominis. As N. aquatica was recovered from sea water, and is phylogenetically unrelated to the ex-type strain of Neocucurbitaria quercina (CBS 115095), we propose it as a new species.



Neocucurbitaria cava (Schulzer) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, comb. nov. MycoBank MB821491. Fig. 21.

Fig. 21.

Neocucurbitaria cava (CBS 257.68). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiophores. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Basionym: Phoma cava Schulzer, Verh. Zool.-bot. Ges. Wien 21:1248. 1871.

Synonyms: Aposphaeria cava (Schulzer) Sacc. & Schulzer, Syll. fung. (Abellini) 3: 174. 1884.

Coniothyrium cavum (Schulzer) Kuntze, Revis. gen. pl. (Leipzig) 3(2): 459. 1898.

Pleurophoma cava (Schulzer) Boerema et al., Persoonia 16: 172. 1996.

Pyrenochaeta cava (Schulzer) Gruyter et al., Mycologia 102: 1076. 2010.



Description from ex-epitype culture (CBS 257.68): Hyphae hyaline to brown, smooth- and thin-walled, septate, 2.5–3.5 μm wide. Conidiomata pycnidial, brown, solitary or confluent, semi-immersed or immersed (OA), glabrous, subglobose, 140–200 × 100–140 μm, with one ostiolar neck; pycnidial wall of textura angularis, composed of brown, flattened polygonal cells of 2.5–5 μm diam. Conidiophores hyaline, smooth-walled, straight or sinuous to slightly curved, slightly tapering towards the apex, branched at the base, 10–22 × 1.5–2.5 μm. Conidiogenous cells integrated to the conidiophore, phialidic, hyaline, smooth-walled, doliiform, with a more or less cylindrical collarette, up to 3 per conidiophore. Conidia aseptate, hyaline, smooth- and thin-walled, mostly cylindrical to slightly allantoid, 2.5–3.5 × 1–1.5 μm, guttulate.



Culture characteristics: Colonies on OA reaching 16 mm diam after 7 d at 25 ± 1 °C, flattened, olive (M. 3F4); reverse dark grey (M. 3F1). Colonies on MEA reaching 14 mm after 7 d at 25 ± 1 °C, flattened, yellowish grey (M. 3B2); reverse olive brown (M. 4E4). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 35 °C.



Materials examined: Germany, Kiel-Kitzeberg, from wheat field soil, 1965, W. Gams (epitype CBS H-20320, ex-epitype living cultures CBS 257.68 = IMI 331911 = FMR 15747). Italy, on branch of Quercus cerris, M. Farras, living cultures CBS 115953 = FMR 15333.



Notes: Pyrenochaeta cava was epitypified by de Gruyter et al. (2010). In our phylogenetic analysis this species clustered in Neocucurbitaria, a genus recently introduced by Wanasinghe et al. (2017b). Therefore, we propose the new combination N. cava.



Neocucurbitaria hakeae (Crous) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, comb. nov. MycoBank MB821492.

Basionym: Pyrenochaeta hakeae Crous, Persoonia 37: 353. 2016.



Description: Crous et al. (2016a).



Material examined: Australia, Western Australia, Denmark, Lights Beach, on leaves of Hakea sp., 19 Sep. 2015, P.W. Crous (holotype CBS H-22894, ex-holotype living cultures CBS 142109 = CPC 28920).



Notes: In our phylogenetic tree, this species forms a sister clade to N. cava. Therefore, we propose a new combination to accommodate this species in the genus Neocucurbitaria. Morphologically, N. hakeae resembles N. unguis-hominis, but the former species is the only species of the genus that produces pale brown conidiophores.



Neocucurbitaria irregularis Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB819769. Fig. 22.



Fig. 22.

Neocucurbitaria irregularis (CBS 142791). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Etymology: From Latin irregularis, irregular, referring to the shape of its conidia.



Description: Hyphae brown, smooth- and thin-walled, septate, 2–5 μm wide. Conidiomata pycnidial, brown, solitary or confluent, superficial (OA), glabrous, subglobose to ovoid, 75–130 × 65–120 μm, with 3–4 papillate ostiolar necks, pycnidial wall of textura angularis, 2–5 layered, 10–35 μm thick, composed of brown, flattened polygonal cells of 3–12 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, doliiform, 2.5 × 3.5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, ellipsoidal to cylindrical, 2.5–4 × 1.5–2. μm, guttulate.



Culture characteristics: Colonies on OA reaching 17–18 mm diam after 7 d at 25 ± 1 °C, flattened, olive brown (M. 4F6); reverse brownish grey (M. 4F2). Colonies on MEA reaching 11 mm after 7 d at 25 ± 1 °C, flattened, pale yellow (M. 4A3); reverse pale yellow (M. 4A4) to greyish yellow (M. 4C6). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 35 °C.



Material examined: USA, from human arm injury, 2000, D.A. Sutton (holotype CBS H-23029, ex-holotype living cultures CBS 142791 = UTHSC DI16-229 = FMR 13719).



Notes: Neocucurbitaria irregularis is proposed to accommodate a clinical isolate previously identified as “Pyrenochaeta unguis-hominis” (Valenzuela-Lopez et al. 2016). This isolate forms a basal clade together with N. keratinophila and N. unguis-hominis. However, it is morphologically well-differentiated from the latter two species, by having small, simple conidiogenous cells instead of filiform conidiophores.



Neocucurbitaria keratinophila (Verkley et al.) Valenzuela-Lopez, Stchigel, Guarro & Cano, comb. nov. MycoBank MB821494.

Basionym: Pyrenochaeta keratinophila Verkley et al., Revta Iberoamer. Micol. 27: 24. 2010.



Description: Verkley et al. (2010).



Material examined: Spain, Alicante, from human corneal scrapings (keratitis), Mar. 2007, A. Rodriguez & J. Guarro (holotype CBS H-20122, ex-holotype living CBS 121759 = FMR 9444).



Notes: This species described by Verkley et al. (2010) was isolated from a human corneal specimen with a case of keratitis. Morphologically it resembles Pyrenochaeta. However, in our phylogenetic analyses this species clustered close to N. irregularis. Therefore, we propose a new combination for this fungus in Neocucurbitaria.



Neocucurbitaria quercina (Kabát & Bubák) Wanas. et al., Mycosphere 8: 412. 2017. Fig. 23.

Fig. 23.

Neocucurbitaria quercina (CBS 115095). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Setae. H. Conidiophores. I. Conidia. Scale bars: F = 50 μm. G–I = 10 μm.

Basionym: Pyrenochaeta quercina Kabát & Bubák, Hedwigia 52: 342. 1912.



Description taken from Bubák & Kabát (1912), which is based on the holotype: Conidiomata pycnidial dark brown, solitary or confluent, setose, globose, 150–220 μm diam. Setae dark brown, tapered towards the apex, erect or decumbent, smooth- and thick-walled, up to 65 μm long, 5 μm broad at the base. Conidiophores cylindrical, tapered toward the apex, erect or slightly curved, hyaline, 25 × 3–3.5 μm. Conidia aseptate, hyaline, bacilliform, 2–3 × 1.5 μm.



Description from the ex-neotype culture (CBS 115095): Hyphae brown, smooth- and thin-walled, septate, 2.5–5 μm wide. Conidiomata pycnidial brown, solitary or confluent, superficial (OA), mostly glabrous or covered with somewhat shortest setae, globose, 70–90 μm diam, 100–230 × 90–130 μm when ovoid, with 1–2 papillate ostiolar necks; pycnidial wall of textura angularis, composed of brown, flattened polygonal cells of 3–12 μm diam; setae brown, erect, rounded at the top, septate, thin-walled, 7–10 × 2.5–3.5 μm,. Conidiophores hyaline, smooth-walled, straight or sinuous to slightly curved, slightly tapering towards the apex, branched at the base, 6.5–14 × 2–3 μm. Conidiogenous cells terminal and lateral on the conidiophore, phialidic, hyaline, smooth-walled, ampulliform when terminal, with a more or less cylindrical collarette, up to 4 per conidiophore. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid to cylindrical, 1.5–3 × 1.2–1.5 μm, guttulate.



