Alternaria redefined

JHC Woudenberg; JZ Groenewald; M Binder; PW Crous

doi:10.3114/sim0015

. 2013 Jun 4;75(1):171–212. doi: 10.3114/sim0015

Alternaria redefined

JHC Woudenberg ^1,^2,^*, JZ Groenewald ¹, M Binder ¹, PW Crous ^1,^2,³

PMCID: PMC3713888 PMID: 24014900

Abstract

Alternaria is a ubiquitous fungal genus that includes saprobic, endophytic and pathogenic species associated with a wide variety of substrates. In recent years, DNA-based studies revealed multiple non-monophyletic genera within the Alternaria complex, and Alternaria species clades that do not always correlate to species-groups based on morphological characteristics. The Alternaria complex currently comprises nine genera and eight Alternaria sections. The aim of this study was to delineate phylogenetic lineages within Alternaria and allied genera based on nucleotide sequence data of parts of the 18S nrDNA, 28S nrDNA, ITS, GAPDH, RPB2 and TEF1-alpha gene regions. Our data reveal a Pleospora/Stemphylium clade sister to Embellisia annulata, and a well-supported Alternaria clade. The Alternaria clade contains 24 internal clades and six monotypic lineages, the assemblage of which we recognise as Alternaria. This puts the genera Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Lewia, Nimbya, Sinomyces, Teretispora, Ulocladium, Undifilum and Ybotromyces in synonymy with Alternaria. In this study, we treat the 24 internal clades in the Alternaria complex as sections, which is a continuation of a recent proposal for the taxonomic treatment of lineages in Alternaria. Embellisia annulata is synonymised with Dendryphiella salina, and together with Dendryphiella arenariae, are placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, which were previously associated with Alternaria, cluster within the Pleosporaceae, outside Alternaria s. str., whereas Alternariaster, a genus formerly seen as part of Alternaria, clusters within the Leptosphaeriaceae. Paradendryphiella is newly described, the generic circumscription of Alternaria is emended, and 32 new combinations and 10 new names are proposed. A further 10 names are resurrected, while descriptions are provided for 16 new Alternaria sections.

Taxonomic novelties:

New combinations - Alternaria abundans (E.G. Simmons) Woudenb. & Crous, Alternaria alternariae (Cooke) Woudenb. & Crous, Alternaria atra (Preuss) Woudenb. & Crous, Alternaria bornmuelleri (Magnus) Woudenb. & Crous, Alternaria botrytis (Preuss) Woudenb. & Crous, Alternaria caespitosa (de Hoog & C. Rubio) Woudenb. & Crous, Alternaria cantlous (Yong Wang bis & X.G. Zhang) Woudenb. & Crous, Alternaria caricis (E.G. Simmons) Woudenb. & Crous, Alternaria cinerea (Baucom & Creamer) Woudenb. & Crous, Alternaria didymospora (Munt.-Cvetk.) Woudenb. & Crous, Alternaria fulva (Baucom & Creamer) Woudenb. & Crous, Alternaria hyacinthi (de Hoog & P.J. Mull. bis) Woudenb. & Crous, Alternaria indefessa (E.G. Simmons) Woudenberg & Crous, Alternaria leptinellae (E.G. Simmons & C.F. Hill) Woudenb. & Crous, Alternaria lolii (E.G. Simmons & C.F. Hill) Woudenb. & Crous, Alternaria multiformis (E.G. Simmons) Woudenb. & Crous, Alternaria obclavata (Crous & U. Braun) Woudenb. & Crous, Alternaria obovoidea (E.G. Simmons) Woudenb. & Crous, Alternaria oudemansii (E.G. Simmons) Woudenb. & Crous, Alternaria oxytropis (Q. Wang, Nagao & Kakish.) Woudenb. & Crous, Alternaria penicillata (Corda) Woudenb. & Crous, Alternaria planifunda (E.G. Simmons) Woudenb. & Crous, Alternaria proteae (E.G. Simmons) Woudenb. & Crous, Alternaria scirpinfestans (E.G. Simmons & D.A. Johnson) Woudenb. & Crous, Alternaria scirpivora (E.G. Simmons & D.A. Johnson) Woudenb. & Crous, Alternaria septospora (Preuss) Woudenb. & Crous, Alternaria slovaca (Svob.-Pol., L. Chmel & Bojan.) Woudenb. & Crous, Alternaria subcucurbitae (Yong Wang bis & X.G. Zhang) Woudenb. & Crous, Alternaria tellustris (E.G. Simmons) Woudenb. & Crous, Alternaria tumida (E.G. Simmons) Woudenb. & Crous, Paradendryphiella salina (G.K. Sutherl.) Woudenb. & Crous, Paradendryphiella arenariae (Nicot) Woudenb. & Crous. New names - Alternaria aspera Woudenb. & Crous, Alternaria botryospora Woudenb. & Crous, Alternaria brassicae-pekinensis Woudenb. & Crous, Alternaria breviramosa Woudenb. & Crous, Alternaria chlamydosporigena Woudenb. & Crous, Alternaria concatenata Woudenb. & Crous, Alternaria embellisia Woudenb. & Crous, Alternaria heterospora Woudenb. & Crous, Alternaria papavericola Woudenb. & Crous, Alternaria terricola Woudenb. & Crous. Resurrected names - Alternaria cetera E.G. Simmons, Alternaria chartarum Preuss, Alternaria consortialis (Thüm.) J.W. Groves & S. Hughes, Alternaria cucurbitae Letendre & Roum., Alternaria dennisii M.B. Ellis, Alternaria eureka E.G. Simmons, Alternaria gomphrenae Togashi, Alternaria malorum (Ruehle) U. Braun, Crous & Dugan, Alternaria phragmospora Emden, Alternaria scirpicola (Fuckel) Sivan. New sections, all in Alternaria - sect. Chalastospora Woudenb. & Crous, sect. Cheiranthus Woudenb. & Crous, sect. Crivellia Woudenb. & Crous, sect. Dianthicola Woudenb. & Crous, sect. Embellisia Woudenb. & Crous, sect. Embellisioides Woudenb. & Crous, sect. Eureka Woudenb. & Crous, sect. Infectoriae Woudenb. & Crous, sect. Japonicae Woudenb. & Crous, sect. Nimbya Woudenb. & Crous, sect. Phragmosporae Woudenb. & Crous, sect. Pseudoulocladium Woudenb. & Crous, sect. Teretispora Woudenb. & Crous, sect. Ulocladioides Woudenb. & Crous, sect. Ulocladium Woudenb. & Crous, sect. Undifilum Woudenb. & Crous. New genus - Paradendryphiella Woudenb. & Crous.

Key words: Allewia, Chalastospora, Crivellia, Embellisia, Lewia, Nimbya, Paradendryphiella, Sinomyces, systematics, Teretispora, Ulocladium, Undifilum

INTRODUCTION

Alternaria is a ubiquitous fungal genus that includes saprobic, endophytic and pathogenic species. It is associated with a wide variety of substrates including seeds, plants, agricultural products, animals, soil and the atmosphere. Species of Alternaria are known as serious plant pathogens, causing major losses on a wide range of crops. Several taxa are also important postharvest pathogens, causative agents of phaeohyphomycosis in immuno-compromised patients or airborne allergens. Because of the significant negative health effects of Alternaria on humans and their surroundings, a correct and rapid identification of Alternaria species would be of great value to researchers, medical mycologists and the public alike.

Alternaria was originally described by Nees (1816), based on A. tenuis as the only species. Characteristics of the genus included the production of dark-coloured phaeodictyospores in chains, and a beak of tapering apical cells. Von Keissler (1912) synonymised both A. tenuis and Torula alternata (Fries 1832) with Alternaria alternata, due to ambiguities in Nees’s description of A. tenuis. Two additional genera, Stemphylium (Wallroth 1833) and Ulocladium (Preuss 1851) were subsequently described for phaeodictyosporic hyphomycetes, further complicating the taxonomic resolution in this group of fungi. Several re-descriptions and revised criteria of these genera (Saccardo 1886, Elliot 1917, Wiltshire 1933, 1938, Joly 1964) resulted in a growing number of new species. Results of a lifetime study on Alternaria taxonomy based upon morphological characteristics were summarised in Simmons (2007), in which 275 Alternaria species were recognised. One species was transferred to the genus Prathoda and three new genera, Alternariaster, Chalastospora and Teretispora, were segregated from Alternaria.

Molecular studies revealed multiple non-monophyletic genera within the Alternaria complex and Alternaria species clades, which do not always correlate to species-groups based upon morphological characteristics (Pryor & Gilbertson 2000, Chou & Wu 2002, de Hoog & Horré 2002, Pryor & Bigelow 2003, Hong et al. 2005, Inderbitzin et al. 2006, Pryor et al. 2009, Runa et al. 2009, Wang et al. 2011, Lawrence et al. 2012). The A. alternata, A. brassicicola, A. infectoria, A. porri and A. radicina species-groups were strongly supported by these studies and two new species-groups, A. sonchi (Hong et al. 2005) and A. alternantherae (Lawrence et al. 2012) and three new genera, Crivellia (Inderbitzin et al. 2006), Undifilum (Pryor et al. 2009) and Sinomyces (Wang et al. 2011), were described. The latest molecular revision of Alternaria (Lawrence et al. 2013) introduced two new species groups, A. panax and A. gypsophilae, and elevated eight species-groups to sections within Alternaria. The sexual phylogenetic Alternaria lineage, the A. infectoria species-group, did not get the status of section, in contrast to the eight asexual phylogenetic lineages in Alternaria. The Alternaria complex currently comprises the genera Alternaria, Chalastospora (Simmons 2007), Crivellia, Embellisia, Nimbya, Stemphylium, Ulocladium, Undifilum and the recently described Sinomyces together with eight sections of Alternaria and the A. infectoria species-group.

The aim of the present study was to delineate the phylogenetic lineages within Alternaria and allied genera, and to create a robust taxonomy. Phylogenetic inferences were conducted on sequence data of parts of the 18S nrDNA (SSU), 28S nrDNA (LSU), the internal transcribed spacer regions 1 and 2 and intervening 5.8S nrDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF1) gene regions of ex-type and reference strains of Alternaria species and all available allied genera.

MATERIAL AND METHODS

Isolates

Based on the ITS sequences of all ex-type or representative strains from the Alternaria identification manual present at the CBS-KNAW Fungal Biodiversity Centre (CBS), Utrecht, The Netherlands (data not shown), 66 Alternaria strains were included in this study together with 61 ex-type or representative strains of 16 related genera (Table 1). Alternaria is represented by the ex-type or representative strains of the seven species-groups and species that clustered outside known Alternaria clades. Because of the size and complexity of the A. alternata, A. infectoria and A. porri species-groups, we only included known species; the complete species-groups will be treated in future studies.

Table 1.

Isolates used in this study and their GenBank accession numbers. Bold accession numbers were generated in other studies.