Culture characteristics: Colonies on OA reaching 21 mm diam after 7 d at 25 ± 1 °C, flattened, olive (M. 3F4); reverse dark grey (M. 3F1). Colonies on MEA reaching 12 mm after 7 d at 25 ± 1 °C, flattened, olive (M. 3F4) to pale grey (M. 3B1); reverse dark grey (M. 3F1). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 15 °C; maximum temperature of growth 35 °C.



Material examined: Italy, from Quercus robur, Nov 1971, S. Mutto Accordi (neotype designated here CBS H-23205, MBT377969, ex-neotype living cultures CBS 115095 = FMR 14868).



Notes: Bubák & Kabát (1912) described Pyrenochaeta quercina from Quercus cerris leaves, in Bukovina forest, Moldavia. The holotype is apparently missing. We studied the isolate CBS 115095, identified previously as P. quercina by de Gruyter et al. (2010), which has been recovered from Quercus robur in Italy. Recently, Wanasinghe et al. (2017b) transferred P. quercina to Neocucurbitaria. In our phylogenetic tree this strain clustered with N. cava and N. hakeae, confirming the right placement into Neocucurbitaria. Because the strain CBS 115095 was isolated from a related host to that of the basionym (both are different species of oaks), we designated this strain as the neotype for Pyrenochaeta quercina, in order to stabilize the taxonomy of the species.



Neocucurbitaria unguis-hominis (Punith. & M.P. English) Wanas. et al., Mycosphere 8: 412. 2017. Fig. 24.

Fig. 24.

Neocucurbitaria unguis-hominis (CBS 112.79). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G, H. Conidiophores. I. Conidia. Scale bars: F = 50 μm. G–I = 10 μm.

Basionym: Pyrenochaeta unguis-hominis Punith. & M.P. English, Trans. Br. mycol. Soc. 64: 539. 1975.



Description: Punithalingam & English (1975).



Materials examined: The Netherlands, Utrecht, from lung sample of Agapornis sp., C. Hoek, living cultures CBS 111112 = FMR 14866. USA, unknown substrate, 2006, D.A. Sutton, living cultures UTHSC DI16-213 = FMR 13703. Wales, Cardiff, from air sample, Apr. 1974, G.H. Boerema, living cultures CBS 112.79 = IMI 386095 = PD 74/1018 = FMR 15748.



Notes: Pyrenochaeta unguis-hominis was established by Punithalingam & English (1975) for a fungus recovered from a human toe-nail. Later, Wanasinghe et al. (2017b) considered this the type species of Neocucurbitaria. Interestingly, the three strains studied by us were able to grow and sporulate at 37 °C, being the only species of the genus that displays such abilities.



Clade C2: Paracucurbitaria



Paracucurbitaria Valenzuela-Lopez, Stchigel, Guarro & Cano, gen. nov. MycoBank MB821453.



Etymology: From Greek παρα-, beside, referring to the morphological similarity with the asexual morph of Cucurbitaria.



Conidiomata pycnidial, pale brown to brown, solitary or confluent, superficial or semi-immersed, pycnidial wall of textura angularis, 2–4 layered, glabrous or ornamented, subglobose to ovoid, ostiolate. Conidiophores if present, septate, hyaline, straight or sinuous to slightly curved, slightly tapering towards the apex. Conidiogenous cells integrated in the conidiophore, phialidic, hyaline, smooth-walled, ampulliform when terminal, with a more or less cylindrical collarette, several per conidiophore. Conidia aseptate, hyaline, smooth- and thin-walled, ellipsoidal to cylindrical, guttulate.



Type species: Paracucurbitaria corni (Bat. & A.F. Vital) Valenzuela-Lopez, Stchigel, Guarro & Cano.



Paracucurbitaria corni (Bat. & A.F. Vital) Valenzuela-Lopez, Stchigel, Guarro & Cano, comb. nov. MycoBank MB821454. Fig. 25.

Fig. 25.

Paracucurbitaria corni (CBS 248.79). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium G. Conidiophores. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Basionym: Plenodomus corni Bat. & A.F. Vital, Anais Soc. Biol. Pernambuco 15: 420. 1957.

Synonyms: Phoma riggenbachii Boerema & J.D. Janse, Eur. J. For. Path. 11: 428. 1981.

Pyrenochaeta corni (Bat. & A.F. Vital) Boerema, Loer. & Hamers, Persoonia 16: 158. 1996.



Description from reference strain (CBS 248.79): Hyphae hyaline to pale brown, smooth- and thin-walled, septate, 2.5–4 μm wide. Conidiomata pycnidial, pale brown to brown, solitary or confluent, superficial or semi-immersed (OA), glabrous, globose to subglobose, 110–210 × 110–190 μm diam, with 2–5 ostiolar necks; pycnidial wall of textura angularis, initially pseudoparenchymatous, scleroplectenchymatous with the age (mainly on MEA), 3–4 layered, 15–30 μm thick, composed of brown to dark brown, flattened polygonal cells of 3–6 μm diam. Conidiophores branched at the base, septate, hyaline, straight or sinuous to slightly curved, slightly tapering towards the apex, 6.5–18 μm long. Conidiogenous cells integrated in the conidiophore, phialidic, hyaline, smooth-walled, doliiform or ampulliform, 3.5–7.5 × 1.3–3.5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, mostly cylindrical or rarely ovoid, 1.8–4 × 1.2–1.6 μm, guttulate.



Culture characteristics: Colonies on OA reaching 14 mm diam after 7 d at 25 ± 1 °C, flattened, olive (M. 2E6); reverse olive (M. 2E6) to dark grey (M. 2F1). Colonies on MEA reaching 10 mm after 7 d at 25 ± 1 °C, flattened, olive brown (M. 4D6) to dark grey (M. 4F1); reverse olive brown (M. 4D6) to dark grey (M. 4F1). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined The Netherlands, Scheerwolde, from Fraxinus excelsior with bacterial canker (also from Prays fraxinella), 1978, deposited by G. H. Boerema, living cultures CBS 248.79 = PD 78/1092 = FMR 16593.



Notes: Plenodomus corni was erected by Batista & Vital (1957) as a new species on branches of Cornus sanguinea from Hungary, and it was characterised by producing brown to black, solitary or clustered, mostly immersed, glabrous, globose to subglobose, pycnidial conidiomata of 115–135 μm diam, with a pseudoparenchymatous wall 12.5–20 μm thick, composed of polygonal to subglobose cells of 2.5–4 μm diam, with phialidic, hyaline, filiform or flask-shaped conidiogenous cells, 3.5–6 × 1–2 μm, and hyaline, bacilliform, 1.5–3 × 1 μm conidia. Later, Janse (1981) isolated a similar fungus from Fraxinus excelsior with a bacterial canker, and also from dead, discoloured tissue surrounding galleries and holes of Prays fraxinella (ash bud moth). This fungus (living culture CBS 248.79) was considered by Boerema et al. (1981) as the same taxon as Plenodomus corni. However, a new name was necessary to transfer Plenodomus corni to the genus Phoma because the species name was occupied (Phoma corni Fuckel ex Sacc.). The strain CBS 248.79 was characterised by the production of pycnidial conidiomata with a scleroplectenchymatous wall, variable in size and in shape, 100–200 μm diam, and of aseptate conidia (measuring 2.1–2.6 × 0.8–1.2 μm), produced on elongated conidiogenous cells. However, CBS 248.79 shows some morphological variation depending of the culture media employed: on MEA it shows a scleroplectenchymatous wall as given in the original description by Janse, but on OA it resembles the description given by Batista & Vital (1957), but it does not produce setose pycnidia as mentioned by Boerema et al. (1996). The strain CBS 248.79 forms a distinct monophyletic clade within the Cucurbitariaceae. Therefore, we propose the new combination, Paracucurbitaria corni.



Paracucurbitaria italica Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, sp. nov. MycoBank MB822116. Fig. 26.



Fig. 26.

Paracucurbitaria italica (CBS 234.92). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiophores. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Etymology: The name of the species refers to the country of origin of the fungus, Italy.



Description: Hyphae hyaline to pale brown, smooth- and thin-walled, septate, 2.5–4 μm wide. Conidiomata pycnidial, brown, solitary or confluent, superficial or semi-immersed (OA), covered by hyphal outgrowths, subglobose to ovoid, 190–240 × 170–190 μm diam, with 1–2 ostiolar necks; pycnidial wall of textura angularis, 2–4 layered, 10–15 μm thick, composed of brown to dark brown, flattened polygonal cells of 5–13 μm diam. Conidiophores septate, hyaline, straight or sinuous to slightly curved, slightly tapering towards the apex, 15–20 μm long. Conidiogenous cells phialidic, hyaline, smooth-walled, filiform or flask-shaped, 4–9 × 2–3.5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, ellipsoidal to cylindrical, 2.5–3 × 1–1.5 μm, guttulate.



Culture characteristics: Colonies on OA reaching 13 mm diam after 7 d at 25 ± 1 °C, flattened, olive (M. 2E6); reverse olive (M. 2E6) to dark grey (M. 2F1). Colonies on MEA reaching 11 mm after 7 d at 25 ± 1 °C, flattened, white (M. 2A1); reverse white (M. 2A1). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: Italy, Rende, from Olea europaea leaves, 26 Feb. 1992, C. Candiano (holotype CBS H-16104, ex-holotype living cultures CBS 234.92 = FMR 14869).



Notes: The strain CBS 234.92 was previously identified as “Pyrenochaeta corni” by de Gruyter et al. (2010). However, this strain is phylogenetically distinct from its closest relative, Paracucurbitaria corni, and differs morphologically by the production of ornamented conidiomata (covered with hyphal outgrowths vs. glabrous). Consequently, we propose CBS 234.92 as the ex-type strain of Paracucurbitaria italica sp. nov.



Clade C3: Allocucurbitaria



Allocucurbitaria Valenzuela-Lopez, Stchigel, Guarro & Cano, gen. nov. MycoBank MB821455.



Etymology: From Greek àλλο-, different, due to is related but phylogenetically and morphologically different to the genus Cucurbitaria.



Conidiomata pycnidial, brown, solitary or confluent, superficial, pycnidial wall of textura angularis, glabrous, subglobose to ovoid, ostiolate. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical to allantoid, guttulate.



Type species: Allocucurbitaria botulispora Valenzuela-Lopez, Stchigel, Guarro & Cano.



Allocucurbitaria botulispora Valenzuela-Lopez, Stchigel, Guarro & Cano, sp. nov. MycoBank MB819770. Fig. 27.



Fig. 27.

Allocucurbitaria botulispora (CBS 142452). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiophores. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Etymology: From Latin botulus-, sausage, and -spora, spores, due to the shape of the conidia.



Description: Hyphae pale brown, smooth- and thin-walled, septate, 1.5–2.5 μm wide. Conidiomata pycnidial, brown, confluent, superficial (OA), glabrous, subglobose to ovoid, 60–160 × 60–120 μm diam, with 1–2 papillate ostiolar necks; pycnidial wall of textura angularis, 2–4 layered, 10–30 μm thick, composed of pale brown to brown, flattened polygonal cells of 3–10 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 5–8 × 2–2.5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical to allantoid, 3–5 × 1–1.5 μm, guttulate.



Culture characteristics: Colonies on OA reaching 26–29 mm diam after 7 d at 25 ± 1 °C, flattened, greyish yellow (M. 4C6); reverse olive brown (M. 4D5). Colonies on MEA reaching 22 mm after 7 d at 25 ± 1 °C, slightly floccose, yellowish white (M. 4A2); reverse pale orange (M. 5A3) to deep orange (M. 5A8). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 15 °C; maximum temperature of growth 37 °C.



Material examined: USA, from human scab on leg, 2009, D.A. Sutton (holotype CBS H-23028, ex-holotype living cultures CBS 142452 = UTHSC DI16-273 = FMR 13764).



Notes: The strain CBS 142452 (= UTHSC DI16-273) was originally assigned to Pyrenochaeta (Valenzuela-Lopez et al. 2016). Morphologically, this strain displays a morphology more similar to phoma-like taxa (with glabrous pycnidia) than to species of Pyrenochaeta (because of its setose conidiomata). In our phylogenetic analysis, this fungus was placed in an uncertain taxonomic position within Cucurbitariaceae. Therefore, we proposed to accommodate CBS 142452 as a new species of the new genus Allocucurbitaria.



Clade D: Pseudopyrenochaetaceae Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, fam. nov. MycoBank MB820426.



Etymology: From Latin pseudo-, resembling but not equalling, because the morphological similarity to Pyrenochaeta.



Conidiomata pycnidial, brown to dark brown, solitary, setose, globose to subglobose, papillate, ostiolate. Conidiophores simple, filiform, septate. Conidiogenous cells phialidic, intercalary, disposed along the conidiophores as short side projections. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical to allantoid.



Type genus: Pseudopyrenochaeta Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano.



Pseudopyrenochaeta Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, gen. nov. MycoBank MB820427.



Etymology: The name refers to the morphological similarity with the genus Pyrenochaeta.



Conidiomata pycnidial, brown to dark brown, solitary, setose, globose to subglobose, with a papillate ostiolar neck. Conidiophores hyaline, simple, filiform, septate. Conidiogenous cells phialidic, hyaline, intercalary along the conidiophore, arising as very short lateral projections immediately below the transverse septa. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical to allantoid.



Type species: Pseudopyrenochaeta lycopersici (R.W. Schneid. & Gerlach) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano.



Pseudopyrenochaeta lycopersici (R.W. Schneid. & Gerlach) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, comb. nov. MycoBank MB820431.

Basionym: Pyrenochaeta lycopersici R.W. Schneid. & Gerlach, Phytopath. Z. 56: 121. 1966.



Description: Schneider & Gerlach (1966).



Material examined: Germany, Berlin, from Lycopersicon esculentum root, Nov. 1971, R. Schneider & G.H. Boerema (isotype CBS H-17628, ex-isotype culture CBS 306.65 = FMR 15746 = BBA 9911 = DSM 62931).



Notes: In previous studies, the ex-isotype strain of Pyrenochaeta lycopersici (CBS 306.65) was phylogenetically located in the Cucurbitariaceae (de Gruyter et al. 2010, Wanasinghe et al. 2017b). However, de Gruyter et al. (2013) placed it as incertae sedis. According to our results, P. lycopersici falls phylogenetically outside the family Cucurbitariaceae and represents a new genus, Pseudopyrenochaeta, in the new family, Pseudopyrenochaetaceae.



Pseudopyrenochaeta terrestris Valenzuela-Lopez, Crous, Cano, Guarro & Stchigel, sp. nov. MycoBank MB822117.



Etymology: The species name refers to soil, the substrate from which the fungus was recovered.



Culture sterile. Pseudopyrenochaeta terrestris differs from its closest phylogenetic species, P. lycopersici, based on the alignment of the concatenated four loci deposited in TreeBASE (S21115), by six bp of LSU, 20 bp of ITS, 16 bp of tub2, and 47 bp of rpb2.



Culture characteristics: Colonies on OA reaching 22 mm diam after 7 d at 25 ± 1 °C, flattened, olive grey (M. 3E3); reverse olive grey (M. 3E3) to dark grey (M. 3F1). Colonies on MEA reaching 11 mm after 7 d at 25 ± 1 °C, slightly flattened, white (M. 3A1); reverse yellowish grey (M. 3C2). NaOH spot test negative. Crystals absent.



Material examined: The Netherlands, Naaldwijk, from greenhouse soil, Feb. 1972, L.H. Kaastra-Höweler (holotype FMR H-15327, ex-holotype living cultures CBS 282.72 = FMR 15327).



Notes: The strain CBS 282.72, deposited as “Pyrenochaeta lycopersici”, clustered with the ex-type strain of Pseudopyrenochaeta lycopersici. However, both strains differ significantly in all nucleotide sequences of the phylogenetic markers used in the present study. Therefore, strain CBS 282.72 is proposed here as the new species Pseudopyrenochaeta terrestris.