Old species name	New species name	Alternaria Section	Strain number¹	Status²	Host / Substrate	Country	Other collection number¹	GenBank accession numbers
								SSU	LSU	RPB2	ITS	GAPDH	TEF1
Alternaria alternantherae	Alternaria alternantherae	Althernantherae	CBS 124392		Solanum melongena	China	HSAUP2798	KC584506	KC584251	KC584374	KC584179	KC584096	KC584633
Alternaria alternata	Alternaria alternata	Alternata	CBS 916.96	T	Arachis hypogaea	India	EGS 34.016	KC584507	DQ678082	KC584375	AF347031	AY278808	KC584634
Alternaria anigozanthi	Alternaria anigozanthi	Eureka	CBS 121920	T	Anigozanthus sp.	Australia	EGS 44.066	KC584508	KC584252	KC584376	KC584180	KC584097	KC584635
Alternaria arborescens	Alternaria arborescens	Alternata	CBS 102605	T	Lycopersicon esculentum	USA	EGS 39.128	KC584509	KC584253	KC584377	AF347033	AY278810	KC584636
Alternaria argyranthemi	Alternaria argyranthemi		CBS 116530	T	Argyranthemum sp.	New Zealand	EGS 44.033	KC584510	KC584254	KC584378	KC584181	KC584098	KC584637
Alternaria armoraciae	Alternaria armoraciae	Chalastospora	CBS 118702	T	Armoracia rusticana	New Zealand	EGS 51.064	KC584511	KC584255	KC584379	KC584182	KC584099	KC584638
Alternaria avenicola	Alternaria avenicola	Panax	CBS 121459	T	Avena sp.	Norway	EGS 50.185	KC584512	KC584256	KC584380	KC584183	KC584100	KC584639
Alternaria axiaeriisporifera	Alternaria axiaeriisporifera	Gypsophilae	CBS 118715	T	Gypsophila paniculata	New Zealand	EGS 51.066	KC584513	KC584257	KC584381	KC584184	KC584101	KC584640
Alternaria brassicae	Alternaria brassicae		CBS 116528	R	Brassica oleracea	USA	EGS 38.032	KC584514	KC584258	KC584382	KC584185	KC584102	KC584641
Alternaria brassicicola	Alternaria brassicicola	Brassicicola	CBS 118699	R	Brassica oleracea	USA	EGS 42.002; ATCC 96836	KC584515	KC584259	KC584383	JX499031	KC584103	KC584642
Alternaria calycipyricola	Alternaria calycipyricola	Panax	CBS 121545	T	Pyrus communis	China	EGS 52.071; RGR 96.0209	KC584516	KC584260	KC584384	KC584186	KC584104	KC584643
Alternaria capsici-annui	Alternaria capsici-annui	Ulocladium	CBS 504.74		Capsicum annuum	-		KC584517	KC584261	KC584385	KC584187	KC584105	KC584644
Alternaria carotiincultae	Alternaria carotiincultae	Radicina	CBS 109381	T	Daucus carota	USA	EGS 26.010	KC584518	KC584262	KC584386	KC584188	KC584106	KC584645
Alternaria cheiranthi	Alternaria cheiranthi	Cheiranthus	CBS 109384	R	Cheiranthus cheiri	Italy	EGS 41.188	KC584519	KC584263	KC584387	AF229457	KC584107	KC584646
Alternaria chlamydospora	Alternaria chlamydospora	Phragmosporae	CBS 491.72	T	Soil	Egypt	EGS 31.060; ATCC 28045; IMI 156427	KC584520	KC584264	KC584388	KC584189	KC584108	KC584647
Alternaria cinerariae	Alternaria cinerariae	Sonchi	CBS 116495	R	Ligularia sp.	USA	EGS 49.102	KC584521	KC584265	KC584389	KC584190	KC584109	KC584648
Alternaria conjuncta	Alternaria conjuncta	Infectoriae	CBS 196.86	T	Pastinaca sativa	Switzerland	EGS 37.139	KC584522	KC584266	KC584390	FJ266475	AY562401	KC584649
Alternaria cumini	Alternaria cumini	Eureka	CBS 121329	T	Cuminum cyminum	India	EGS 04.158a	KC584523	KC584267	KC584391	KC584191	KC584110	KC584650
Alternaria dauci	Alternaria dauci	Porri	CBS 117097	R	Daucus carota	USA	EGS 46.006	KC584524	KC584268	KC584392	KC584192	KC584111	KC584651
Alternaria daucifolii	Alternaria daucifolii	Alternata	CBS 118812	T	Daucus carota	USA	EGS 37.050	KC584525	KC584269	KC584393	KC584193	KC584112	KC584652
Alternaria dianthicola	Alternaria dianthicola	Dianthicola	CBS 116491	R	Dianthus × allwoodii	New Zealand	EGS 51.022	KC584526	KC584270	KC584394	KC584194	KC584113	KC584653
Alternaria elegans	Alternaria elegans	Dianthicola	CBS 109159	T	Lycopersicon esculentum	Burkina Faso	EGS 45.072; IMI 374542	KC584527	KC584271	KC584395	KC584195	KC584114	KC584654
Alternaria ellipsoidea	Alternaria ellipsoidea	Gypsophilae	CBS 119674	T	Dianthus barbatus	USA	EGS 49.104	KC584528	KC584272	KC584396	KC584196	KC584115	KC584655
Alternaria eryngii	Alternaria eryngii	Panax	CBS 121339	R	Eryngium sp.	-	EGS 41.005	KC584529	KC584273	KC584397	JQ693661	AY562416	KC584656
Alternaria ethzedia	Alternaria ethzedia	Infectoriae	CBS 197.86	T	Brassica napus	Switzerland	EGS 37.143	KC584530	KC584274	KC584398	AF392987	AY278795	KC584657
Alternaria gaisen	Alternaria gaisen	Alternata	CBS 632.93	R	Pyrus pyrifolia cv. Nijiseiki	Japan	EGS 90.512	KC584531	KC584275	KC584399	KC584197	KC584116	KC584658
Alternaria geniostomatis	Alternaria geniostomatis	Eureka	CBS 118701	T	Geniostoma sp.	New Zealand	EGS 51.061	KC584532	KC584276	KC584400	KC584198	KC584117	KC584659
Alternaria gypsophilae	Alternaria gypsophilae	Gypsophilae	CBS 107.41	T	Gypsophila elegans	-	EGS 07.025; IMI 264349	KC584533	KC584277	KC584401	KC584199	KC584118	KC584660
Alternaria helianthiinficiens	Alternaria helianthiinficiens		CBS 117370	R	Helianthus annuus	UK	EGS 50.174; IMI 388636	KC584534	KC584278	KC584402	KC584200	KC584119	KC584661
Alternaria helianthiinficiens	Alternaria helianthiinficiens		CBS 208.86	T	Helianthus annuus	USA	EGS 36.184	KC584535	KC584279	KC584403	JX101649	KC584120	EU130548
Alternaria infectoria	Alternaria infectoria	Infectoriae	CBS 210.86	T	Triticum aestivum	UK	EGS 27.193	KC584536	KC584280	KC584404	DQ323697	AY278793	KC584662
Alternaria japonica	Alternaria japonica	Japonicae	CBS 118390	R	Brassica chinensis	USA	EGS 50.099	KC584537	KC584281	KC584405	KC584201	KC584121	KC584663
Alternaria juxtiseptata	Alternaria juxtiseptata	Gypsophilae	CBS 119673	T	Gypsophila paniculata	Australia	EGS 44.015; DAR 43414	KC584538	KC584282	KC584406	KC584202	KC584122	KC584664
Alternaria limaciformis	Alternaria limaciformis	Phragmosporae	CBS 481.81	T	Soil	UK	EGS 07.086; IMI 052976; QM 1790	KC584539	KC584283	KC584407	KC584203	KC584123	KC584665
Alternaria limoniasperae	Alternaria limoniasperae	Alternata	CBS 102595	T	Citrus jambhiri	USA	EGS 45.100	KC584540	KC584284	KC584408	FJ266476	AY562411	KC584666
Alternaria longipes	Alternaria longipes	Alternata	CBS 540.94	R	Nicotiana tabacum	USA	EGS 30.033; QM 9589	KC584541	KC584285	KC584409	AY278835	AY278811	KC584667
Alternaria macrospora	Alternaria macrospora	Porri	CBS 117228	T	Gossypium barbadense	USA	EGS 50.190	KC584542	KC584286	KC584410	KC584204	KC584124	KC584668
Alternaria mimicula	Alternaria mimicula	Brassicicola	CBS 118696	T	Lycopersicon esculentum	USA	EGS 01.056; QM 26a	KC584543	KC584287	KC584411	FJ266477	AY562415	KC584669
Alternaria molesta	Alternaria molesta	Phragmosporae	CBS 548.81	T	Phocaena phocaena	Denmark	EGS 32.075	KC584544	KC584288	KC584412	KC584205	KC584125	KC584670
Alternaria mouchaccae	Alternaria mouchaccae	Phragmosporae	CBS 119671	T	Soil	Egypt	EGS 31.061	KC584545	KC584289	KC584413	KC584206	AY562399	KC584671
Alternaria nepalensis	Alternaria nepalensis	Japonicae	CBS 118700	T	Brassica sp.	Nepal	EGS 45.073; IMI 374543	KC584546	KC584290	KC584414	KC584207	KC584126	KC584672
Alternaria nobilis	Alternaria nobilis	Gypsophilae	CBS 116490	R	Dianthus caryophyllus	New Zealand	EGS 51.027; NZMAF Lynfield 743	KC584547	KC584291	KC584415	KC584208	KC584127	KC584673
Alternaria oregonensis	Alternaria oregonensis	Infectoriae	CBS 542.94	T	Triticum aestivum	USA	EGS 29.194	KC584548	KC584292	KC584416	FJ266478	FJ266491	KC584674
Alternaria panax	Alternaria panax	Panax	CBS 482.81	R	Aralia racemosa	USA	EGS 29.180	KC584549	KC584293	KC584417	KC584209	KC584128	KC584675
Alternaria perpunctulata	Alternaria perpunctulata	Althernantherae	CBS 115267	T	Alternanthera philoxeroides	USA		KC584550	KC584294	KC584418	KC584210	KC584129	KC584676
Alternaria petroselini	Alternaria petroselini	Radicina	CBS 112.41	T	Petroselinum sativum	-	EGS 06.196	KC584551	KC584295	KC584419	KC584211	KC584130	KC584677
Alternaria photistica	Alternaria photistica	Panax	CBS 212.86	T	Digitalis purpurea	UK	EGS 35.172	KC584552	KC584296	KC584420	KC584212	KC584131	KC584678
Alternaria porri	Alternaria porri	Porri	CBS 116698	R	Allium cepa	USA	EGS 48.147	KC584553	KC584297	KC584421	DQ323700	KC584132	KC584679
Alternaria pseudorostrata	Alternaria pseudorostrata	Porri	CBS 119411	T	Euphorbia pulcherrima	USA	EGS 42.060	KC584554	KC584298	KC584422	JN383483	AY562406	KC584680
Alternaria radicina	Alternaria radicina	Radicina	CBS 245.67	T	Daucus carota	USA	EGS 03.145; ATCC 6503; IMI 124939; QM 1301; QM 6503	KC584555	KC584299	KC584423	KC584213	KC584133	KC584681
“Alternaria resedae”	Alternaria sp.	Cheiranthus	CBS 115.44		Reseda odorata	-	EGS 07.030	KC584556	KC584300	KC584424	KC584214	KC584134	KC584682
Alternaria saponariae	Alternaria saponariae	Gypsophilae	CBS 116492	R	Saponaria officinalis	USA	EGS 49.199	KC584557	KC584301	KC584425	KC584215	KC584135	KC584683
Alternaria selini	Alternaria selini	Radicina	CBS 109382	T	Petroselinum crispum	Saudi Arabia	EGS 25.198; IMI 137332	KC584558	KC584302	KC584426	AF229455	AY278800	KC584684
Alternaria septorioides	Alternaria septorioides	Brassicicola	CBS 106.41	T	Reseda odorata	Netherlands	EGS 52.089; MUCL 20298	KC584559	KC584303	KC584427	KC584216	KC584136	KC584685
Alternaria simsimi	Alternaria simsimi	Dianthicola	CBS 115265	T	Sesamum indicum	Argentina	EGS 13.110	KC584560	KC584304	KC584428	JF780937	KC584137	KC584686
Alternaria smyrnii	Alternaria smyrnii	Radicina	CBS 109380	R	Smyrnium olusatrum	UK	EGS 37.093	KC584561	KC584305	KC584429	AF229456	KC584138	KC584687
Alternaria solani	Alternaria solani	Porri	CBS 116651	R	Solanum tuberosum	USA	EGS 45.020	KC584562	KC584306	KC584430	KC584217	KC584139	KC584688
Alternaria soliaridae	Alternaria soliaridae		CBS 118387	T	Soil	USA	EGS 33.024	KC584563	KC584307	KC584431	KC584218	KC584140	KC584689
Alternaria solidaccana	Alternaria solidaccana	Brassicicola	CBS 118698	T	Soil	Bangladesh	EGS 36.158; IMI 049788	KC584564	KC584308	KC584432	KC584219	KC584141	KC584690
Alternaria sonchi	Alternaria sonchi	Sonchi	CBS 119675	R	Sonchus asper	Canada	EGS 43.131; IMI 366167	KC584565	KC584309	KC584433	KC584220	KC584142	KC584691
Alternaria tagetica	Alternaria tagetica	Porri	CBS 479.81	R	Tagetes erecta	UK	EGS 33.081	KC584566	KC584310	KC584434	KC584221	KC584143	KC584692
Alternaria tenuissima	Alternaria tenuissima	Alternata	CBS 918.96	R	Dianthus sp.	UK	EGS 34.015	KC584567	KC584311	KC584435	AF347032	AY278809	KC584693
Alternaria thalictrigena	Alternaria thalictrigena		CBS 121712	T	Thalictrum sp.	Germany		KC584568	KC584312	KC584436	EU040211	KC584144	KC584694
Alternaria triglochinicola	Alternaria triglochinicola	Eureka	CBS 119676	T	Triglochin procera	Australia	EGS 41.070	KC584569	KC584313	KC584437	KC584222	KC584145	KC584695
Alternaria vaccariae	Alternaria vaccariae	Gypsophilae	CBS 116533	R	Vaccaria hispanica	USA	EGS 47.108	KC584570	KC584314	KC584438	KC584223	KC584146	KC584696
Alternaria vaccariicola	Alternaria vaccariicola	Gypsophilae	CBS 118714	T	Vaccaria hispanica	USA	EGS 46.003; ATCC 26038	KC584571	KC584315	KC584439	KC584224	KC584147	KC584697
Alternariaster helianthi	Alternariaster helianthi		CBS 119672	R	Helianthus sp.	USA	EGS 36.007	KC584626	KC584368	KC584493
Alternariaster helianthi	Alternariaster helianthi		CBS 327.69		Helianthus annuus	-		KC584627	KC584369	KC584494
Ascochyta pisi	Ascochyta pisi		CBS 126.54		Pisum sativum	Netherlands		EU754038	DQ678070	DQ677967
Boeremia exigua	Boeremia exigua		CBS 431.74		Solanum tuberosum	Netherlands	PD 74/2447	EU754084	EU754183	GU371780
Brachycladium papaveris	Alternaria papavericola	Crivellia	CBS 116606	T	Papaver somniferum	USA		KC584579	KC584321	KC584446	FJ357310	FJ357298	KC584705
Brachycladium penicillatum	Alternaria penicillata	Crivellia	CBS 116608	T	Papaver rhoeas	Austria	DAOM 230457	KC584572	KC584316	KC584440	FJ357311	FJ357299	KC584698
Chaetodiplodia sp.	Chaetodiplodia sp.		CBS 453.68		Halimione portulacoides	Netherlands		DQ678001	DQ678054	KC584499
Chaetosphaeronema hispidulum	Chaetosphaeronema hispidulum		CBS 216.75		Anthyllis vulneraria	Germany		EU754045	EU754144	GU371777
Chalastospora cetera	Alternaria cetera	Chalastospora	CBS 121340	T	Elymus scabrus	Australia	EGS 41.072	KC584573	KC584317	KC584441	JN383482	AY562398	KC584699
Chalastospora ellipsoidea	Alternaria breviramosa	Chalastospora	CBS 121331	T	Triticum sp.	Australia		KC584574	KC584318	KC584442	FJ839608	KC584148	KC584700
Chalastospora obclavata	Alternaria obclavata	Chalastospora	CBS 124120	T	Air	USA	EGS 12.128	KC584575	FJ839651	KC584443	KC584225	KC584149	KC584701
Chmelia slovaca	Alternaria slovaca	Infectoriae	CBS 567.66	T	Human	Slovakia	ATCC 24279	KC584576	KC584319	KC584444	KC584226	KC584150	KC584702
Clathrospora elynae	Clathrospora elynae		CBS 161.51		Carex curvula	Switzerland		KC584628	KC584370	KC584495
Clathrospora elynae	Clathrospora elynae		CBS 196.54		Carex curvula	Switzerland		KC584629	KC584371	KC584496
Clathrospora heterospora	Alternaria sp.	Alternata	CBS 175.52		Juncus mertensianus	USA	EGS 35.1619; IMI 068085; QM 1277	KC584577	KC584320	KC584445	KC584227	KC584151	KC584703
Cochliobolus heterostrophus	Cochliobolus heterostrophus		CBS 134.39		Zea mays	-	DSM 1149	AY544727	AY544645	DQ247790
Cochliobolus sativus	Cochliobolus sativus		DAOM 226212		Hordeum vulgare	Canada		DQ677995	DQ678045	DQ677939
Comoclathris magna	Alternaria sp.	Alternata	CBS 174.52		Anemone occidentalis	USA	EGS 39.1613; IMI 068086; QM 1278	KC584578	DQ678068	DQ677964	KC584228	KC584152	KC584704
Comoclathris compressa	Comoclathris compressa		CBS 156.53		Castilleja miniata	USA	EGS No. C-20285-I	KC584630	KC584372	KC584497
Comoclathris compressa	Comoclathris compressa		CBS 157.53		Ligusticum purpureum	USA	EGS No. 1952a-1633	KC584631	KC584373	KC584498
Coniothyrium palmarum	Coniothyrium palmarum		CBS 400.71		Chamaerops humilis	Italy		EU754054	EU754153	DQ677956
Crivellia papaveracea	Alternaria penicillata	Crivellia	CBS 116607	T	Papaver rhoeas	Austria	DAOM 230456	KC584580	KC584322	KC584447	KC584229	KC584153	KC584706
Dendryphiella arenariae	Paradendryphiella arenariae		CBS 181.58	T	Coastal sand	France	DAOM 63738; IMI 067735; MUCL 4129	KC793336	KC793338	DQ470924
Dendryphiella salina	Paradendryphiella salina		CBS 142.60		Spartina sp.	UK	MUCL 9639	KC793337	KC793339	KC793340
Embellisia abundans	Alternaria abundans	Chalastospora	CBS 534.83	T	Fragaria sp.	New Zealand	EGS 29.159	KC584581	KC584323	KC584448	JN383485	KC584154	KC584707
Embellisia allii	Alternaria embellisia	Embellisia	CBS 339.71	R	Allium sativum	USA	ATCC 22412; IMI 155707; MUCL 18571; QM 8609	KC584582	KC584324	KC584449	KC584230	KC584155	KC584708
Embellisia annulata	Cicatricea salina		CBS 302.84	T	Cancer pagurus	North Sea, Skagerrak		KC584583	KC584325	KC584450	JN383486	JN383467	KC584709
Embellisia chlamydospora	Alternaria chlamydosporigena	Embellisia	CBS 341.71	R	Air	USA	EGS 10.073; ATCC 22409; IMI 155709; MUCL 18573; QM 7287	KC584584	KC584326	KC584451	KC584231	KC584156	KC584710
Embellisia conoidea	Alternaria conoidea	Brassicicola	CBS 132.89		Ricinus communis	Saudi Arabia		KC584585	KC584327	KC584452	AF348226	FJ348227	KC584711
Embellisia dennisii	Alternaria dennisii		CBS 110533		Senecio jacobaea	New Zealand		KC584586	KC584328	KC584453	KC584232	KC584157	KC584712
Embellisia dennisii	Alternaria dennisii		CBS 476.90	T	Senecio jacobaea	Isle of Man	IMI 151744	KC584587	KC584329	KC584454	JN383488	JN383469	KC584713
Embellisia didymospora	Alternaria didymospora	Phragmosporae	CBS 766.79		Seawater	Adriatic Sea		KC584588	KC584330	KC584455	FJ357312	FJ357300	KC584714
Embellisia eureka	Alternaria eureka	Eureka	CBS 193.86	T	Medicago rugosa	Australia	IMI 273162	KC584589	KC584331	KC584456	JN383490	JN383471	KC584715
Embellisia hyacinthi	Alternaria hyacinthi	Embellisioides	CBS 416.71	T	Hyacinthus orientalis	Netherlands	EGS 19.102; IMI 279179	KC584590	KC584332	KC584457	KC584233	KC584158	KC584716
Embellisia indefessa	Alternaria indefessa	Cheiranthus	CBS 536.83	T	Soil	USA	EGS 30.195	KC584591	KC584333	KC584458	KC584234	KC584159	KC584717
Embellisia leptinellae	Alternaria leptinellae	Eureka	CBS 477.90	T	Leptinella dioica	New Zealand	EGS 39.101	KC584592	KC584334	KC584459	KC584235	KC584160	KC584718
Embellisia lolii	Alternaria lolii	Embellisioides	CBS 115266	T	Lolium perenne	New Zealand		KC584593	KC584335	KC584460	JN383492	JN383473	KC584719
Embellisia novaezelandiae	Alternaria botryospora	Embellisioides	CBS 478.90	T	Leptinella dioica	New Zealand	EGS 39.099	KC584594	KC584336	KC584461	AY278844	AY278831	KC584720
Embellisia phragmospora	Alternaria phragmospora	Phragmosporae	CBS 274.70	T	Soil	The netherlands	EGS 27.098; ATCC 18914	KC584595	KC584337	KC584462	JN383493	JN383474	KC584721
Embellisia planifunda	Alternaria planifunda	Embellisioides	CBS 537.83	T	Triticum aestivum	Australia	IMI 115034	KC584596	KC584338	KC584463	FJ357315	FJ357303	KC584722
Embellisia proteae	Alternaria proteae	Embellisioides	CBS 475.90	T	Protea sp.	Australia	IMI 320290; IMI 341684	KC584597	KC584339	KC584464	AY278842	KC584161	KC584723
Embellisia tellustris	Alternaria tellustris	Embellisia	CBS 538.83	T	Soil	USA	EGS 33.026	KC584598	KC584340	KC584465	FJ357316	AY562419	KC584724
Embellisia tumida	Alternaria tumida	Embellisioides	CBS 539.83	T	Triticum aestivum	Australia		KC584599	KC584341	KC584466	FJ266481	FJ266493	KC584725
Heterospora chenopodii	Heterospora chenopodii		CBS 115.96		Chenopodium album	Netherlands	PD 94/1576	EU754089	EU754188	GU371775
Julella avicenniae	Julella avicenniae		BCC 18422		Mangrove wood	Thailand		GU371831	GU371823	GU371787
Leptosphaerulina australis	Leptosphaerulina australis		CBS 317.83		Eugenia aromatica	Indonesia		GU296160	GU301830	GU371790
Loratospora aestuarii	Loratospora aestuarii		JK 5535B		Juncus roemerianus	USA		GU296168	GU301838	GU371760
Neophaeosphaeria filamentosa	Neophaeosphaeria filamentosa		CBS 102202		Yucca rostrata	Mexico		GQ387516	GQ387577	GU371773
Nimbya caricis	Alternaria caricis	Nimbya	CBS 480.90	T	Carex hoodii	USA	EGS 13.094	KC584600	KC584342	KC584467	AY278839	AY278826	KC584726
“Nimbya gomphrenae”	Alternaria sp.	Alternata	CBS 108.27		Gomphrena globosa	-		KC584601	KC584343	KC584468	KC584236	KC584162	KC584727
Nimbya scirpicola	Alternaria scirpicola	Nimbya	CBS 481.90	R	Scirpus sp.	UK	EGS 19.042	KC584602	KC584344	KC584469	KC584237	KC584163	KC584728
Ophiosphaerella herpotricha	Ophiosphaerella herpotricha		CBS 620.86		Bromus erectus	Switzerland	ETH 9373	DQ678010	DQ678062	DQ677958
Paraleptosphaeria dryadis	Paraleptosphaeria dryadis		CBS 643.86		Dryas octopetala	Switzerland	ETH 9446	KC584632	GU301828	GU371733
Peyronellaea glomerata	Peyronellaea glomerata		CBS 528.66		Chrysanthemum sp.	Netherlands	PD 63/590	EU754085	EU754184	GU371781
Peyronellaea zeaemaydis	Peyronellaea zeaemaydis		CBS 588.69	T	Zea mays	USA		EU754093	EU754192	GU371782
Phaeosphaeria ammophilae	Phaeosphaeria ammophilae		CBS 114595		Ammophila arenaria	Sweden	UPSC 3568	GU296185	GU304859	GU371724
Phaeosphaeria avenaria	Phaeosphaeria avenaria		DAOM 226215		Avena sativa	Canada	OSC 100096	AY544725	AY544684	DQ677941
Phaeosphaeria eustoma	Phaeosphaeria eustoma		CBS 573.86		Dactylis glomerata	Switzerland	ETH 9239	DQ678011	DQ678063	DQ677959
Phoma complanata	Phoma complanata		CBS 268.92		Anglica sylvestris	Netherlands	PD 75/3	EU754081	EU754180	GU371778
Phoma herbarum	Phoma herbarum		CBS 276.37		Wood pulp	Sweden		DQ678014	DQ678066	DQ677962
Plenodomus lingam	Plenodomus lingam		DAOM 229267		Brassica sp.	France		DQ470993	DQ470946	DQ470894
Pleospora betae	Pleospora betae		CBS 109410		Beta vulgaris	Netherlands	PD 77/113	EU754079	EU754178	GU371774
Pleospora calvescens	Pleospora calvescens		CBS 246.79		Atriplex hastata	Germany	PD 77/655	EU754032	EU754131	KC584500
Pleospora chenopodii	Pleospora chenopodii		CBS 206.80		Chenopodium quinoa	Bolivia	PD 74/1022	JF740095	JF740266	KC584501
Pleospora fallens	Pleospora fallens		CBS 161.78		Olea europaea	New Zealand		GU238215	GU238074	KC584502
Pleospora halimiones	Pleospora halimiones		CBS 432.77		Halimione portulacoides	Netherlands	IMI 282137	JF740096	JF740267	KC584503
Pleospora incompta	Pleospora incompta		CBS 467.76		Olea europaea	Greece		GU23822	GU238087	KC584504
Pleospora tarda	Pleospora tarda		CBS 714.68	T	Medicago sativa	Canada	EGS 04.118C; IMI 135456; MUCL 11717; QM 1379	KC584603	KC584345	AF107804	KC584238	AF443881	KC584729
Pleospora typhicola	Pleospora typhicola		CBS 132.69		Typha angustifolia	Netherlands		JF740105	JF740325	KC584505
Pyrenochaeta nobilis	Pyrenochaeta nobilis		CBS 407.76	T	Laurus nobilis	Italy		EU754107	DQ678096	DQ677991
Pyrenophora phaeocomes	Pyrenophora phaeocomes		DAOM 222769		Calamagrostis villosa	Switzerland		DQ499595	DQ499596	DQ497614
Saccothecium sepincola	Saccothecium sepincola		CBS 278.32		Ribes nigrum	USA		GU296195	GU301870	GU371745
Setomelanomma holmii	Setomelanomma holmii		CBS 110217		Picea pungens	USA		GU296196	GQ37633	GU371800
Sinomyces alternariae	Alternaria alternariae	Ulocladium	CBS 126989	T	Daucus carota	USA	EGS 46.004	KC584604	KC584346	KC584470	AF229485	AY278815	KC584730
Stemphylium herbarum	Stemphylium herbarum		CBS 191.86	T	Medicago sativa	India	EGS 36.138; IMI 276975	GU238232	GU238160	KC584471	KC584239	AF443884	KC584731
Teretispora leucanthemi	Alternaria leucanthemi	Teretispora	CBS 421.65	T	Chrysanthemum maximum	Netherlands	ATCC 16028; IFO 9085; IMI 111986; QM 7227	KC584605	KC584347	KC584472	KC584240	KC584164	KC584732
Teretispora leucanthemi	Alternaria leucanthemi		CBS 422.65	R	Chrysanthemum maximum	USA	EGS 17.063; ATCC 16029; IMI 111987; QM 8579	KC584606	KC584348	KC584473	KC584241	KC584165	KC584733
Ulocladium arborescens	Alternaria aspera	Pseudoulocladium	CBS 115269	T	Pistacia vera	Japan	IMI 369777	KC584607	KC584349	KC584474	KC584242	KC584166	KC584734
Ulocladium atrum	Alternaria atra	Ulocladioides	CBS 195.67	T	Soil	USA	ATCC 18040; IMI 124944; QM 8408	KC584608	KC584350	KC584475	AF229486	KC584167	KC584735
Ulocladium botrytis	Alternaria botrytis	Ulocladium	CBS 197.67	T	Contaminant	USA	ATCC 18042; IMI 124942; MUCL 18556; QM 7878	KC584609	KC584351	KC584476	KC584243	KC584168	KC584736
Ulocladium botrytis	Alternaria sp.	Ulocladioides	CBS 198.67	R	Soil	USA	ATCC 18043; IMI 124949; MUCL 18557; QM 8619	KC584610	KC584352	KC584477	AF229487	KC584169	KC584737
Ulocladium brassicae	Alternaria brassicaepekinensis	Ulocladioides	CBS 121493	T	Brassica pekinensis	China	HSAUPwy0037	KC584611	KC584353	KC584478	KC584244	KC584170	KC584738
Ulocladium cantlous	Alternaria cantlous	Ulocladioides	CBS 123007	T	Cucumis melo	China	HSAUP0209	KC584612	KC584354	KC584479	KC584245	KC584171	KC584739
Ulocladium capsici	Alternaria concatenata	Pseudoulocladium	CBS 120006	T	-	-	HSAUPIII00035	KC584613	KC584355	KC584480	KC584246	AY762950	KC584740
Ulocladium chartarum	Alternaria chartarum	Pseudoulocladium	CBS 200.67	T	Populus sp.	Canada	ATCC 18044; DAOM 59616b; IMI 124943; MUCL 18564; QM 8328	KC584614	KC584356	KC584481	AF229488	KC584172	KC584741
Ulocladium consortiale	Alternaria consortialis	Ulocladioides	CBS 104.31	T	-	-		KC584615	KC584357	KC584482	KC584247	KC584173	KC584742
Ulocladium cucurbitae	Alternaria cucurbitae	Ulocladioides	CBS 483.81	R	Cucumis sativus	New Zealand	EGS 31.021; LEV 7067	KC584616	KC584358	KC584483	FJ266483	AY562418	KC584743
Ulocladium multiforme	Alternaria multiformis	Ulocladioides	CBS 102060	T	Soil	Canada		KC584617	KC584359	KC584484	FJ266486	KC584174	KC584744
Ulocladium obovoideum	Alternaria obovoidea	Ulocladioides	CBS 101229		Cucumis sativus	New Zealand		KC584618	KC584360	KC584485	FJ266487	FJ266498	KC584745
Ulocladium oudemansii	Alternaria oudemansii	Ulocladium	CBS 114.07	T	-	-	ATCC 18047; IMI 124940; MUCL 18563; QM 1744	KC584619	KC584361	KC584486	FJ266488	KC584175	KC584746
Ulocladium septosporum	Alternaria septospora	Pseudoulocladium	CBS 109.38		Wood	Italy		KC584620	KC584362	KC584487	FJ266489	FJ266500	KC584747
Ulocladium solani	Alternaria heterospora	Ulocladioides	CBS 123376	T	Lycopersicon esculentum	China	HSAUP 0521	KC584621	KC584363	KC584488	KC584248	KC584176	KC584748
Ulocladium subcucurbitae	Alternaria subcucurbitae	Ulocladioides	CBS 121491	T	Chenopodium glaucum	China		KC584622	KC584364	KC584489	KC584249	EU855803	KC584749
Ulocladium tuberculatum	Alternaria terricola	Ulocladioides	CBS 202.67	T	Soil	USA	ATCC 18048; IMI 124947; MUCL 18560; QM 8614	KC584623	KC584365	KC584490	FJ266490	KC584177	KC584750
Undifilum bornmuelleri	Alternaria bornmuelleri	Undifilum	DAOM 231361	T	Securigera varia	Austria	DAOM 231361	KC584624	KC584366	KC584491	FJ357317	FJ357305	KC584751
Ybotromyces caespitosus	Alternaria caespitosa	Infectoriae	CBS 177.80	T	Human	Spain		KC584625	KC584367	KC584492	KC584250	KC584178	KC584752