Clade E: Neopyrenochaetaceae Valenzuela-Lopez, Crous, Cano, Guarro & Stchigel, fam. nov. MycoBank MB820416.



Etymology: Relating to the distinct phenotypic and genetic relationship to the genus Pyrenochaeta and its relatives.



Conidiomata pycnidial, pale brown to brown, solitary, pycnidial wall of textura angularis, setose, ovoid to globose, with a non-papillate or papillate ostiolar neck. Conidiogenous cells phialidic, ampulliform or lageniform. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid to subcylindrical.



Type genus: Neopyrenochaeta Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano.



Neopyrenochaeta Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, gen. nov. MycoBank MB820313.



Etymology: Referring to its morphological similarity to the genus Pyrenochaeta.



Conidiomata pycnidial, pale brown to brown, solitary, pycnidial wall of textura angularis, setose, ovoid to globose, ostiolate. Conidiogenous cells phialidic, ampulliform or lageniform. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid to subcylindrical.



Type species: Neopyrenochaeta acicola (Moug. & Lév.) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano.



Neopyrenochaeta acicola (Moug. & Lév.) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, comb. nov. MycoBank MB820314. Fig. 28.

Fig. 28.

Neopyrenochaeta acicola (CBS 812.95). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G, H. Conidiogenous cells. I. Conidia. Scale bars: F = 50 μm. G–I = 10 μm.

Basionym: Vermicularia acicola Moug. & Lév. apud Léveillé, Annls Sci. nat. (Bot.) III, 9:259. 1848 (as “Moug. Lév.”; non Phoma acicola sensu Saccardo), Syll. Fung. 3:100. 1884 [as “(Lév.) Sacc.”; = Sclerophoma pythiophila (Corda) Höhn.].

Synonym: Phoma leveillei var. leveillei Boerema & G.J. Bollen, Persoonia 8: 115. 1975.



Description and synonymy: Boerema et al. (2004).



Material examined: The Netherlands, from water pipe sample, 1995, Y. Driessen (neotype CBS H-20314, ex-neotype living cultures CBS 812.95 = FMR 14872).



Notes: Pyrenochaeta acicola was neotypified and relegated to the Cucurbitariaceae by de Gruyter et al. (2010). Although Neopyrenochaeta acicola morphologically resembles a Pyrenochaeta species, our phylogenetic analyses revealed that this taxon is distant from the type species of Pyrenochaeta, P. nobilis, and therefore we proposed the new genus Neopyrenochaeta for this and a few related species.



Neopyrenochaeta fragariae Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, sp. nov. MycoBank MB820316. Fig. 29.



Fig. 29.

Neopyrenochaeta fragariae (CBS 101634). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: Relating to the host from the fungus was isolated, Fragaria (strawberry).



Description: Hyphae pale brown, smooth- and thin-walled, septate, 2.5–3 μm wide. Conidiomata pycnidial, pale brown to brown, solitary, superficial (OA), ovoid to globose, 170–220 × 160–210 μm, covered with brown to dark brown, septate, erect, smooth- and thick-walled setae tapering towards the apex, 110–120 × 2.5–5.5 μm, mainly disposed around the ostiole, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–5 layered, 20–60 μm thick, composed of brown, flattened polygonal cells of 5–15 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 4.5–7 × 3.5–4 μm. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid to ellipsoidal, 3.5–5 × 2–3 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 14 mm diam after 7 d at 25 ± 1 °C, flattened, olive brown (M. 4E8); reverse olive brown (M. 4F2). Colonies on MEA reaching 11 mm after 7 d at 25 ± 1 °C, flattened, yellowish-brown (M. 5F4); reverse yellowish brown (M. 5E4). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: The Netherlands, Arnhem, from Fragaria sp., 1976, M.M.J. Dorenbosch (holotype CBS H-23206, ex-holotype living cultures CBS 101634 = PD 76/416 = FMR 14871).



Notes: The strain CBS 101634 was previously named Pyrenochaeta acicola. Although it is morphologically similar to the latter mentioned species (now in Neopyrenochaeta), these fungi differ in 23 and 11 nucleotides for rpb2 and tub2, respectively. Therefore, a new species name is proposed for CBS 101634.



Neopyrenochaeta inflorescentiae (Crous et al.) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, comb. nov. MycoBank MB820317.

Basionym: Pyrenochaeta inflorescentiae Crous et al., CBS Diversity Ser. (Utrecht) 7: 115. 2008.



Description: Marincowitz et al. (2008).



Material examined: South Africa, Western Cape Province, from Protea neriifolia, 6 Jun. 2000, S. Marincowitz (holotype PREM 58657, ex-holotype living cultures CBS 119222 = CPC 13163 = FMR 15334).



Notes: In our phylogenetic analysis, the ex-type strain of Pyrenochaeta inflorescentiae (CBS 119222) clustered with N. acicola and N. fragariae in a terminal clade distant from the type species of the genus Pyrenochaeta, P. nobilis, and outside the family Cucurbitariaceae, where that fungus was previously placed. For that reason, we accommodate P. inflorescentiae in the new genus Neopyrenochaeta (Neopyrenochaetaceae).



Neopyrenochaeta telephoni (Rohit Sharma et al.) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, comb. nov. MycoBank MB820318.

Basionym: Pyrenochaeta telephoni Rohit Sharma et al., Persoonia 35: 321. 2015.



Description: Crous et al. (2015b).



Material examined: India, Maharashtra, Pune, from screen of mobile phone, 2013, R. Kurli & P. Rahi (holotype MCC H1001, ex-holotype living cultures MCC 1159 = CBS 119222 = FMR 15754).



Notes: Recently, Sharma et al. (in Crous et al. 2015b) proposed the new species Pyrenochaeta telephoni, recovered from a mobile phone. Morphologically, it resembles other species of Pyrenochaeta; however, in our phylogenetic analysis this fungus forms a basal terminal clade in Neopyrenochaeta, which is distant from Cucurbitariaceae s. str.



Clade F: Pyrenochaetopsidaceae Valenzuela-Lopez, Crous, Cano, Guarro & Stchigel, fam. nov. MycoBank MB820308.



Conidiomata pycnidial, pale brown to brown, solitary or confluent; pycnidial wall of textura angularis, glabrous or setose, subglobose to ovoid, with a non-papillate or papillate ostiolar neck. Conidiogenous cells phialidic, hyaline, discrete or integrated in septate, acropleurogenous conidiophores. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid, cylindrical to allantoid, guttulate.



Type genus: Pyrenochaetopsis Gruyter, Aveskamp & Verkley.



Clade F1: Pyrenochaetopsis



Pyrenochaetopsis Gruyter, Aveskamp & Verkley, Mycologia 102: 1076. 2010.



Conidiomata pycnidial, honey to citrine or olivaceous to olivaceous black, solitary to confluent, superficial or submerged, with a non-papillate or papillate ostiolar neck; pycnidial wall pseudoparenchymatous, setose, globose to subglobose. Conidiogenous cells phialidic, hyaline, discrete and integrated in septate, acropleurogenous conidiophores. Conidia aseptate, cylindrical to allantoid, guttulate (de Gruyter et al. 2010).



Type species: Pyrenochaetopsis leptospora (Sacc. & Briard) Gruyter et al.



Pyrenochaetopsis americana Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB822115.



Etymology: The species name denotes the geographic area where the fungus is from.



Culture sterile. Pyrenochaetopsis americana differs from its closest phylogenetic species, Pyrenochaetopsis uberiformis, in five nucleotides for ITS, 19 for tub2 and 34 for rpb2, based on alignment of the concatenated four loci deposited in TreeBASE (S21115).



Culture characteristics: Colonies on OA reaching 30 mm diam after 7 d at 25 ± 1 °C, flattened, dark olive (M. 3F3); reverse olive grey (M. 3D2). Colonies on MEA reaching 19 mm diam after 7 d at 25 ± 1 °C, flattened, olive grey (M. 3D2) to white (M. 3A1); reverse white (M. 3A1). NaOH spot test negative. Crystals absent.