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^¹

ATCC: American Type Culture Collection, Manassas, VA, USA; BCC: BIOTEC Culture Collection, Thailand; CBS: Culture collection of the Centraalbureau voor Schimmelcultures, Fungal Biodiversity Centre, Utrecht, The Netherlands; DAOM: Canadian Collection of Fungal Cultures, Ottawa, Canada; DAR: Plant Pathology Herbarium, Orange Agricultural Institute, Australia; DSM: German Collection of Microorganisms and Cell Cultures, Leibniz Institute, Braunschweig, Germany; EGS: Personal collection of Dr. E.G. Simmons; ETH: Swiss Federal Institute of Technology, Switzerland; HSAUP: Department of Plant Pathology, Shandong Agricultural University, China; IFO: Institute for Fermentation Culture Collection, Osaka, Japan; IMI: Culture collection of CABI EUrope UK Centre, Egham UK; JK: Personal collection of Dr. J. Kohlmeyer; LEV: Plant Health and Diagnostic Station, Levin, New Zealand; MUCL: (Agro)Industrial Fungi and Yeast Collection of the Belgian Co-ordinated Collections of Micro-organisms (BCCM), Louvain-la Neuve, Belgium; NZMAF: New Zealand Ministry of Agriculture and Forestry; OSC: Oregon State University Herbarium, USA; PD: Plant Protection Service, Wageningen, The Netherlands; RGR: Personal collection of Dr. R.G. Roberts; UPSC: Uppsala University Culture Collection, Sweden; QM: Quarter Master Culture Collection, Amherst, MA, USA.

^²

T: ex-type strain; R: representative strain.

Freeze-dried strains were revived in 2 mL malt/peptone (50 % / 50 %) and subsequently transferred to oatmeal agar (OA) (Crous et al. 2009a). Strains of the CBS collection stored in liquid nitrogen were transferred to OA directly from -80 °C. DNA extraction was performed using the UltraClean Microbial DNA Isolation Kit (MoBio laboratories, Carlsbad, CA, USA), according to the manufacturer’s instructions.