Material examined: USA, substrate unknown, 2007, D.A. Sutton (holotype FMR H-13715, ex-holotype living cultures UTHSC DI16-225 = FMR 13715).



Notes: The strain UTHSC DI16-225, which remained sterile in all culture media tested in this study, forms an unsupported sister clade with P. uberiformis, from which it is phylogenetically distant. Therefore, UTHSC DI16-225 is proposed here as a new species different from P. uberiformis.



Pyrenochaetopsis botulispora Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB819764. Fig. 30.



Fig. 30.

Pyrenochaetopsis botulispora (CBS 142458). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: From Latin botulus-, sausage, and -spora, spore, relating to the morphology of the conidia.



Description: Hyphae brown, smooth- and thin-walled, septate, 2–7 μm wide. Conidiomata pycnidial, brown, solitary or confluent, superficial (OA), glabrous, subglobose or globose, 140–190 × 130–160 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–3 layered, 15–35 μm thick, composed of brown, flattened polygonal cells of 5–8 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, subglobose, ca. 4 × 5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical, 4.5–6 × 2–2.5 μm, guttulate.



Culture characteristics: Colonies on OA reaching 25–30 mm diam after 7 d at 25 ± 1 °C, flattened, with abundant production of pycnidia, yellowish brown (M. 5E8); reverse yellowish-brown (M. 5F6). Colonies on MEA reaching 30 mm diam after 7 d at 25 ± 1 °C, flattened, orange grey (M. 5B2) to brownish orange (M. 5C5); reverse yellowish brown (M. 5E7) to greyish orange (M. 5B5). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 15 °C; maximum temperature of growth 30 °C.



Material examined: USA, from human sputum sample, 2011, D.A. Sutton (holotype CBS H-23035, ex-holotype living cultures CBS 142458 = UTHSC DI16-298 = FMR 13791); from human bronchial wash sample, 2010, D.A. Sutton, living culture UTHSC DI16-289 = FMR 13781; from human foot skin, 2011, D.A. Sutton, living culture UTHSC DI16-297 = FMR 13790.



Notes: Pyrenochaetopsis botulispora is proposed to accommodate three isolates from clinical specimens, which form a sister clade to P. paucisetosa, being well differentiated phylogenetically from their closest relatives. Morphologically, P. botulispora is characterised by producing glabrous pycnidia, which are setose in P. paucisetosa, and by its slightly longer conidia (4.5–6 × 2–2.5 μm vs. 3–4 × 2–2.5 μm in in P. paucisetosa).



Pyrenochaetopsis confluens Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB819763. Fig. 31.



Fig. 31.

Pyrenochaetopsis confluens (CBS 142459). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Etymology: From Latin confluens, confluent, due to the production of tightly aggregated conidiomata.



Description: Hyphae pale brown, smooth- and thin-walled, septate, 2–5 μm wide. Conidiomata pycnidial, pale brown, translucent, aggregated, immersed (MEA), subglobose or globose, 80–140 × 70–90 μm, with 1–2 papillate ostiolar necks, covered by brown setae around the ostiole; setae erect, smooth- and thick- walled, septate, 15–22.5(–35) × 2.5–4.5 μm; pycnidial wall of textura angularis, 2–3 layered, 13–20 μm thick, composed of brown, flattened polygonal cells of 5–8 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, subglobose, 4.5–7.5 × 6.5–7.5 μm. Conidia aseptate, hyaline, aseptate, smooth- and thin-walled, guttulate, ovoid to cylindrical, 2–4 × 2–2.5 μm.



Culture characteristics: Colonies on OA reaching 15 mm diam after 7 d at 25 ± 1 °C, flattened, white (M. 4A1) to olive brown (M. 4E4); reverse olive brown (M. 4F3). Colonies on MEA reaching 10 mm diam after 7 d at 25 ± 1 °C, flattened, white (M. 4A1) to brownish-grey (M. 4F2); reverse brownish-grey (M. 4F2). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: USA, from human blood sample, 2011, D.A. Sutton (holotype CBS H-23036, ex-holotype living cultures CBS 142459 = UTHSC DI16-303 = FMR = 13796).



Notes: The strain CBS 142459 forms a distinct clade phylogenetically distant from P. decipiens and P. indica. This new species grows slowly on all culture media tested and produces aggregated conidiomata.



Pyrenochaetopsis decipiens (Marchal) Gruyter et al., Mycologia 102: 1077. 2010.

Basionym: Pyrenochaeta decipiens Marchal, Bull. Soc. Roy. Bot. Belg. 30:139. 1891.

Synonym: Phoma terricola Boerema, Versl. Meded. plziektenk. Dienst Wageningen 163 (Jaarb. 1984): 38. 1985.



Material examined: The Netherlands, Hoofddorp, on cyst of Globodera pallida, May 1985, D. Hugo, No. 727 (neotype CBS H-20315, ex-neotype living cultures CBS 343.85 = IMI 386097 = FMR 14880).



Notes: In this study, newer genomic sequences data from the ex-type strain of Pyrenochaetopsis decipiens are provided. Unfortunately, we have not been able to induce this fungus to sporulate.



Pyrenochaetopsis globosa Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB821496. Fig. 32.



Fig. 32.

Pyrenochaetopsis globosa (CBS 143034). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Etymology: From Latin globosus, globose, due to the production of globose conidiomata.



Description: Hyphae hyaline to pale brown, smooth- and thin-walled, septate, 2–4 μm wide. Conidiomata pycnidial, pale olivaceus-brown to brown, solitary or aggregated, semi-immersed or immersed, mainly globose (70–200 μm diam), sometimes ovoid (150–220 × 140–190 μm), glabrous or covered by hyphal outgrowths, with 1–2 papillate ostiolar necks; pycnidial wall of textura angularis, 3–5 layered, 25–35 μm thick, composed of pale olive-brown to brown, flattened polygonal cells of 3–10 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, lageniform to ampulliform, 3.5–5 × 2.5–3 μm. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid to cylindrical, 3–5.5 × 1.5–2 μm, guttulate.



Culture characteristics: Colonies on OA reaching 27 mm diam after 7 d at 25 ± 1 °C, flattened, yellowish brown (M. 5E5); reverse greyish brown (M. 5F3). Colonies on MEA reaching 20 mm diam after 7 d at 25 ± 1 °C, flattened, brownish-orange (M. 5C3); reverse pale brown (M. 5D4). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: USA, from human dermatitis sample, 2009, D.A. Sutton (holotype CBS H-23208 ex-holotype living cultures CBS 143034 = UTHSC DI16-275 = FMR 13766).



Notes: The strain CBS 143034, which is morphologically similar to P. uberiformis (slightly different in pycnidial and conidial size), forms a large clade wherein there is P. uberiformis and several other species of the genus Pyrenochaetopsis. Because the nucleotide sequences of both fungi differ in 19 bp for rpb2 and 13 bp for tub2, P. globosa is proposed as a new species for the genus.



Pyrenochaetopsis indica (T.S. Viswan.) Gruyter et al., Mycologia 102: 1077. 2010.

Basionym: Pyrenochaeta indica T.S. Viswan., Curr. Sci. 26:118. 1957.

Synonym: Phoma indica (T.S. Viswan.) Gruyter & Boerema, Persoonia 17: 556. 2002.



Description: Boerema et al. (2004).



Material examined: India, Poona, on leaf spot of Saccharum officinarum (holotype AMH-11, ex-holotype living cultures IMI 062569 = CBS 124454 = FMR 14879).



Notes: We studied the ex-type strain of Pyrenochaetopsis indica, providing new genomic sequence data. It is morphologically characterised by its setose pycnidia, and the production of globose to subglobose, olivaceous chlamydospores solitary or in chains. Morphologically it is difficult to differentiate this species from P. decipiens. However, Pyrenochaetopsis indica clearly differs genetically from the latter in its tub2 and rpb2 sequences. Unfortunately, all cultures remained sterile.



Pyrenochaetopsis leptospora (Sacc. & Briard) Gruyter et al., Mycologia 102: 1076. 2010. Fig. 33.

Fig. 33.

Pyrenochaetopsis leptospora (CBS 101635). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Basionym: Pyrenochaeta leptospora Sacc. & Briard, Revue Mycol. 11: 16. 1889.

Synonyms: Pyrenochaeta spegazziniana Trotter, Syll. Fung. 25: 190. 1931.

Phoma briardii Gruyter & Boerema, Persoonia 17: 555. 2002.



Description: Boerema et al. (2004).



Material examined: Germany, subtrate unknown, J.W. Veenbaas, living cultures CBS 122787 = FMR 14873. The Netherlands, on Secale cereal (epitype CBS H-20313, ex-epitype living cultures CBS 101635 = PD 71/1027 = FMR 14877).



Notes: We received isolate CBS 122787 as “Coniothyrium cerealis”, but it was identified as P. leptospora in our phylogenetic study.



Pyrenochaetopsis microspora (Gruyter & Boerema) Gruyter et al., Mycologia 102: 1077. 2010. Fig. 34.

Fig. 34.

Pyrenochaetopsis microspora (CBS 102876). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Basionym: Phoma leveillei var. microspora Gruyter & Boerema, Persoonia 17: 553. 2002.



Description: Boerema et al. (2004).



Materials examined: Montenegro, Lake of Skadar, from water, 1975 (holotype HLB 999-242399, ex-holotype living cultures CBS 102876 = PD 75/911 = FMR 14874). USA, from human sinusitis sample, 2006, D.A. Sutton, living cultures UTHSC DI16-193 = FMR 13688.



Notes: In this paper, the ex-type strain of Pyrenochaetopsis microspora was examined, and new genomic sequence data and illustrations are provided. Furthermore, one human clinical specimen clustered with the ex-type living culture, being morphologically and genetically very closely related.



Pyrenochaetopsis paucisetosa Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB819766. Fig. 35.



Fig. 35.

Pyrenochaetopsis paucisetosa (CBS 142460). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Etymology: From Latin paucus, few, and -setosus, setose, because the conidiomata are covered by a few setae.



Description: Hyphae brown, smooth- and thin-walled, septate, 2–3 μm wide. Conidiomata pycnidial, brown, solitary, superficial or immersed (OA), setose, globose to ovoid, 150–190 × 140–160 μm, with a papillate ostiolar neck, covered by a few, brown, erect or slightly curved, smooth- and thick-walled, septate setae, (50–)63–68(–83) × 2–3.5 μm; pycnidial wall of textura angularis, 2–5 layered, 20–50 μm thick, composed of brown, flattened polygonal cells of 4–13 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 3.5–4 × 3–3.5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical, 3–4 × 2–2.5 μm, guttulate.



Culture characteristics: Colonies on OA reaching 25 mm diam after 7 d at 25 ± 1 °C, flattened, olive brown (M. 4F5); reverse brownish grey (M. 4F2). Colonies on MEA reaching 21 mm diam after 7 d at 25 ± 1 °C, floccose, pale grey (M. 4C1); reverse medium-grey (M. 4E1). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 15 °C; maximum temperature of growth 35 °C.



Material examined: USA, from human toe nail, 2005, D.A. Sutton (holotype CBS H-23037, ex-holotype living cultures CBS 142460 = UTHSC DI16-193 = FMR 13683).



Notes: Pyrenochaetopsis paucisetosa, recovered from a specimen of superficial human tissue, produces pycnidia covered by a few setae, and conidia smaller than in other species of the genus. Phylogenetically, P. paucisetosa is well-separated from P. botulispora.



Pyrenochaetopsis poae Crous & Quaedvlieg, Persoonia 32: 197. 2014.



Description: Crous et al. (2014).



Material examined: Netherlands, Raalte, on Poa sp. (Poaceae), 2013, W. Quaedvlieg (holotype CBS H-21677, ex-holotype living cultures CBS 136769 = D779 = FMR 14876).



Notes: We studied the ex-type strain of Pyrenochaetopsis poae, which is morphologically similar to the generic type of P. leptospora. In this paper, we provide rpb2 sequence that, together with tub2, are useful to differentiate these taxa.



Pyrenochaetopsis setosissima Valenzuela-Lopez, Cano, Crous, Guarro & Stchigel, sp. nov. MycoBank MB819767. Fig. 36.



Fig. 36.

Pyrenochaetopsis setosissima (CBS 119739). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Etymology: From Latin –setosissimus, bearing many setae, relating to the ornamentation of the pycnidia.



Description: Hyphae brown, smooth- and thin-walled, septate, 2–5 μm wide. Conidiomata pycnidial, brown, solitary or confluent, superficial (OA), subglobose to ovoid, 150–230 × 150–200 μm, with a papillate ostiolar neck, covered by many dark brown, erect, smooth- and thick-walled, septate setae, 33–83 × 2–4 μm; pycnidial wall of textura angularis, 2–4 layered, 20–50 μm thick, composed of brown, flattened polygonal cells of 5–15 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 5–4.5 × 4–4.5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical, 4–5 × 2–2.5 μm, guttulate.



Culture characteristics: Colonies on OA reaching 25 mm diam after 7 d at 25 ± 1 °C, flattened, olive brown (M. 4F4); reverse brownish grey (M. 4F2). Colonies on MEA reaching 18 mm diam after 7 d at 25 ± 1 °C, flattened, light orange (M. 5A4); reverse orange white (M. 5A2). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: Brazil, Minas Gerais, Lavras, from Coffea arabica leaf, Jun. 1999, L.H. Pfenning (holotype CBS H-23209, ex-holotype living cultures CBS 119739 = FMR 14875).



Notes: The isolate CBS 119739 was identified as P. microspora by de Gruyter et al. (2010) using SSU and LSU sequences as phylogenetic markers. However, in our phylogenetic study employing more markers, it clusters distant from the latter species. Pyrenochaetopsis setosissima is morphologically very similar to P. microspora, and can only be distinguished based on molecular data (differing in 19 bp for tub2 and 31 bp for rpb2).



Pyrenochaetopsis uberiformis Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB819765. Fig. 37.



Fig. 37.

Pyrenochaetopsis uberiformis (CBS 142461). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: From Latin –ubera, mammaries, and -forma, shape, relating to the anatomy of its pycnidia.



Description: Hyphae brown, smooth- and thin-walled, septate, 2–3 μm wide. Conidiomata pycnidial, brown, solitary or confluent, superficial or immersed (OA), glabrous, globose or ovoid, 200–440 × 130–410 μm, with a papillate ostiolar neck; pycnidial wall of textura angularis, 2–4 layered, 15–30 μm thick, composed of pale brown to brown, flattened polygonal cells of 5–10 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 3–4 × 4–5 μm. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical, 4–6 × 2–2.5 μm, guttulate.



Culture characteristics: Colonies on OA reaching 27 mm diam after 7 d at 25 ± 1 °C, flattened, yellowish brown (M. 5E5); reverse greyish brown (M. 5F3). Colonies on MEA reaching 20 mm diam after 7 d at 25 ± 1 °C, flattened, brownish orange (M. 5C3); reverse pale brown (M. 5D4). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: USA, from human ear lesion, 2009, D.A. Sutton (holotype CBS H-23038, ex-holotype living cultures CBS 142461 = UTHSC DI16-277 = FMR 13769).



Notes: The strain CBS 142461 clustered within the Pyrenochaetopsis clade, distant from other species of the genus, with the exception of P. americana, which forms a sister clade. Both strains differ in their rpb2 and tub2 sequences. Therefore, we propose strain CBS 142461 as representative of the new species P. uberiformis.



Clade F2: Xenopyrenochaetopsis



Xenopyrenochaetopsis Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, gen. nov. MycoBank MB820311.



Etymology: From Greek ξένος-, strange, alien, because it is phylogenetically distinct from the genus Pyrenochaetopsis.



Conidiomata pycnidial, pale brown to brown, solitary or confluent; pycnidial wall of textura angularis, glabrous, globose, ostiolate. Conidiogenous cells phialidic, hyaline. Conidia aseptate, hyaline, smooth- and thin-walled, cylindrical, guttulate.