Taxonomy

Morphological descriptions were made for isolates grown on synthetic nutrient-poor agar plates (SNA, Nirenberg 1976) with a small piece of autoclaved filter paper placed onto the agar surface. Cultures were incubated at moderate temperatures (∼ 22 °C) under CoolWhite fluorescent light with an 8 h photoperiod for 7 d. The sellotape technique was used for making slide preparations (Crous et al. 2009a) with Shear’s medium as mounting fluid. Photographs of characteristic structures were made with a Nikon Eclipse 80i microscope using differential interference contrast (DIC) illumination. Growth rates were measured after 5 and 7 d. Colony characters were noted after 7 d, colony colours were rated according to Rayner (1970). Nomenclatural data were deposited in MycoBank (Crous et al. 2004).

PCR and sequencing

The SSU region was amplified with the primers NS1 and NS4 (White et al. 1990), the LSU region with LSU1Fd (Crous et al. 2009b) and LR5 (Vilgalys & Hester 1990), the ITS region with V9G (De Hoog & Gerrits van den Ende 1998) and ITS4 (White et al. 1990), the GAPDH region with gpd1 and gpd2 (Berbee et al. 1999), the RPB2 region with RPB2-5F2 (Sung et al. 2007) and fRPB2-7cR (Liu et al. 1999) and the TEF1 gene with the primers EF1-728F and EF1-986R (Carbone & Kohn 1999) or EF2 (O’Donnell et al. 1998). The PCRs were performed in a MyCycler™ Thermal Cycler (Bio-Rad Laboratories B.V., Veenendaal, The Netherlands) in a total volume of 12.5 μL. The SSU and LSU PCR mixtures consisted of 1 μL genomic DNA, 1′ GoTaq® Flexi buffer (Promega, Madison, WI, USA), 2 μM MgCl₂, 40 μM of each dNTP, 0.2 μM of each primer and 0.25 Unit GoTaq® Flexi DNA polymerase (Promega). The ITS and GAPDH PCR mixtures differed from the original mix by containing 1 μM MgCl₂, the RPB2 and TEF1 PCR mixtures differed from the original mix by containing 2 μL genomic DNA and the RPB2 mixture differed from the original mix by containing 0.5 U instead of 0.25 U GoTaq® Flexi DNA polymerase. Conditions for PCR amplification consisted of an initial denaturation step of 5 min at 94 °C followed by 35 cycles of 30 s at 94 °C, 30 s at 48 °C and 90 s at 72 °C for SSU, LSU, ITS and 40 cycles of 30 s at 94 °C, 30 s at 52 °C / 59 °C and 45 s at 72 °C for TEF1 using respectively EF2 or EF1-986R as reverse primer and a final elongation step of 7 min at 72 °C. The partial RPB2 gene was obtained by using a touchdown PCR protocol of 5 cycles of 45 s at 94 °C, 45 s at 60 °C and 2 min at 72 °C, followed by 5 cycles with a 58 °C annealing temperature and 30 cycles with a 54 °C annealing temperature. The PCR products were sequenced in both directions using the PCR primers and the BigDye Terminator v. 3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA), according to the manufacturer’s recommendations, and analysed with an ABI Prism 3730XL Sequencer (Applied Biosystems) according to the manufacturer’s instructions. Consensus sequences were computed from forward and reverse sequences using the BioNumerics v. 4.61 software package (Applied Maths, St-Martens-Latem, Belgium). All generated sequences were deposited in GenBank (Table 1).

Phylogenetic analyses

Multiple sequence alignments were generated with MAFFT v. 6.864b (http://mafft.cbrc.jp/alignment/server/index.html), and adjusted by eye. Two different datasets were used to estimate two phylogenies; an Alternaria complex phylogeny and a Pleosporineae family tree. The first tree focusses on the Alternaria complex, the second one was produced to place the genera Comoclathris, Clathrospora and Alternariaster in the context of the Alternaria complex. The relatives of the three genera were determined with standard nucleotide blast searches, with both the SSU and LSU sequences, against the nucleotide database in GenBank. This resulted in a selection of 35 species (Table 1) for which the SSU, LSU and RPB2 sequence data set was present or could be completed. Blast searches with Embellisia annulata gave hits with two marine Dendryphiella species, Dendryphiella arenariae and Dendryphiella salina, which we also included. Phylogenetic analyses of the sequence data consisted of Bayesian and Maximum likelihood analyses of both the individual data partitions as well as the combined aligned dataset. Bayesian analyses were performed with MrBayes v. 3.2.1 (Huelsenbeck & Ronquist 2001, Ronquist & Huelsenbeck 2003). The Markov Chain Monte Carlo (MCMC) analysis used four chains and started from a random tree topology. The sample frequency was set at 100 and the temperature value of the heated chain was 0.1. The temperature value was lowered to 0.05 when the average standard deviation of split frequencies did not fall below 0.01 after 5M generations (RPB2 and Pleosporineae phylogeny). Burn-in was set to 25 % after which the likelihood values were stationary. Maximum likelihood analyses including 500 bootstrap replicates were run using RAxML v. 7.2.6 (Stamatakis & Alachiotis 2010). The online tool Findmodel (http://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html) was used to determine the best nucleotide substitution model for each partition. For the SSU (Pleosporineae family tree), LSU, ITS, RPB2 and TEF1 partitions a GTR model with a gamma-distributed rate variation was suggested, and for the SSU (Alternaria complex) and GAPDH partitions a TrN model with gamma-distributed rate variation. Sequences of Stemphylium herbarum (CBS 191.86) were used as outgroup in the Alternaria phylogeny and those of Jullella avenicae (BCC 18422) in the Pleosporineae phylogeny. The resulting trees were printed with TreeView v. 1.6.6 (Page 1996) and together with the alignments deposited into TreeBASE (http://www.treebase.org).

RESULTS

Phylogeny

For defining the taxonomy of Alternaria and allied genera, 121 strains were included in the Alternaria complex alignment. The alignment length and unique site patterns of the different genes and gene combinations are stated in Table 2. The original ITS alignment consisted of 577 characters of which the first 78 are excluded as this contained a non-alignable region. In the original TEF1 alignment (375 characters) we coded the major inserts (Table 3), which otherwise would negatively influence the phylogeny, resulting in a TEF1 alignment of 269 characters. All phylogenies, different phylogenetic methods and gene regions or gene combinations used on this dataset (data not shown, trees and alignments lodged in TreeBASE), show a weak support at the deeper nodes of the tree. The only well-supported node (Bayesian posterior probability of 1.0, RAxML Maximum Likelihood support value of 100) in all phylogenies separates Embellisia annulata CBS 302.84 and the Pleospora/Stemphylium clade from the Alternaria complex (Fig. 1). In the Alternaria clade, six monotypic lineages and 24 internal clades occur consistently in the individual and combined phylogenies, although positions vary between the different gene regions or combinations used. The support values for the clades within Alternaria (called sections) are plotted in a heat map (Table 2) per gene and phylogenetic method used. The support values for the different phylogenetic methods vary, with the Bayesian posterior probabilities being higher than the RAxML bootstrap support values (Table 2). The SSU, LSU and ITS phylogenies display a low resolution, which reflects in poor to no support of the sections. Therefore, we chose not to include them in the multi-gene alignments, except in the all-gene alignment. In the GAPDH phylogenies, sect. Cheiranthus, sect. Nimbya and sect. Pseudoulocladium are poorly supported and “A. resedae” clusters separate from sect. Cheiranthus. In the RPB2 phylogenies the support values for sect. Alternata, sect. Embellisioides and sect. Eureka are relatively low; A. cumini clusters in sect. Embellisioides instead of sect. Eureka and U. capsici clusters separate from sect. Pseudoulocladium. The TEF1 phylogenies did not support sect. Nimbya and show relative low support for sect. Cheiranthus, sect. Dianthicola, sect. Embellisioides, sect. Panax, sect. Phragmosporae and sect. Radicina, and A. cumini clusters outside sect. Eureka. In the 2-region phylogenies U. capsici clusters outside sect. Pseudoulocladium based on GAPDH and RPB2, E. indefessa clusters outside sect. Cheiranthus based on GAPDH and TEF1, and sect. Eureka is poorly supported based on RPB2 and TEF1. The combined phylogeny based on the GAPDH, RPB2 and TEF1 sequences (Fig. 1) is displayed, as these are the genes with the best resolution.

Table 2.

Summary of locus and phylogenetic results as well as a heat map of the Bayesian posterior probabilities and RAxML boostrap support values per Alternaria section.

graphic file with name table001.jpg

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Table 3.

Coded inserts in the TEF1 sequence alignment.

Species	Nt position	Coded	Nt position	Coded
Alternaria elegans	23 to 39	TC
Alternaria simsimi	23 to 39	TCC
Alternaria dauci	186 to 205	C	221 to 269	TACTT
Alternaria macrospora	186 to 205	C	221 to 269	TCCCC
Alternaria porri	186 to 205	C	221 to 269	ACTTA
Alternaria pseudorostrata	186 to 205	C	221 to 269	TGGTA
Alternaria solani	186 to 205	C	221 to 269	-AAGG
Alternaria tegetica	186 to 205	C	221 to 269	CACAC

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Fig. 1. — Bayesian 50 % majority rule consensus tree based on the GAPDH, RPB2 and TEF1 sequences of 121 strains representing the *Alternaria* complex. The Bayesian posterior probabilities (PP) and RAxML bootstrap support values (ML) are given at the nodes (PP/ML). Thickened lines indicate a PP of 1.0 and ML of 100. The tree was rooted to *Stemphylium herbarum* (CBS 191.86). The monotypic lineages are indicated by black dots.

The final Pleosporineae alignment included 74 strains, representing six families, and consisted of 2 506 characters (SSU 935, LSU 796, RPB2 775) of which 700 were unique site patterns (SSU 111, LSU 145, RPB2 444). In the SSU alignment a large insertion at position 446 in the isolates Chaetosphaeronema hispidulum CBS 216.75, Pleospora fallens CBS 161.78, Pleospora flavigena CBS 314.80 and Ophiosphaerella herpotrichia CBS 620.86 was excluded from the phylogenetic analyses. A total of 43 202 trees were sampled after the burn-in. The type species of Clathrospora, C. elynae, forms a well-supported clade, located basal to the Pleosporaceae (Fig. 2), outside the Alternaria complex. The type species of Comoclathris, C. lanata, was not available for study but the two Comoclathris compressa strains cluster in a well-supported clade within the Pleosporaceae outside Alternaria s. str. The genus Alternariaster, with Alternariaster helianthi as type and only species, also clusters outside the Alternaria complex and even outside Pleosporaceae; it belongs to the Leptosphaeriaceae instead (Fig. 2). Embellisia annulata is identical to Dendryphiella salina, and forms a well-supported clade in the Pleosporaceae together with Dendryphiella arenariae. As the type species of Dendryphiella, D. vinosa, clusters outside the Pleosporineae (dela Cruz 2006, Jones et al. 2008), Dendryphiella salina and D. arenariae are placed in a new genus, Paradendryphiella, below.

Fig. 2. — Bayesian 50 % majority rule consensus tree based on the SSU, LSU and RPB2 sequences of 74 strains representing the *Pleosporineae*. The Bayesian posterior probabilities (PP) and RAxML bootstrap support values (ML) are given at the nodes (PP/ML). Thickened lines indicate a PP of 1.0 and ML of 100. The tree was rooted to *Julella avicenniae* (BCC 18422).

Taxonomy

Based on DNA sequence data in combination with a review of literature and morphology, the species within the Alternaria clade are all recognised here as Alternaria (Fig 1). This puts the genera Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Lewia, Nimbya, Sinomyces, Teretispora, Ulocladium, Undifilum and Ybotromyces in synonymy with Alternaria, resulting in the proposal of 32 new combinations, 10 new names and the resurrection of 10 names. Species of Alternaria were assigned to 24 Alternaria sections, of which 16 are newly described, and six monotypic lineages. The (emended) description of the genus Alternaria, the Alternaria sections and monotypic lineages with new Alternaria names and name combinations are treated below in alphabetical order. Finally the description of the new genus Paradendryphiella is also provided.

Alternaria Nees, Syst. Pilze (Würzburg): 72. 1816 [1816-1817].

= Elosia Pers., Mycol. Eur. (Erlanga) 1: 12. 1822.
= Macrosporium Fr., Syst. Mycol. (Lundae) 3: 373. 1832.
= Rhopalidium Mont., Ann. Sci. Nat., Bot., Sér. 2, 6: 30. 1836.
= Brachycladium Corda, Icon. Fungorum hucusque Cogn. (Prague) 2: 14. 1838.
= Ulocladium Preuss, Linnaea 24: 111. 1851.
= Chmelia Svob.-Pol., Biologia (Bratislava) 21: 82. 1966.
= Embellisia E.G. Simmons, Mycologia 63: 380. 1971.
= Trichoconiella B.L. Jain, Kavaka 3: 39. 1976 [1975].
= Botryomyces de Hoog & C. Rubio, Sabouraudia 20: 19. 1982. (nom. illegit.)
= Lewia M.E. Barr & E.G. Simmons, Mycotaxon 25: 289. 1986.
= Ybotromyces Rulamort, Bull. Soc. Bot. Centre-Ouest, Nouv. Sér. 17: 192. 1986.
= Nimbya E.G. Simmons, Sydowia 41: 316. 1989.
= Allewia E.G. Simmons, Mycotaxon 38: 260. 1990.
= Crivellia Shoemaker & Inderb., Canad. J. Bot. 84: 1308. 2006.
= Chalastospora E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 668. 2007.
= Teretispora E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 674. 2007.
= Undifilum B.M. Pryor, Creamer, Shoemaker, McLain-Romero & Hambl., Botany 87: 190. 2009.
= Sinomyces Yong Wang bis & X.G. Zhang, Fungal Biol. 115: 192. 2011.

Colonies effuse, usually grey, dark blackish brown or black. Mycelium immersed or partly superficial; hyphae colourless, olivaceous-brown or brown. Stroma rarely formed. Setae and hyphopodia absent. Conidiophores macronematous, mononematous, simple or irregularly and loosely branched, pale brown or brown, solitary or in fascicles. Conidiogenous cells integrated, terminal becoming intercalary, polytretic, sympodial, or sometimes monotretic, cicatrized. Conidia catenate or solitary, dry, ovoid, obovoid, cylindrical, narrowly ellipsoid or obclavate, beaked or non-beaked, pale or medium olivaceous-brown to brown, smooth or verrucose, with transverse and with or without oblique or longitudinal septa. Septa can be thick, dark and rigid and an internal cell-like structure can be formed. Species with meristematic growth are known.

Ascomata small, solitary to clustered, erumpent to (nearly) superficial at maturity, globose to ovoid, dark brown, smooth, apically papillate, ostiolate. Papilla short, blunt. Peridium thin. Hamathecium of cellular pseudoparaphyses. Asci few to many per ascoma, (4-6-)8-spored, basal, bitunicate, fissitunicate, cylindrical to cylindro-clavate, straight or somewhat curved, with a short, furcate pedicel. Ascospores muriform, ellipsoid to fusoid, slightly constricted at septa, yellow-brown, without guttules, smooth, 3-7 transverse septa, 1-2 series of longitudinal septa through the two original central segments, end cells without septa, or with 1 longitudinal or oblique septum, or with a Y-shaped pair of septa.

Type species: Alternaria alternata (Fr.) Keissl.

ALTERNARIA SECTIONS

Section Alternantherae D.P. Lawr., Gannibal, Peever & B.M. Pryor, Mycologia 105: 540. 2013. Fig. 3.

Type species: Alternaria alternantherae Holcomb & Antonop.

Diagnosis: Section Alternantherae contains short to moderately long conidiophores with a conidiogenous tip which can be enlarged. Conidia are narrowly ellipsoid or ovoid, sometimes subcylindrical, solitary or rarely paired, sometimes slightly constricted near some septa, longitudinal or oblique septa occasionally occur, disto- and euseptate, with a long apical narrow beak. The conidial beak is unbranched, septate or aseptate, long filiform, and sometimes swollen at the end. Internal compartmentation occurs, cell lumina tend to be broadly octagonal to rounded.

Notes: Section Alternantherae was recently established by Lawrence et al. (2013) after first being described as species-group A. alternantherae (Lawrence et al. 2012). The described section consists of three former Nimbya species which formed a separate clade amidst the Alternaria species-groups based on sequences of the GAPDH, ITS and Alt a 1 genes (Lawrence et al. 2012). Nimbya celosiae is placed in this section based on the data of Lawrence et al. (2012), while N. gomphrenae is placed in the section based on ITS sequence data from Chou & Wu (2002).

Alternaria alternantherae Holcomb & Antonop., Mycologia 68: 1126. 1976.

≡ Nimbya alternantherae (Holcomb & Antonop.) E.G. Simmons & Alcorn, Mycotaxon 55: 142. 1995.

Alternaria celosiicola Jun. Nishikawa & C. Nakash., J. Phytopathol.: doi: 10.1111/jph.12108 (p. 3). 2013.

Basionym: Nimbya celosiae E.G. Simmons & Holcomb, Mycotaxon 55: 144. 1995.

≡ Alternaria celosiae (E.G. Simmons & Holcomb) D.P. Lawr., M.S. Park & B.M. Pryor, Mycol. Progr. 11: 811. 2012. (nom. illegit., homonym of Alternaria celosiae (Tassi) O. Savul. 1950).

Alternaria gomphrenae Togashi, Bull. Imp. Coll. Agric. 9: 6. 1926.

≡ Nimbya gomphrenae (Togashi) E.G. Simmons, Sydowia 41: 324. 1989.

Alternaria perpunctulata (E.G. Simmons) D.P. Lawr., M.S. Park & B.M. Pryor, Mycol. Progr. 11: 811. 2012.

Basionym: Nimbya perpunctulata E.G. Simmons, Stud. Mycol. 50: 115. 2004.

Section Alternata D.P. Lawr., Gannibal, Peever & B.M. Pryor, Mycologia 105: 538. 2013. Fig. 4.

Type species: Alternaria alternata (Fr.) Keissl.

Diagnosis: Section Alternata contains straight or curved primary conidiophores, short to long, simple or branched, with one or several apical conidiogenous loci. Conidia are obclavate, long ellipsoid, small or moderate in size, septate, slightly constricted near some septa, with few longitudinal septa, in moderately long to long, simple or branched chains. The conidium body can narrow gradually into a tapered beak or secondary conidiophore. Secondary conidiophores can be formed apically or laterally with one or a few conidiogenous loci.

Notes: Next to the species that are displayed in our phylogeny, 14 more are included in sect. Alternata based on the study of Lawrence et al. (2013) and confirmed by our molecular data (not shown). We chose not to include 11 species from the study of Lawrence et al. (2013). The species A. gossypina, A. grisae, A. grossulariae, A. iridis, A. lini, A. maritima and A. nelumbii were not recognised by Simmons (2007) and the strains of A. malvae, A. rhadina, A. resedae and A. tomato used by Lawrence et al. (2013) were not authentic. Section Alternata comprises almost 60 Alternaria species based on ITS sequence data (data not shown). The molecular variation within this section is low.

Alternaria alternata (Fr.) Keissl., Beih. Bot. Centralbl., Abt. 2, 29: 434. 1912.

Basionym: Torula alternata Fr., Syst. Mycol. (Lundae) 3: 500. 1832 (nom. sanct.).

= Alternaria tenuis Nees, Syst. Pilze (Würzburg): 72. 1816 [1816-1817].

Additional synonyms listed in Simmons (2007)

Alternaria angustiovoidea E.G. Simmons, Mycotaxon 25: 198. 1986.

Alternaria arborescens E.G. Simmons, Mycotaxon 70: 356. 1999.

Alternaria burnsii Uppal, Patel & Kamat, Indian J. Agric. Sci. 8: 49. 1938.

Alternaria cerealis E.G. Simmons & C.F. Hill, CBS Biodiversity Ser. (Utrecht) 6: 600. 2007.

Alternaria citriarbusti E.G. Simmons, Mycotaxon 70: 287. 1999.

Alternaria citrimacularis E.G. Simmons, Mycotaxon 70: 277. 1999.

Alternaria colombiana E.G. Simmons, Mycotaxon 70: 298. 1999.

Alternaria daucifollii E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 518. 2007.

Alternaria destruens E.G. Simmons, Mycotaxon 68: 419. 1998.

Alternaria dumosa E.G. Simmons, Mycotaxon 70: 310. 1999.

Alternaria gaisen Nagano ex Hara, Sakumotsu Byorigaku, Edn 4: 263. 1928.

= Alternaria gaisen Nagano, J. Jap. Soc. Hort. Sci. 32: 16-19. 1920. (nom. illegit.)
= Alternaria kikuchiana S. Tanaka, Mem. Coll. Agric. Kyoto Univ., Phytopathol. Ser. 28: 27. 1933.
= Macrosporium nashi Miura, Flora of Manchuria and East Mongolia, Part III Cryptogams, Fungi: 513. 1928.

Alternaria herbiphorbicola E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 608. 2007.

Alternaria limoniasperae E.G. Simmons, Mycotaxon 70: 272. 1999.

Alternaria longipes (Ellis & Everh.) E.W. Mason, Mycol. Pap. 2: 19. 1928.

Basionym: Macrosporium longipes Ellis & Everh., J. Mycol. 7: 134. 1892.

= Alternaria brassicae var. tabaci Preissecker, Fachliche Mitt. Österr. Tabakregie 16: 4. 1916.

Alternaria perangusta E.G. Simmons, Mycotaxon 70: 303. 1999.

Alternaria postmessia E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 598. 2007.

Alternaria tangelonis E.G. Simmons, Mycotaxon 70: 282. 1999.

Alternaria tenuissima (Nees & T. Nees: Fr.) Wiltshire, Trans. Brit. Mycol. Soc. 18: 157. 1933.

Basionym: Macrosporium tenuissimum (Nees & T. Nees) Fr., Syst. Mycol. (Lundae) 3: 374. 1832 (nom. sanct.).

≡ Helminthosporium tenuissimum Kunze ex Nees & T. Nees, Nova Acta Acad. Caes. Leop.-Carol. German. Nat. Cur. 9: 242. 1818.

Additional synonyms listed in Simmons (2007).

Alternaria toxicogenica E.G. Simmons, Mycotaxon 70: 294. 1999.

Alternaria turkisafria E.G. Simmons, Mycotaxon 70: 290. 1999.

Section Brassicicola D.P. Lawr., Gannibal, Peever & B.M. Pryor, Mycologia 105: 541. 2013. Fig. 5.

Type species: Alternaria brassicicola (Schwein.) Wiltshire

Diagnosis: Section Brassicicola contains short to moderately long, simple or branched primary conidiophores with one or several apical conidiogenous loci. Conidia are ellipsoid, ovoid or somewhat obclavate, small or moderate in size, septate, slightly or strongly constricted at most of their transverse septa, with no to many longitudinal septa, in moderately long to long, simple or branched chains, with dark septa and cell walls. Secondary conidiophores can be formed apically or laterally with one or a few conidiogenous loci. Chlamydospores may occur.

Notes: Our molecular data support the morphological placement of A. septorioides and A. solidaccana in section Brassicicola (Simmons 2007). The other three species were already assigned to this section based on previous molecular studies (Pryor et al. 2009, Runa et al. 2009, Lawrence et al. 2012). Alternaria japonica was previously linked to the A. brassicicola species-group (Pryor & Gilbertson 2000, Pryor & Bigelow 2003, Lawrence et al. 2013), but this association was questioned by Hong et al. (2005). In our analyses, A. japonica clustered in sect. Japonicae.

Alternaria brassicicola (Schwein.) Wiltshire, Mycol. Pap. 20: 8. 1947.

Basionym: Helminthosporium brassicicola Schwein., Trans. Amer. Philos. Soc., Ser. 2, 4: 279. 1832.

Additional synonyms listed in Simmons (2007)

Alternaria conoidea (E.G. Simmons) D.P. Lawr., Gannibal, Peever & B.M. Pryor, Mycologia 105: 542. 2013.

Basionym: Embellisia conoidea E.G. Simmons, Mycotaxon 17: 226. 1983.

Alternaria mimicula E.G. Simmons, Mycotaxon 55: 129. 1995.

Alternaria septorioides (Westend.) E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 570. 2007.

Basionym: Sporidesmium septorioides Westend., Bull. Acad. Roy. Sci. Belgique., Cl. Sci., Sér. 2, 21: 236. 1854.

= Alternaria resedae Neerg., Annual Rep. Phytopathol. Lab. J.E. Ohlsens Enkes, Seed Growers, Copenhagen 7: 9. 1942 (nom. nud.).
= Alternaria resedae Neerg., Danish species of Alternaria & Stemphylium: 150. 1945.

Alternaria solidaccana E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 572. 2007.

Section Chalastospora (E.G. Simmons) Woudenb. & Crous, comb. et stat. nov. MycoBank MB803733. Fig. 6.

Basionym: Chalastospora E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 668. 2007.

Type species: Alternaria cetera E.G. Simmons

Diagnosis: Section Chalastospora contains short to long, simple or branched primary conidiophores with one or several conidiogenous loci. Conidia are pale to medium brown, narrowly ellipsoid to ellipsoid or ovoid, beakless, with no to multiple transverse eusepta and rarely longitudinal septa, solitary or in chains. Secondary conidiophores can be formed apically or laterally with one or a few conidiogenous loci.

Notes: Previous studies already placed E. abundans in the Chalastospora-clade (Andersen et al. 2009, Lawrence et al. 2012). Our study also placed Alternaria armoraciae in this section, while Crous et al. (2009c) showed that Chalastospora gossypii, formerly Alternaria malorum, belonged to this section based on sequences of the ITS and LSU genes.

Alternaria abundans (E.G. Simmons) Woudenb. & Crous, comb. nov. MycoBank MB803688.

Basionym: Embellisia abundans E.G. Simmons, Mycotaxon 17: 222. 1983.

Alternaria armoraciae E.G. Simmons & C.F. Hill, CBS Biodiversity Ser. (Utrecht) 6: 660. 2007.

Alternaria breviramosa Woudenb. & Crous, nom. nov. MycoBank MB803690.

Basionym: Chalastospora ellipsoidea Crous & U. Braun, Persoonia 22: 145. 2009, non Alternaria ellipsoidea E.G. Simmons, 2002.

Etymology: Name refers to the short lateral branches.

Alternaria cetera E.G. Simmons, Mycotaxon 57: 393. 1996.

≡ Chalastospora cetera (E.G. Simmons) E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 668. 2007.

Alternaria malorum (Ruehle) U. Braun, Crous & Dugan, Mycol. Progr. 2: 5. 2003.

Basionym: Cladosporium malorum Ruehle, Phytopathology 21: 1146. 1931.

= Cladosporium gossypii Jacz., Khlopkovoe Delo, 1929 (5-6): 564. 1929, non Alternaria gossypii (Jacz.) Y. Nisik., K. Kimura & Miyaw., 1940.
- ≡ Chalastospora gossypii (Jacz.) U. Braun & Crous, Persoonia 22: 144. 2009.
= Cladosporium malorum Heald, Wash. State Agric. Exp. Sta. Bull., Special Ser. 245: 48. 1930. (nom. nud.)

Additional synonyms in Crous et al. (2009c).

Alternaria obclavata (Crous & U. Braun) Woudenb. & Crous, comb. nov. MycoBank MB803689.

Basionym: Chalastospora obclavata Crous & U. Braun, Persoonia 22: 146. 2009.

Section Cheiranthus Woudenb. & Crous, sect. nov. MycoBank MB803734. Fig. 7.

Type species: Alternaria cheiranthi (Lib.) P.C. Bolle

Diagnosis: Section Cheiranthus contains short to moderately long, simple or branched primary conidiophores with one or several conidiogenous loci. Conidia are ovoid, broadly ellipsoid with transverse and longitudinal septa, slightly or strongly constricted at the septa, in short to long, simple or branched chains. Secondary conidiophores can be formed apically or laterally with a single conidiogenous locus.

Notes: Next to Alternaria cheiranthi and Embellisia indefessa, sect. Cheiranthus contains a non-sporulating strain formerly known as Alternaria resedae, CBS 115.44. Because Alternaria resedae is synonymised with Alternaria septorioides (Simmons 2007), which clusters in section Brassisicola, CBS 115.44 will be treated as “Alternaria sp.”. Alternaria cheiranthi and E. indefessa have been linked to Ulocladium (Pryor & Gilbertson 2000, Pryor & Bigelow 2003, Hong et al. 2005, Pryor et al. 2009, Runa et al. 2009, Lawrence et al. 2012), but based on morphology could not be placed here. Our extensive dataset showed that they form a sister section to section Ulocladioides.

Alternaria cheiranthi (Lib.) P.C. Bolle, Meded. Phytopathol. Lab. “Willie Commelin Scholten” 7: 43. 1924.

Basionym: Helminthosporium cheiranthi Lib. [as “Helmisporium”], in Desmazières, Plantes Cryptogames du Nord de la France, edn 1: 213. 1827.

≡ Macrosporium cheiranthi (Lib.) Fr., Syst. Mycol. (Lundae) 3: 374. 1832.

Alternaria indefessa (E.G. Simmons) Woudenberg & Crous, comb. nov. MycoBank MB803691.

Basionym: Embellisia indefessa E.G. Simmons, Mycotaxon 17: 228. 1983.

Section Crivellia (Shoemaker & Inderb.) Woudenb. & Crous, comb. et stat. nov. MycoBank MB803735. Fig. 8.

Basionym: Crivellia Shoemaker & Inderb., Canad. J. Bot. 84: 1308. 2006.

Type species: Alternaria penicillata (Corda) Woudenb. & Crous (= Cucurbitaria papaveracea De Not.).

Diagnosis: Section Crivellia is characterised by straight or curved, simple or branched primary conidiophores, with geniculate, sympodial proliferations. Conidia are cylindrical, straight to curved to inequilateral, with transverse eusepta, rarely constricted at septa, single or in short, simple or branched chains. Secondary conidiophores are formed apically or laterally. Microsclerotia or chlamydospores may occur. Sexual morphs observed.

Notes: Section Crivellia contains the type species of the sexual morph Crivellia, C. papaveracea, with Brachycladium penicillatum asexual morph, and Brachycladium papaveris. The genus was established by Inderbitzin et al. (2006) based on the finding that C. papaveraceae, formerly Pleospora papaveraceae, belonged to the Alternaria-complex instead of Pleospora s. str. based on ITS, GAPDH and TEF1 sequences.