Type species: Xenopyrenochaetopsis pratorum (P.R. Johnst. & Boerema) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano.



Xenopyrenochaetopsis pratorum (P.R. Johnst. & Boerema) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, comb. nov. MycoBank MB820312. Fig. 38.

Fig. 38.

Xenopyrenochaetopsis pratorum (CBS 445.81). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium. G. Conidiogenous cells. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Basionym: Phoma pratorum P.R. Johnst. & Boerema, New Zealand J. Bot. 19: 395. 1981.

Synonym: Pyrenochaetopsis pratorum (P.R. Johnst. & Boerema) Gruyter et al., Stud. Mycol. 75: 24. 2012.



Description from ex-isotype (CBS 445.81): Hyphae pale brown to brown, smooth- and thin-walled, septate, 2.5–5 μm wide. Conidiomata pycnidial, pale brown to brown, solitary or confluent, semi-immersed or immersed (OA), glabrous, globose to irregular, (88–)160–270 × (80–)100–250 μm, with 1–3 papillate ostiolar necks; pycnidial wall of textura angularis, 2–4 layered, 10–30 μm thick, composed of pale brown to brown, flattened polygonal cells of 2.5–8 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform, 3–3.5 × 1.5–2 μm. Conidia aseptate, hyaline, smooth- and thin-walled, subreniform to oblong or cylindrical, 4–5 × 1.5–2 μm, guttulate.



Culture characteristics: Colonies on OA reaching 5 mm diam after 7 d at 25 ± 1 °C, flattened, olive (M. 3D4) to olive grey (M.3F2); reverse olive (M.3F4). Colonies on MEA reaching 4 mm diam after 7 d at 25 ± 1 °C, flattened, yellowish white (M. 3A2); reverse ash blonde (M. 3C3). NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 15 °C; maximum temperature of growth 25 °C.



Material examined: New Zealand, Rakura, near Hamilton, from a leaf of Lolium perenne (Poaceae), 1980, P.R. Johnston (isotype CBS H-7625, CBS H-7626, ex-isotype living cultures CBS 445.81 = PDDCC 7049 = PD 80/1254 = FMR 14878).



Notes: Pyrenochaetopsis pratorum was proposed as a new combination for Phoma pratorum by de Gruyter et al. (2013). In that study, it clustered with Pyrenochaetopsis but was situated phylogenetically distinct from P. leptospora. However, in our phylogenetic analysis this species clustered outside Pyrenochaetopsis s. str. Moreover, Phoma pratorum differs in the main distinctive morphological feature of the genus Pyrenochaetopsis, the production of setose pycnidia (glabrous in P. pratorum). Therefore, we accommodate this species in the new genus Xenopyrenochaetopsis.



Clade F3: Neopyrenochaetopsis



Neopyrenochaetopsis Valenzuela-Lopez, Cano, Guarro & Stchigel, gen. nov. MycoBank MB820309.



Etymology: Referring to its close phylogenetic relationship with the genus Pyrenochaetopsis.



Conidiomata pycnidial, brown, solitary or confluent, pycnidial wall of textura angularis, glabrous, subglobose to ovoid, ostiolate. Conidiogenous cells phialidic, ampulliform to globose. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid to cylindrical.



Type species: Neopyrenochaetopsis hominis Valenzuela-Lopez, Cano, Guarro & Stchigel.



Neopyrenochaetopsis hominis Valenzuela-Lopez, Cano, Guarro & Stchigel, sp. nov. MycoBank MB820310. Fig. 39.



Fig. 39.

Neopyrenochaetopsis hominis (CBS 143033). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiogenous cell. H. Conidia. Scale bars: F = 100 μm. G, H = 10 μm.

Etymology: Relating to its isolation from a human specimen.



Description: Hyphae pale yellow to pale brown, smooth- and thin-walled, septate, 2–3 μm wide. Conidiomata pycnidial, brown, solitary or confluent, superficial or immersed (OA), glabrous, subglobose to ovoid, 160–170 × 140–160 μm, with a single papillate ostiolar neck; pycnidial wall of textura angularis, 2–4 layered, 15–40 μm thick, composed of brown, flattened polygonal cells of 2.5–8 μm diam. Conidiogenous cells phialidic, hyaline, smooth-walled, ampulliform to globose, 4–5 μm diam wide. Conidia aseptate, hyaline, smooth- and thin-walled, ovoid to narrowly ellipsoidal, 3–3.5 × 1.5–2 μm, guttulate. Chlamydospores absent.



Culture characteristics: Colonies on OA reaching 31 mm diam after 7 d at 25 ± 1 °C, flattened, greyish yellow (M. 3B4); reverse greyish yellow (M. 3C4); yellow pigment diffusing into the agar. Colonies on MEA reaching 29 mm diam after 7 d at 25 ± 1 °C, floccose, dull yellow (M. 3B3) to white (M. 3A1); reverse brownish yellow (M. 5C8); diffusible pigment yellowish. NaOH spot test negative. Crystals absent. Optimal temperature of growth and sporulation 25 °C; minimum temperature of growth 5 °C; maximum temperature of growth 30 °C.



Material examined: USA, from human skin tissue, 2007, D. A. Sutton (holotype CBS H-23207, culture ex-holotype living cultures CBS 143033 = UTHSC DI16-238 = FMR 13728).



Notes: The strain CBS 143033, recovered from a clinical sample, forms a distinct basal clade within the Pyrenochaetopsidaceae. Morphologically, N. hominis can be differentiated from the other taxa mainly by the production of smaller-sized conidia, and a yellow diffusing pigment on MEA and OA.



Clade N: Parapyrenochaetaceae Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, fam. nov. MycoBank MB820418.



Etymology: Named after its close morphological relationship with Pyrenochaeta.



Conidiomata pycnidial, brown, solitary, pycnidial wall of textura angularis, setose, globose, ostiolate. Conidiogenous cells phialidic, ampulliform or lageniform. Conidia aseptate, hyaline, smooth- and thin-walled, allantoid or ellipsoidal.



Type genus: Parapyrenochaeta Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano.



Parapyrenochaeta Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, gen. nov. MycoBank MB820319.



Etymology: Based on its close morphological relationship to Pyrenochaeta.



Conidiomata pycnidial, pale brown to brown, solitary, setose, globose, ostiolate; pycnidial wall of textura angularis. Conidiogenous cells phialidic, ampulliform or lageniform. Conidia aseptate, hyaline, smooth- and thin-walled, allantoid or ellipsoidal.



Type species: Parapyrenochaeta protearum (Crous) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano.



Parapyrenochaeta acaciae (Crous et al.) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, comb. nov. MycoBank MB820321. Fig. 40.

Fig. 40.

Parapyrenochaeta acaciae (CBS 141291). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidia. G. Conidiogenous cells. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Basionym: Pyrenochaeta acaciae Crous et al., Persoonia 36: 349. 2016.



Description: Crous et al. (2016b).



Material examined: Australia, Victoria, on leaf of Acacia sp. (Fabaceae), 7 Nov. 2014, J. Edwards, I.G. Pascoe & P.W. Crous (holotype CBS H-22601, ex-holotype living cultures CPC 25527 = CBS 141291 = FMR 15755).



Notes: Pyrenochaeta acaciae was described by Crous et al. (2016b) based on morphological and nucleotide sequence data, highlighting the close relationship with P. protearum. In our phylogenetic study, P. acaciae clustered distant from the Cucurbitariaceae s. str., forming a distinct clade related to P. protearum.



Parapyrenochaeta protearum (Crous) Valenzuela-Lopez, Crous, Stchigel, Guarro & Cano, comb. nov. MycoBank MB820320. Fig. 41.

Fig. 41.

Parapyrenochaeta protearum (CBS 131315). A, B. Colony on OA (front and reverse). C, D. Colony on MEA (front and reverse). E. Pycnidia forming on OA. F. Pycnidium G. Conidiophores. H. Conidia. Scale bars: F = 50 μm. G, H = 10 μm.

Basionym: Pyrenochaeta protearum Crous, Persoonia 27: 153. 2011.