Alternaria papavericola Woudenb. & Crous, nom. nov. MycoBank MB803749.

Basionym: Helminthosporium papaveris Sawada, J. Nat. Hist. Soc. Formosa 31: 1. 1917.

≡ Dendryphion papaveris (Sawada) Sawada, Special Publ. Coll. Agric. Natl. Taiwan Univ. 8: 200. 1959, non Alternaria papaveris (Bres.) M.B. Ellis, 1976.
≡ Brachycladium papaveris (Sawada) Shoemaker & Inderb., Canad. J. Bot. 84: 1310. 2006.

Etymology: Name refers to the host.

Alternaria penicillata (Corda) Woudenb. & Crous, comb. nov. MycoBank MB803692.

Basionym: Brachycladium penicillatum Corda, Icon. Fungorum hucusque Cogn. (Prague) 2: 14. 1838.

- ≡ Dendryphion penicillatum (Corda) Fr., Summa Veg. Scand., Sect. Post. (Stockholm): 504. 1849.
= Cucurbitaria papaveracea De Not., Sferiacei Italici: 62. 1863.
- ≡ Pleospora papaveracea (De Not.) Sacc., Syll. Fungorum (Abellini) 2: 243. 1883.
- ≡ Crivellia papaveracea (De Not.) Shoemaker & Inderb., Canad. J. Bot. 84: 1308. 2006.

Note: The asexual name, Brachycladium penicillatum is older than the sexual name, Cucurbitaria papaveracea, and therefore the species epithet penicillatum is chosen above papaveracea.

Section Dianthicola Woudenb. & Crous, sect. nov. MycoBank MB803736. Fig. 9.

Type species: Alternaria dianthicola Neerg.

Diagnosis: Section Dianthicola contains simple or branched primary conidiophores, with or without apical geniculate proliferations. Conidia are narrowly ovoid or narrowly ellipsoid with transverse and few longitudinal septa, slightly constricted at the septa, with a long (filamentous) beak or apical secondary conidiophore, solitary or in short chains.

Note: Based on the ITS sequence, Alternaria dianthicola clustered near Ulocladium (Chou & Wu 2002). Our extensive dataset places it in a sister section to section Ulocladioides.

Alternaria dianthicola Neerg., Danish species of Alternaria & Stemphylium: 190. 1945.

Alternaria elegans E.G. Simmons & J.C. David, Mycotaxon 75: 89. 2000.

Alternaria simsimi E.G. Simmons, Stud. Mycol. 50: 111. 2004.

Section Embellisia (E.G. Simmons) Woudenb. & Crous, comb. et stat. nov. MycoBank MB803737. Fig. 10.

Basionym: Embellisia E.G. Simmons, Mycologia 63: 380. 1971.

Type species: Alternaria embellisia Woudenb. & Crous (≡ Helminthosporium allii Campan., Embellisia allii (Campan.) E.G. Simmons).

Diagnosis: Section Embellisia contains simple, septate conidiophores, straight or with geniculate sympodial proliferation. Condia are solitary, ovoid to subcylindrical, straight to inequilateral, transseptate; septa can be thick, dark and rigid in contrast to the external wall. Chlamydospores may occur.

Notes: Section Embellisia contains the first two species described in the genus Embellisia, Embellisia allii (type species) and Embellisia chlamydospora (Simmons 1971) together with Embellisia tellustris. This clade is also resolved in the latest molecular revision of Embellisia based on sequences of the GAPDH, ITS and Alt a 1 genes as Embellisia group I (Lawrence et al. 2012).

Alternaria chlamydosporigena Woudenb. & Crous, nom. nov. MycoBank MB803694.

Basionym: Pseudostemphylium chlamydosporum Hoes, G.W. Bruehl & C.G. Shaw, Mycologia 57: 904. 1965, non Alternaria chlamydospora Mouch., 1973.

≡ Embellisia chlamydospora (Hoes, G.W. Bruehl & C.G. Shaw) E.G. Simmons, Mycologia 63: 384. 1971.

Etymology: Name refers to the formation of chlamydospores during growth.

Alternaria embellisia Woudenb. & Crous, nom. nov. MycoBank MB803693.

Basionym: Helminthosporium allii Campan., Nuovi Ann. Agric. Roma 4: 87. 1924, non Alternaria allii Nolla, 1927.

≡ Embellisia allii (Campan.) E.G. Simmons, Mycologia 63: 382. 1971.

Etymology: Name refers to the genus Embellisia for which it served as type species.

Alternaria tellustris (E.G. Simmons) Woudenb. & Crous, comb. nov. MycoBank MB803695.

Basionym: Embellisia tellustris E.G. Simmons [as “telluster”], Mycotaxon 17: 234. 1983.

Section Embellisioides Woudenb. & Crous, sect. nov. MycoBank MB803738. Fig. 11.

Type species: Alternaria hyacinthi (de Hoog & P.J. Mull. bis) Woudenb. & Crous

Diagnosis: Section Embellisioides contains simple, septate conidiophores, straight or with multiple, geniculate, sympodial proliferations. Apical or lateral, short secondary conidiophores may occur. Condia are solitary or in short chains, obovoid to ellipsoid, with transverse and longitudinal septa; transverse septa can be thick, dark and rigid in contrast to the external wall. Chlamydospores and a sexual morph may occur.

Note: In Lawrence et al. (2012) the section is named Embellisia group III.

Alternaria botryospora Woudenb. & Crous, nom. nov. MycoBank MB803705.

Basionym: Embellisia novae-zelandiae E.G. Simmons & C.F. Hill, Mycotaxon 38: 252. 1990, non Alternaria novae-zelandiae E.G. Simmons, 2002.

Etymology: Name refers to the clusters of conidia.

Alternaria hyacinthi (de Hoog & P.J. Mull. bis) Woudenb. & Crous, comb. nov. MycoBank MB803703.

Basionym: Embellisia hyacinthi de Hoog & P.J. Mull. bis, Netherlands J. Pl. Pathol. 79: 85. 1973.

Alternaria lolii (E.G. Simmons & C.F. Hill) Woudenb. & Crous, comb. nov. MycoBank MB803704.

Basionym: Embellisia lolii E.G. Simmons & C.F. Hill, Stud. Mycol. 50: 113. 2004.

Alternaria planifunda (E.G. Simmons) Woudenb. & Crous, comb. nov. MycoBank MB803706.

Basionym: Embellisia planifunda E.G. Simmons, Mycotaxon 17: 233. 1983.

Alternaria proteae (E.G. Simmons) Woudenb. & Crous, comb. nov. MycoBank MB803707.

Basionym: Embellisia proteae E.G. Simmons, Mycotaxon 38: 258. 1990.

= Allewia proteae E.G. Simmons, Mycotaxon 38: 262. 1990.

Alternaria tumida (E.G. Simmons) Woudenb. & Crous, comb. nov. MycoBank MB803708.

Basionym: Embellisia tumida E.G. Simmons, Mycotaxon 17: 236. 1983.

Section Eureka Woudenb. & Crous, sect. nov. MycoBank MB803739. Fig. 12.

Type species: Alternaria eureka E.G. Simmons

Diagnosis: Section Eureka contains simple, septate conidiophores, straight or with geniculate, sympodial proliferations. Apical or lateral, short secondary conidiophores may occur. Condia are solitary or in short chains, narrowly ellipsoid to cylindrical, with transverse and longitudinal septa, slighty constricted at the septa, with a blunt rounded apex. Chlamydospores and a sexual morph may occur.

Notes: Section Eureka contains four Alternaria species and two former Embellisia species. From the Alternaria species only the ITS sequence of A. geniostomatis was previously used in a molecular study (Toth et al. 2011), showing it to cluster separate from the other Alternaria spp. The two Embellisia species were included in the latest molecular-based revision of Embellisia (Lawrence et al. 2012) where they formed Embellisia group IV. A sexual morph is known for the type species of this section.

Alternaria anigozanthi Priest, Australas. Pl. Pathol. 24: 239. 1995.

Alternaria cumini E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 664. 2007.

Alternaria eureka E.G. Simmons, Mycotaxon 25: 306. 1986.

- ≡ Embellisia eureka (E.G. Simmons) E.G. Simmons, Mycotaxon 38: 260. 1990.
= Lewia eureka E.G. Simmons, Mycotaxon 25: 304. 1986.
- ≡ Allewia eureka (E.G. Simmons) E.G. Simmons, Mycotaxon 38: 264. 1990.

Alternaria geniostomatis E.G. Simmons & C.F. Hill, CBS Biodiversity Ser. (Utrecht) 6: 412. 2007.

Alternaria leptinellae (E.G. Simmons & C.F. Hill) Woudenb. & Crous, comb. nov. MycoBank MB803696.

Basionym: Embellisia leptinellae E.G. Simmons & C.F. Hill, Mycotaxon 38: 254. 1990.

Alternaria triglochinicola Alcorn & S.M. Francis, Mycotaxon 46: 359. 1993.

Section Gypsophilae D.P. Lawr., Gannibal, Peever & B.M. Pryor, Mycologia 105: 541. 2013. Fig. 13

Type species: Alternaria gypsophilae Neerg.

Diagnosis: Section Gypsophilae contains simple, or occasionally branched, primary conidiophores, with one or a few conidiogenous loci. Conidia are ellipsoid to long ovoid, with multiple transverse and longitudinal septa, conspicuously constricted near some transverse septa, solitary or in short chains. Secondary conidiophores are formed apically with one or two conidiogenous loci or laterally with a single conidiogenous locus. Species from this section occur on Caryophyllaceae.

Notes: Section Gypsophilae was recently established by Lawrence et al. (2013) containing the four Alternaria species, A. gypsophilae, A. nobilis, A. vaccariae and A. vaccariicola. Our dataset adds four Alternaria species, A. axiaeriisporifera, A. ellipsoidea, A. saponariae, and A. juxtiseptata to this section. Simmons (2007) noted the similarity of the primary conidia of A. ellipsoidea to A. gypsophilae, A. nobilis, A. saponariae and A. vaccariae. This section contains all Alternaria species that occur on Caryophyllaceae (Simmons 2002), except A. dianthicola which resides in sect. Dianthicola.

Alternaria axiaeriisporifera E.G. Simmons & C.F. Hill, CBS Biodiversity Ser. (Utrecht) 6: 662. 2007.

Alternaria ellipsoidea E.G. Simmons, Mycotaxon 82: 31. 2002.

Alternaria gypsophilae Neerg., Danish species of Alternaria & Stemphylium: 207. 1945.

Alternaria juxtiseptata E.G. Simmons, Mycotaxon 82: 32. 2002.

Alternaria nobilis (Vize) E.G. Simmons, Mycotaxon 82: 7. 2002.

Basionym: Macrosporium nobile Vize, Grevillea 5(35): 119. 1877.

Alternaria saponariae (Peck) Neerg., Annual Rep. Phytopathol. Lab. J.E. Ohlsens Enkes, Seed Growers, Copenhagen 3: 6. 1938 [1937-1938].

Basionym: Macrosporium saponariae Peck, Rep. (Annual) NewYork State Mus. Nat. Hist. 28: 62. 1876 [1875].

Alternaria vaccariae (Săvul. & Sandu) E.G. Simmons & S.T. Koike, Mycotaxon 82: 21. 2002.

Basionym: Macrosporium vaccariae Săvul. & Sandu, Hedwigia 73: 130. 1933.

Alternaria vaccariicola E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 594. 2007.

Section Infectoriae Woudenb. & Crous, sect. nov. MycoBank MB803740. Fig. 14.

Type species: Alternaria infectoria E.G. Simmons

Diagnosis: Section Infectoriae contains short to long, simple or branched primary conidiophores with one or several conidiogenous loci. Conidia are obclavate, long-ellipsoid, small or moderate in size, septate, slightly constricted near some septa, with few longitudinal septa, in moderately long to long, branched chains. Long, geniculate, multi-locus secondary conidiophores can be formed apically or laterally. Sexual morphs are known, and meristematic growth has been reported.

Notes: In addition to the six species that are displayed in our phylogeny, 19 more are included based on the study of Lawrence et al. (2013), confirmed with our molecular data (not shown). From these 25 species, nine species have a known sexual morph in Lewia. Three species from the study of Lawrence et al. (2013) are not included; A. photistica (sect. Panax) and A. dianthicola (sect. Dianthicola) cluster elsewhere in our phylogenies and A. peglionii is marked as a taxon incertae sedis by Simmons (2007). The human pathogenic genera Ybotromyces and Chmelia are also embedded in sect. Infectoriae.

Alternaria alternarina E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 644. 2007.

= Pyrenophora alternarina M.D. Whitehead & J. Dicks., Mycologia 44: 748. 1952.
- ≡ Lewia alternarina (M.D. Whitehead & J.G. Dicks.) E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 644. 2007.

Alternaria arbusti E.G. Simmons, Mycotaxon 48: 103. 1993.

Alternaria caespitosa (de Hoog & C. Rubio) Woudenb. & Crous, comb. nov. MycoBank MB803698.

Basionym: Botryomyces caespitosus de Hoog & C. Rubio, Mycotaxon 14: 19. 1982.

≡ Ybotromyces caespitosus (de Hoog & C. Rubio) Rulamort, Bull. Soc. Bot. Centre-Ouest, Nouv. Sér. 21: 512. 1990.

Alternaria californica E.G. Simmons & S.T. Koike, CBS Biodiversity Ser. (Utrecht) 6: 602. 2007.

Alternaria conjuncta E.G. Simmons, Mycotaxon 25: 294. 1986.

= Sphaeria scrophulariae Desm., Ann. Sci. Nat., Bot., Sér. 2, 6: 245. 1836.
- ≡ Leptosphaeria scrophulariae (Desm.) Sacc., Syll. Fungorum (Abellini) 2: 57. 1883.
- ≡ Heptameria scrophulariae (Desm.) Cooke, Grevillea 18(no. 86): 31. 1889.
- ≡ Pleospora scrophulariae (Desm.) Höhn., Sitzungsber. Kaiserl. Akad. Wiss., Math.-Naturwiss. Cl., Abt. 1. 126(4-5): 374. 1917.
- ≡ Lewia scrophulariae (Desm.) M.E. Barr & E.G. Simmons, Mycotaxon 25: 294. 1986.

Alternaria daucicaulis E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 640. 2007.

= Lewia daucicaulis E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 640. 2007.

Alternaria ethzedia E.G. Simmons, Mycotaxon 25: 300. 1986.

= Lewia ethzedia E.G. Simmons, Mycotaxon 25: 299. 1986.

Alternaria frumenti E.G. Simmons & C.F. Hill, CBS Biodiversity Ser. (Utrecht) 6: 620. 2007.

Alternaria graminicola E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 626. 2007.

Alternaria hordeiaustralica E.G. Simmons & Alcorn, CBS Biodiversity Ser. (Utrecht) 6: 614. 2007.

= Lewia hordeiaustralica E.G. Simmons & Alcorn, CBS Biodiversity Ser. (Utrecht) 6: 614. 2007.

Alternaria hordeicola E.G. Simmons & Kosiak, CBS Biodiversity Ser. (Utrecht) 6: 630. 2007.

= Lewia hordeicola Kwaśna & Kosiak, Mycologia 98: 663. 2006.

Alternaria humuli E.G. Simmons, Mycotaxon 83: 139. 2002.

Alternaria incomplexa E.G. Simmons, Mycotaxon 57: 394. 1996.

Alternaria infectoria E.G. Simmons, Mycotaxon 25: 298. 1986.

= Pleospora infectoria Fuckel, Jahrb. Nassauischen Vereins Naturk. 23-24: 132. 1870 [1869-70].
- ≡ Sphaeria infectoria (Fuckel) Cooke, Handb. Brit. Fungi 2: 897. 1871.
- ≡ Pleospora phaeocomoides var. infectoria (Fuckel) Wehm., A World Monograph of the Genus Pleospora and its Segregates: 121. 1961.
- ≡ Lewia infectoria (Fuckel) M.E. Barr & E.G. Simmons, Mycotaxon 25: 296. 1986.

Alternaria intercepta E.G. Simmons, Mycotaxon 83: 134. 2002.

= Lewia intercepta E.G. Simmons & McKemy, Mycotaxon 83: 133. 2002.

Alternaria merytae E.G. Simmons, Mycotaxon 83: 136. 2002.

Alternaria metachromatica E.G. Simmons, Mycotaxon 50: 418. 1994.

Alternaria novae-zelandiae E.G. Simmons, Mycotaxon 83: 142. 2002.

Alternaria oregonensis E.G. Simmons, Mycotaxon 50: 417. 1994.

Alternaria slovaca (Svob.-Pol., L. Chmel & Bojan.) Woudenb. & Crous, comb. nov. MycoBank MB803699.

Basionym: Aureobasidium slovacum Svob.-Pol., L. Chmel & Bojan., Conspect. Verruc. 5: 116. 1966.

≡ Chmelia slovaca (Svob.-Pol., L. Chmel & Bojan.) Svob.-Pol., Biologia (Bratislava) 21: 83. 1966.

Alternaria triticimaculans E.G. Simmons & Perelló, Mycotaxon 50: 413. 1994.

Alternaria triticina Prasada & Prabhu, Indian Phytopathol. 15 (3-4): 292. 1963. [1962]

Alternaria ventricosa R.G. Roberts, Mycotaxon 100: 164. 2007.

Alternaria viburni E.G. Simmons, Mycotaxon 83: 132. 2002.

= Lewia viburni E.G. Simmons & McKemy, Mycotaxon 83: 130. 2002.

Section Japonicae Woudenb. & Crous, sect. nov. MycoBank MB803741. Fig. 15.

Type species: Alternaria japonica Yoshii

Diagnosis: Section Japonicae contains short to long, simple or occasionally branched primary conidiophores with a single conidiogenous locus. Conidia are short, to long-ovoid with transverse and longitudinal septa, conspicuously constricted at most of the transverse septa, in short chains. Apical secondary conidiophores are produced with a single conidiogenous locus. The species within this section occur on Brassicaceae.

Note: Alternaria japonica was previously connected to the A. brassicicola species-group (Pryor & Gilbertson 2000, Pryor & Bigelow 2003, Lawrence et al. 2013), but this association was questioned by Hong et al. (2005).

Alternaria japonica Yoshii, J. Pl. Protect. 28: 17. 1941.

= Alternaria matthiolae Neerg., Danish species of Alternaria and Stemphylium: 184. 1945.

Alternaria nepalensis E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 480. 2007.

Section Nimbya (E.G. Simmons) Woudenb. & Crous, comb. et stat. nov. MycoBank MB803742. Fig. 16.

Basionym: Nimbya E.G. Simmons, Sydowia 41: 316. 1989.

Type species: Alternaria scirpicola (Fuckel) Sivan.

Diagnosis: Section Nimbya contains simple, short to moderately long conidiophores, which may form one or a few short to long, geniculate, sympodial proliferations. Conidia are narrowly elongate-obclavate, gradually tapering apically, solitary or in short chains, with transverse disto- and eusepta, sometimes slightly constricted near eusepta. Apical condiophores with a single conidiogenous locus can be formed. Internal compartmentation occurs, cell lumina tend to be broadly octagonal to rounded. A sexual morph may occur.

Notes: Section Nimbya contains the type species of Nimbya, N. scirpicola, and N. caricis (Simmons 1989). A more extensive study on Nimbya (Lawrence et al. 2012) found that N. scirpinfestans and N. scirpivora also belonged to this section based on sequences of the GAPDH, ITS and Alt a 1 genes.

Alternaria caricis (E.G. Simmons) Woudenb. & Crous, comb. nov. MycoBank MB803700.

Basionym: Nimbya caricis E.G. Simmons, Sydowia 41: 328. 1989.

Alternaria scirpicola (Fuckel) Sivan., Bitunicate Ascomycetes and their Anamorphs (Vaduz): 526. 1984.

Basionym: Sporidesmium scirpicola Fuckel, Jahrb. Nassauischen Vereins Naturk. 23-24: 140. 1870 [1869-70].

- ≡ Clasterosporium scirpicola (Fuckel) Sacc., Syll. Fungorum (Abellini) 4: 393. 1886.
- ≡ Cercospora scirpicola (Fuckel) Zind.-Bakker, Rev. Mycol. (Paris) 5: 66. 1940.
- ≡ Alternaria scirpicola (Fuckel) M.T. Lucas & J. Webster, Čas. Slez. Mus., Ser. A, Hist. Nat. 23: 151. 1974 (nom. inval.).
- ≡ Nimbya scirpicola (Fuckel) E.G. Simmons, Sydowia 41: 316. 1989.
= Sphaeria scirpicola DC., in Lamarck & de Candolle, Fl. Franç., Edn 3 (Paris) 2: 300. 1805.
- ≡ Clathrospora scirpicola (DC.) Höhn., Ann. Mycol. 18(1/3): 77. 1920.
- ≡ Macrospora scirpicola (DC.) Fuckel, Jahrb. Nassauischen Vereins Naturk. 23-24: 139. 1870 [1869-70].
- ≡ Pyrenophora scirpicola (DC.) E. Müll., Sydowia 5(3-6): 256. 1951.

Note: Although Sphaeria scirpicola DC. (de Candolle 1805) predates Sporidesmium scirpicola Fuckel (Fuckel 1870), a valid combination in Alternaria already exists, thus we choose to retain Alternaria scirpicola (Fuckel) Sivan., which is also a well established name.

Alternaria scirpinfestans (E.G. Simmons & D.A. Johnson) Woudenb. & Crous, comb. nov. MycoBank MB803701.

Basionym: Nimbya scirpinfestans E.G. Simmons & D.A. Johnson, Mycotaxon 84: 420. 2002.

= Macrospora scirpinfestans E.G. Simmons & D.A. Johnson, Mycotaxon 84: 417. 2002.

Alternaria scirpivora (E.G. Simmons & D.A. Johnson), Woudenb. & Crous, comb. nov. MycoBank MB803702.

Basionym: Nimbya scirpivora E.G. Simmons & D.A. Johnson, Mycotaxon 84: 424. 2002.

= Macrospora scirpivora E.G. Simmons & D.A. Johnson, Mycotaxon 84: 422. 2002.

Section Panax D.P. Lawr., Gannibal, Peever & B.M. Pryor, Mycologia 105: 541. 2013. Fig. 17.

Type species: Alternaria panax Whetzel

Diagnosis: Section Panax contains simple or branched, short to moderately long primary conidiophores, with one or a few conidiogenous loci. Conidia are obclavate to ovoid, with multiple transverse and longitudinal septa, conspicuously constricted near several transverse septa, solitary or in simple or branched, short chains. Apical secondary conidiophores are formed with one or several conidiogenous loci, multiple lateral secondary conidiophores with a single conidiogenous locus may occur.

Notes: Section Panax was recently described by Lawrence et al. (2013) and consists of A. calycipyricola, A. eryngii and A. panax. Our extended dataset added the species A. avenicola and A. photistica to this section. Three species, A. avenicola, A. calycipyricola, and A. photistica have earlier been placed in the A. infectoria species-group based on their morphological characters (Simmons 2007), and two of them have a known sexual morph; Lewia avenicola (Simmons 2007) and Lewia photistica (Simmons 1986). A phylogenetic study based on Alt a 1 and GAPDH sequences placed A. photistica in the A. infectoria species-group (Hong et al. 2005) but an extensive study on the A. infectoria species-group (Andersen et al. 2009) confirmed our finding, and placed this species outside the A. infectoria species-group. Additional research performed on multiple A. photistica strains support our sequence data (data not shown).

Alternaria avenicola E.G. Simmons, Kosiak & Kwaśna, in Simmons, CBS Biodiversity Ser. (Utrecht) 6: 114. 2007.

= Lewia avenicola Kosiak & Kwaśna, Mycol. Res. 107: 371. 2003.

Alternaria calycipyricola R.G. Roberts, Mycotaxon 100: 162. 2007.

Alternaria eryngii (Pers.) S. Hughes & E.G. Simmons, Canad. J. Bot. 36: 735. 1958.

Basionym: Conoplea eryngii Pers., Mycol. Eur. (Erlanga) 1: 11. 1822.

≡ Exosporium eryngianum (Pers.) Chevall., Flore Générale des Environs de Paris 1: 39. 1826.
≡ Exosporium eryngii (Pers.) Duby, Bot. Gallicum., Edn 2 (Paris) 2: 882. 1830.
≡ Helminthosporium eryngii (Pers.) Fr., Syst. Mycol. (Lundae) 3: 361. 1832.

Alternaria panax Whetzel, Bull. U.S.D.A. 250: 11. 1912.

= Macrosporium araliae Dearn. & House, Circ. New York State Mus. 24: 58. 1940.
= Alternaria araliae H.C. Greene, Trans. Wisconsin Acad. Sci. 42: 80. 1953.

Alternaria photistica E.G. Simmons, Mycotaxon 25: 304. 1986.

= Lewia photistica E.G. Simmons, Mycotaxon 25: 302. 1986.

Section Phragmosporae Woudenb. & Crous, sect. nov. MycoBank MB803743. Fig. 18.

Type species: Alternaria phragmospora Emden

Diagnosis: Section Phragmosporae contains simple, short to moderately long, primary conidiophores, with one or multiple geniculate, sympodial proliferations. Conidia are (broad) ovoid to long ovoid, ellipsoid, curved, or limaciform, with multiple transverse and few to multiple longitudinal septa, some septa darkened, slightly to conspicuously constricted near several transverse septa, solitary or in simple short chains. Apical secondary conidiophores are formed with one or several conidiogenous loci. All species within the section are known from soil and seawater environments.

Note: Section Phragmosporae contains six species of which two were linked to Embellisia.

Alternaria chlamydospora Mouch. [as “chlamydosporum”], Mycopathol. Mycol. Appl. 50: 217. 1973.

Alternaria didymospora (Munt.-Cvetk.) Woudenb. & Crous, comb. nov. MycoBank MB803709.

Basionym: Embellisia didymospora Munt.-Cvetk., Mycologia 68: 49. 1976.

Alternaria limaciformis E.G. Simmons, Mycotaxon 13: 24. 1981.

Alternaria molesta E.G. Simmons, Mycotaxon 13: 17. 1981.

Alternaria mouchaccae E.G. Simmons, Mycotaxon 13: 18. 1981.

≡ Ulocladium chlamydosporum Mouch., Rev. Mycol. (Paris) 36: 114. 1971, non Alternaria chlamydospora Mouch., 1973.

Alternaria phragmospora Emden, Acta Bot. Neerl. 19: 393. 1970.

≡ Embellisia phragmospora (Emden) E.G. Simmons, Mycotaxon 17: 232. 1983.

Section Porri D.P. Lawr., Gannibal, Peever & B.M. Pryor, Mycologia 105: 541. 2013. Fig. 19

Type species: Alternaria porri (Ellis) Cif.

Diagnosis: Section Porri is characterised by broadly ovoid, obclavate, ellipsoid, subcylindrical or obovoid (medium) large conidia, disto- and euseptate, solitary or in short to moderately long chains, with a simple or branched, long to filamentous beak. Conidia contain multiple transverse and longitudinal septa and are slightly constricted near some transverse septa. Secondary conidiophores can be formed apically or laterally.

Notes: In addition to the six species that are displayed in our phylogeny, 40 more are included based on the study of Lawrence et al. (2013), confirmed with own molecular data (not shown). With almost 80 species section Porri is the largest Alternaria section (data not shown). The section displays a higher level of genetic variation than the second largest section; section Alternata.

Alternaria acalyphicola E.G. Simmons, Mycotaxon 50: 260. 1994.

Alternaria agerati Sawada ex E.G. Simmons, Mycotaxon 65: 63. 1997.

= Alternaria agerati Sawada, Rep. Dept. Agric. Gov. Res. Inst. Formosa 86: 165. 1943. (nom. inval., Art. 36.1)

Alternaria agripestis E.G. Simmons & K. Mort., Mycotaxon 50: 255. 1994.

Alternaria anagallidis A. Raabe, Hedwigia 78: 87. 1939.

Alternaria aragakii E.G. Simmons, Mycotaxon 46: 181. 1993.

Alternaria argyroxiphii E.G. Simmons & Aragaki, Mycotaxon 65: 40. 1997.

Alternaria bataticola Ikata ex W. Yamam., Trans. Mycol. Soc. Japan 2(5): 89. 1960.

= Macrosporium bataticola Ikata, Agric. Hort. (Tokyo) 22: 241. 1947 (nom. inval., Art. 36.1).

Alternaria blumeae E.G. Simmons & Sontirat, Mycotaxon 65: 81. 1997.

Alternaria calendulae Ondřej, Čas. Slez. Mus. v Opave˘, Ser. A, Hist. Nat. 23(2): 150. 1974.

= Alternaria calendulae W. Yamam. 1939 (nom. nud.).
= Macrosporium calendulae Nelen, Bull. Centr. Bot. Gard. (Moscow) 35: 90. 1959 (nom. inval., Art. 36.1).
= Macrosporium calendulae Nelen, Bot. Mater. Otd. Sporov. Rast. Bot. Inst. Akad. Nauk S.S.S.R. 15: 144. 1962.
= Alternaria calendulae Nirenberg, Phytopathol. Z. 88(2): 108. 1977 (nom. illegit., Art. 53.1).

Alternaria capsici E.G. Simmons, Mycotaxon 75: 84. 2000.

Alternaria carthami S. Chowdhury, J. Indian Bot. Soc. 23: 65. 1944.

= Macrosporium anatolicum A. Săvul., Bull. Sect. Sci. Acad. Roumaine 26: 709. 1944.

Alternaria cassiae Jurair & A. Khan, Pakistan J. Sci. Industr. Res. 3(1): 72. 1960.

Alternaria cichorii Nattrass, First List of Cyprus Fungi: 29. 1937.

≡ Alternaria porri f.sp. cichorii (Natrass) T. Schmidt, Pflanzenschutz-berichte 32: 181. 1965.
≡ Macrosporium cichorii (Nattrass) Gordenko, Mikol. Fitopatol. 9(3): 241. 1975.

Alternaria cirsinoxia E.G. Simmons & K. Mort., Mycotaxon 65: 72. 1997.

Alternaria crassa (Sacc.) Rands, Phytopathology 7: 337. 1917.

Basionym: Cercospora crassa Sacc., Michelia 1(no. 1): 88. 1877.

Alternaria cretica E.G. Simmons & Vakal., Mycotaxon 75: 64. 2000.