Synonym: Pyrenochaeta pinicola Crous, Persoonia 32: 255. 2014.



Description: Crous et al. (2011).



Materials examined: France, Nice, L’aire d’Esterel petrol filling station, on needles of Pinus sp., 20 Jul. 2013, P.W. Crous, living cultures ex-type of P. pinicola, CPC 23455 = CBS 137997 = FMR 15753. South Africa, Western Cape Province, on leaves of Protea mundii, 4 May 2010, P.W. Crous (holotype of P. protearum, CBS H-20772, ex-holotype living cultures CPC 18322 = CBS 131315 = FMR 15752).



Notes: Pyrenochaeta protearum morphologically resembles phoma-like taxa in producing single phialides covering the inner source of the pycnidia, and having small, ((3–)4–5(–6) × (2–)2.5(–3) μm), aseptate, hyaline conidia, but also resembles pyrenochaeta-like species due to its setose pycnidia (Crous et al. 2011). Based on ITS and LSU nucleotide sequences, this fungus has been related to Leptosphaeria, Pyrenochaeta and Pyrenochaetopsis, and was included in the genus Pyrenochaeta (Crous et al. 2011). However, our results revealed that this fungus is phylogenetically distant from Pyrenochaeta spp., and from the members of the Cucurbitariaceae, and therefore we accommodated it in the new genus Parapyrenochaeta. We also studied the ex-type strain of Pyrenochaeta pinicola (Crous et al. 2014), which was morphologically and genetically very closely related to Pa. protearum. Therefore, we reduce Py. pinicola to synonymy under Pa. protearum.

Discussion

The taxonomy of the coelomycetes has undergone major changes in recent years, mainly due to the extensive use of molecular techniques, which has resulted in a more natural classification of these fungi. In this regard, the taxonomic circumscription of the genera Phoma (Didymellaceae) and Pyrenochaeta (Cucurbitariaceae) have proven to be especially complex. In recent studies on Didymellaceae, Chen et al., 2015, Chen et al., 2017 restricted Phoma to P. herbarum, accepting 17 genera in the family Didymellaceae. They demonstrated that by combining four loci, but especially by using the rpb2 marker, it was possible to resolve the phylogeny of the Didymellaceae. However, in recent studies, several Phoma species accepted by Aveskamp et al. (2010) such as P. bulgarica, P. crystallifera, P. destructiva, P. eupyrena, P. multirostrata, P. omnivirens, P. pereupyrena and P. saxea, were not included. Currently, several genera such as Didymellocamarosporium, Endocoryneum, Heracleicola, Neodidymella, Platychora and Pseudohendersonia have been added to the Didymellaceae based mainly on the ribosomal gene analyses (Ariyawansa et al., 2015a, Hyde et al., 2016, Wijayawardene et al., 2016). However, recently, Chen et al. (2017) demonstrated that the genera mentioned above are simple synonyms of previous genera of that family such as Ascochyta, Boeremia, Stagonosporopsis and Neomicrosphaeropsis. Therefore, sequences of those taxa need to be verified with proper genes to resolve their taxonomic placement within the Didymellaceae. For this reason, our proposal was to revise this family testing a large set of coelomycetous fungi recently isolated from clinical specimens (Valenzuela-Lopez et al. 2016), but also including several reference species of Phoma from the prior study of Aveskamp et al. (2010). This resulted in the proposal of six new genera, viz. Cumuliphoma, Ectophoma, Juxtiphoma, Remotididymella, Similiphoma and Vacuiphoma, 14 new species, and nine new combinations.

The taxonomic placement of Pyrenochaeta continues to be a topic of discussion, as this genus accommodates at least 163 epithets (www.indexfungorum.org). It is currently related to the Cucurbitariaceae, but an earlier phylogenetic study involving Pyrenochaeta species performed by Schoch et al. (2006), showed that P. nobilis, its type species, occupied an unclear taxonomic placement within the Pleosporales. Subsequently, this genus occupied an intermediate position as incertae sedis between the Leptosphaeriaceae and Didymellaceae (de Gruyter et al. 2009), or belonging to the Leptosphaeriaceae (Zhang et al. 2009). Later, de Gruyter et al. (2010) placed Pyrenochaeta in Cucurbitariaceae, and several species of Phoma in the new genus Pyrenochaetopsis. However, by employing additional gene loci in our phylogeny, the type species P. nobilis clustered distant from Cucurbitariaceae s. str., being placed as incertae sedis in the Pleosporineae. Moreover, several species previously identified as Pyrenochaeta have proved to be phylogenetically scattered within the Pleosporineae. Therefore, we introduced four new families with several new genera to accommodate all Pyrenochaeta species which clustered outside the Cucurbitariaceae, i.e. Neopyrenochaetaceae (which includes Neopyrenochaeta gen. nov.), Parapyrenochaetaceae (within Parapyrenochaeta gen. nov.), Pseudopyrenochaetaceae (including Pseudopyrenochaeta gen. nov.) and Pyrenochaetopsidaceae (including the two new genera, Neopyrenochaetopsis and Xenopyrenochaetopsis).

In the revision of Cucurbitariaceae by Doilom et al. (2013), the authors accepted six genera in the family, although Curreya, Rhytidiella and Syncarpella were not sequenced. This family was recently enlarged by Wanasinghe et al. (2017b) proposing the new genus Neocucurbitaria to accommodate N. acerina, N. unguis-hominis (syn. Pyrenochaeta unguis-hominis, the type species of that genus) and N. quercina (syn. Pyrenochaeta quercina) and considering the genus Fenestella as belonging to this family; however, the type species and more species of this genus should be studied to clarify its taxonomy. Neocucurbitaria has been also modified in our study to include N. cava (syn. Pyrenochaeta cava), N. hakeae (syn. Pyrenochaeta hakeae), N. keratinophila (syn. Pyrenochaeta keratinophila), and the new species N. aquatica and N. irregularis. Here, we have also enlarged the current concept of Cucurbitariaceae with the proposal of the new genera Allocucurbitaria (with the only species A. botulispora), which is closely related to Cucurbitaria and Paracucurbitaria, with P. corni and the new species P. italica forming a clade distinct from Neocucurbitaria. In fact, Cucurbitariaceae is currently circumscribed with four genera, i.e. the three mentioned above, and Cucurbitaria. In contrast, Camarosporium, which was included in Cucurbitariaceae by Doilom et al. (2013), has been recently placed in Coniothyriaceae by Crous & Groenewald (2017), who studied and epitypified the generic type of Camarosporium and several phoma-like species, proposing the new family Libertasomycetaceae within Pleosporineae. In the same year, Wanasinghe et al. (2017a) have studied a large set of camarosporium-like fungi proposing the new families Camarosporidiellaceae and Neocamarosporiaceae and resurrected the family Camarosporiaceae. However, in our phylogeny, several members of Coniothyriaceae and Leptosphaeriaceae remain in an ambiguous taxonomic position within Pleosporineae. Furthermore, in our study the family Camarosporidiellaceae was phylogenetically unsupported, which is probably caused by the lack of rpb2 or tub2 sequences; therefore further studies are needed to understand the relationships of this family with the other members of this suborder.

At the present study, we have clarified the generic concept of two of the largest genera of coelomycetes (Phoma and Pyrenochaeta) through a polyphasic approach that included the analysis of four phylogenetic markers of 143 additional isolates. This approach allowed a better delimitation of members of Cucurbitariaceae and Didymellaceae of the suborder Pleosporineae that currently encompasses the following 19 families: Camarosporiaceae, Camarosporidiellaceae, Coniothyriaceae, Cucurbitariaceae, Didymellaceae, Dothidotthiaceae, Halojulellaceae, Leptosphaeriaceae, Libertasomycetaceae, Microsphaeropsidaceae, Neocamarosporiaceae, Neophaeosphaeriaceae, Neopyrenochaetaceae, Parapyrenochaetaceae, Phaeosphaeriaceae, Pleosporaceae, Pseudopyrenochaetaceae, Pyrenochaetopsidaceae and Shiraiaceae.