Alternaria cucumerina (Ellis & Everh.) J.A. Elliott, Amer. J. Bot. 4: 472. 1917.

Basionym: Macrosporium cucumerinum Ellis & Everh., Proc. Acad. Nat. Sci. Philadelphia 47: 440. 1895.

Alternaria cyphomandrae E.G. Simmons, Mycotaxon 75: 86. 2000.

Alternaria danida E.G. Simmons, Mycotaxon 65: 78. 1997.

Alternaria dauci (J.G. Kühn) J.W. Groves & Skolko, Canad. J. Res., Sect. C, Bot. Sci. 22: 222. 1944.

Basionym: Sporidesmium exitiosum var. dauci J.G. Kühn, Hedwigia 1: 91. 1855.

Additional synonyms in Simmons 2007.

Alternaria dichondrae Gambogi, Vannacci & Triolo, Trans. Brit. Mycol. Soc. 65(2): 323. 1975.

Alternaria euphorbiicola E.G. Simmons & Engelhard, Mycotaxon 25: 196. 1986.

≡ Macrosporium euphorbiae Reichert, Bot. Jahrb. Syst. 56: 723. 1921. (nom. illegit., Art 53.1).

Alternaria grandis E.G. Simmons, Mycotaxon 75: 96. 2000.

Alternaria hawaiiensis E.G. Simmons, Mycotaxon 46: 184. 1993.

Alternaria limicola E.G. Simmons & M.E. Palm, Mycotaxon 37: 82. 1990.

Alternaria linicola J.W. Groves & Skolko, Canad. J. Res., Sect. C, Bot. Sci. 22: 223. 1944.

Alternaria macrospora Zimm., Ber. Land-Forstw. Deutsch-Ostafrika 2: 24. 1904.

- ≡ Macrosporium macrosporum (Zimm.) Nishikado & Oshima, Agric. Res. (Kurashiki) 36: 391. 1944.
= Sporidesmium longipedicellatum Reichert, Bot. Jahrb. Syst. 56: 723. 1921.
- ≡ Alternaria longipedicellata (Reichert) Snowden, Rep. Dept. Agric. Uganda: 31. 1927 [1926].

Alternaria multirostrata E.G. Simmons & C.R. Jacks., Phytopathology 58: 1139. 1968.

Alternaria nitrimali E.G. Simmons & M.E. Palm, Mycotaxon 75: 93. 2000.

Alternaria passiflorae J.H. Simmonds, Proc. Roy. Soc. Queensland. 49: 151. 1938.

Alternaria poonensis Ragunath, Mycopathol. Mycol. Appl. 21: 315. 1963.

Alternaria porri (Ellis) Cif., J. Dept. Agric. Porto Rico 14: 30. 1930 [1929].

Basionym: Macrosporium porri Ellis, Grevillea 8 (no. 45): 12. 1879.

Alternaria protenta E.G. Simmons, Mycotaxon 25: 207. 1986.

Alternaria pseudorostrata E.G. Simmons, Mycotaxon 57: 398. 1996.

Alternaria ricini (Yoshii) Hansf., Proc. Linn. Soc. Lond.: 53. 1943.

Basionym: Macrosporium ricini Yoshii, Bult. Sci. Fak. Terk. Kjusu Imp. Univ. 3(4): 327. 1929.

Alternaria rostellata E.G. Simmons, Mycotaxon 57: 401. 1996.

Alternaria scorzonerae (Aderh.) Loer., Netherlands J. Pl. Pathol. 90(1): 37. 1984.

Basionym: Sporidesmium scorzonerae Aderh.,Arbeiten Kaiserl. Biol. Anst. Land-Forstw. 3: 439. 1903.

Alternaria sesami (E. Kawam.) Mohanty & Behera, Curr. Sci. 27: 493. 1958.

Basionym: Macrosporium sesami E. Kawam., Fungi 1(2): 27. 1931.

Alternaria solani Sorauer, Z. Pflanzenkrankh. Pflanzenschutz 6: 6. 1896.

= Macrosporium solani Ellis & G. Martin, Amer. Naturalist 16(12): 1003. 1882
- ≡ Alternaria solani (Ellis & G. Martin) L.R. Jones & Grout, Vermont Agric. Exp. Sta. Annual Rep. 9: 86. 1896.

Additional synonyms in Simmons (2007).

Alternaria solani-nigri R. Dubey, S.K. Singh & Kamal [as “solani-nigrii”], Microbiol. Res. 154(2): 120. 1999.

Alternaria steviae Ishiba, T. Yokoy. & Tani, Ann. Phytopathol. Soc. Japan 48(1): 46. 1982.

Alternaria subcylindrica E.G. Simmons & R.G. Roberts, Mycotaxon 75: 62. 2000.

Alternaria tagetica S.K. Shome & Mustafee, Curr. Sci. 35: 370. 1966.

Alternaria tomatophila E.G. Simmons, Mycotaxon 75: 53. 2000.

Alternaria tropica E.G. Simmons, Mycotaxon 46: 187. 1993.

Alternaria zinniae H.Pape ex M.B. Ellis, Mycol. Pap. 131: 22. 1972.

= Alternaria zinniae H. Pape, Angew. Bot. 24: 61. 1942. (nom. inval., Art. 36.1)

Section Pseudoulocladium Woudenb. & Crous, sect. nov. MycoBank MB803744. Fig. 20.

Type species: Alternaria chartarum Preuss

Diagnosis: Section Pseudoulocladium is characterised by simple or branched conidiophores with short, geniculate, sympodial proliferations. Conidia are obovoid, non-beaked with a narrow base, in simple or (mostly) branched chains. Apical secondary conidiophores with multiple conidiogenous loci and lateral secondary conidiophores with a single conidiogenous locus can be formed.

Note: It forms a sister clade to section Ulocladioides.

Alternaria aspera Woudenb. & Crous, nom. nov. MycoBank MB803712.

Basionym: Ulocladium arborescens E.G. Simmons, Stud. Mycol. 50: 117. 2004, non Alternaria arborescens E.G. Simmons, 1999.

Etymology: Name refers to the conspicuously ornamented conidia.

Alternaria chartarum Preuss, Bot. Zeitung 6: 412, 1848.

- ≡ Sporidesmium polymorphum var. chartarum (Preuss) Cooke, Fungi Brit. Exs., ser. 2: 329. 1875.
- ≡ Ulocladium chartarum (Preuss) E.G. Simmons, Mycologia 59: 88. 1967.
= Alternaria stemphylioides Bliss, Mycologia 36: 538. 1944.
- ≡ Alternaria chartarum f. stemphylioides (Bliss) P. Joly, Encycl. Mycol. (Paris) 33: 161. 1964.

Alternaria concatenata Woudenb. & Crous, nom. nov. MycoBank MB803713.

Basionym: Ulocladium capsici F. Xue & X.G. Zhang [as “capsicuma”], Sydowia 59: 174. 2007, non Alternaria capsici E.G. Simmons, 2000.

Eymology: Name refers to the concatenated conidia.

Alternaria septospora (Preuss) Woudenb. & Crous, comb. nov. MycoBank MB803714.

Basionym: Helminthosporium septosporum Preuss, Linnaea 24: 117. 1851.

≡ Macrosporium septosporum (Preuss) Rabenh., Bot. Zeitung 9: 454. 1851.
≡ Ulocladium septosporum (Preuss) E.G. Simmons, Mycologia 59: 87. 1967.

Section Radicina D.P. Lawr., Gannibal, Peever & B.M. Pryor, Mycologia 105: 541. 2013. Fig. 21.

Type species: Alternaria radicina Meier, Drechsler & E.D. Eddy

Diagnosis: Section Radicina contains straight, simple or branched, short or long, primary conidiophores with multiple, short geniculate, sympodial proliferations with single or a few conidiogenous loci at the apex. Sporulation resembles a cluster or clumps of conidia. Conidia are widely ovoid to narrowly ellipsoid, moderate in size, beakless, with several transverse and longitudinal septa, solitary or in short chains. Solitary, short, apical secondary conidiophores may occur. The species from this section occur on Umbelliferae.

Note: This section was first recognised by Pryor & Gilbertson (2000) based on sequence data of the ITS and mitochondrial SSU.

Alternaria carotiincultae E.G. Simmons, Mycotaxon 55: 103. 1995.

Alternaria petroselini (Neerg.) E.G. Simmons, More dematiaceous hyphomycetes (Kew): 417. 1976.

Basionym: Stemphylium petroselini Neerg., Zentralbl. Bakteriol., 2. Abt., 104: 411. 1942.

≡ Stemphylium radicinum var. petroselini (Neerg.) Neerg., Danish species of Alternaria & Stemphylium: 357. 1945.
≡ Alternaria radicina var. petroselini (Neerg.) Neerg., Encycl. Mycol. 33: 123. 1964.

Alternaria radicina Meier, Drechsler & E.D. Eddy, Phytopathology 12: 157. 1922.

≡ Stemphylium radicinum (Meier, Drechsler & E.D. Eddy) Neerg., Annual Rep. Phytopathol. Lab. J.E. Ohlsens Enkes, Seed Growers, Copenhagen 4: 14. 1939.
≡ Thyrospora radicina (Meier, Drechsler & E.D. Eddy) Neerg., Bot. Tidsskr. 44: 361. 1939.
≡ Pseudostemphylium radicinum (Meier, Drechsler & E.D. Eddy) Subram., Curr. Sci. 30: 423. 1961.

Alternaria selini E.G. Simmons, Mycotaxon 55: 109. 1995.

Alternaria smyrnii (P. Crouan & H. Crouan) E.G. Simmons, Mycotaxon 55: 41. 1995.

Basionym: Helminthosporium smyrnii P. Crouan & H. Crouan, Florule Finistère (Paris): 11. 1867.

≡ Macrosporium smyrnii (P. Crouan & H. Crouan) Sacc., Syll. Fungorum (Abellini) 4: 527. 1886.

Section Sonchi D.P. Lawr., Gannibal, Peever & B.M. Pryor, Mycologia 105: 542. 2013. Fig. 22.

Type species: Alternaria sonchi Davis

Diagnosis: Section Sonchi is characterised by subcylindrical, broadly ovoid, broadly ellipsoid or obclavate, (medium) large conidia, single or in short chains, with multiple transverse and few longitudinal septa, slightly constricted at the septa, with a blunt taper which can form secondary conidiophores.

Notes: The species-group was described by Hong et al. (2005) based on molecular data of the GAPDH and Alt a 1 regions. Lawrence et al. (2013) included A. brassicae as a basal lineage in sect. Sonchi, which is supported as a monotypic lineage in our analyses. The species from section Sonchi occur on multiple hosts within the Compositae.

Alternaria cinerariae Hori & Enjoji, J. Pl. Protect. 18: 432. 1931.

Alternaria sonchi Davis, in Elliott, Bot. Gaz. 62: 416. 1916.

Section Teretispora (E.G. Simmons) Woudenb. & Crous, comb. et stat. nov. MycoBank MB803745. Fig. 23.

Basionym: Teretispora E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 674. 2007.

Type species: Alternaria leucanthemi Nelen

Diagnosis: Section Teretispora is characterised by simple conidiophores, sometimes extending at the apex with one or two, geniculate, sympodial proliferations, bearing single, long cylindrical mature conidia lacking a beak portion, with many transverse and a few longitudinal septa, constricted at most of the transverse septa. Secondary conidiophores with a single conidium are rarely formed at the apex; instead, they may form from the base of the primary conidium.

Notes: The genus Teretispora had Teretispora leucanthemi, formerly Alternaria leucanthemi (= Alternaria chrysanthemi), as type and only species (Simmons 2007). We choose to treat this as a section, which retains the name Teretispora, rather than a monotypic lineage.

Alternaria leucanthemi Nelen, in Nelen & Vasiljeva, Bot. Mater. Otd. Sporov. Rast. Bot. Inst. Akad. Nauk S.S.S.R. 15: 148. 1962.

- ≡ Teretispora leucanthemi (Nelen) E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 674. 2007.
= Alternaria leucanthemi Nelen, Bull. Centr. Bot. Gard. (Moscow) 35: 83. 1959. (nom. inval., Art. 36.1)
= Alternaria chrysanthemi E.G. Simmons & Crosier, Mycologia 57: 142. 1965.

Section Ulocladioides Woudenb. & Crous, sect. nov. MycoBank MB803746. Fig. 24.

Type species: Alternaria cucurbitae Letendre & Roum.

Diagnosis: Section Ulocladioides is characterised by conidiophores with short, geniculate, sympodial proliferations. Conidia are obovoid, non-beaked with a narrow base, single or in chains, which may form secondary conidiophores at the apex.

Note: Section Ulocladioides resembles section Ulocladium and contains the majority of the species included in this study from the genus Ulocladium (11/17).

Alternaria atra (Preuss) Woudenb. & Crous, comb. nov. MycoBank MB803717.

Basionym: Ulocladium atrum Preuss, Linnaea 25: 75. 1852.

≡ Stemphylium atrum (Preuss) Sacc., Syll. Fungorum (Abellini) 4: 520. 1886.

Alternaria brassicae-pekinensis Woudenb. & Crous, nom. nov. MycoBank MB803723.

Basionym: Ulocladium brassicae Yong Wang bis & X.G. Zhang, Mycologia 100: 457. 2008, non Alternaria brassicae (Berk.) Sacc., 1880.

Etymology: Name refers to the host from which it was originally isolated.

Alternaria cantlous (Yong Wang bis & X.G. Zhang) Woudenb. & Crous, comb. nov. MycoBank MB803719.

Basionym: Ulocladium cantlous Yong Wang bis & X.G. Zhang, Mycologia 102: 376. 2010.

Alternaria consortialis (Thüm.) J.W. Groves & S. Hughes [as “consortiale”], Canad. J. Bot. 31: 636. 1953.

Basionym: Macrosporium consortiale Thüm., Herb. Mycol. Oecon. 9: no. 450. 1876.

- ≡ Stemphylium consortiale (Thüm.) J.W. Groves & Skolko, Canad. J. Res., Sect. C, Bot. Sci.: 196. 1944.
- ≡ Pseudostemphylium consortiale (Thüm.) Subram., Curr. Sci. 30: 423. 1961.
- ≡ Ulocladium consortiale (Thüm.) E.G. Simmons, Mycologia 59: 84. 1967.
= Stemphylium ilicis Tengwall, Meded. Phytopathol. Lab. “Willie Commelin Scholten” 6: 44. 1924.

Alternaria cucurbitae Letendre & Roum., in Roumeguère, Rev. Mycol. (Toulouse) 8 (no. 30): 93. 1886.

≡ Ulocladium cucurbitae (Letendre & Roum.) E.G. Simmons, Mycotaxon 14: 48. 1982.

Alternaria heterospora Woudenb. & Crous, nom. nov. MycoBank MB803724.

Basionym: Ulocladium solani Yong Wang bis & X.G. Zhang, Mycol. Progr. 8: 209. 2009, non Alternaria solani Sorauer, 1896.

Etymology: Name refers to the various conidial morphologies observed during growth.

Alternaria multiformis (E.G. Simmons) Woudenb. & Crous, comb. nov. MycoBank MB803720.

Basionym: Ulocladium multiforme E.G. Simmons, Canad. J. Bot. 76: 1537. 1999 [1998].

Alternaria obovoidea (E.G. Simmons) Woudenb. & Crous, comb. nov. MycoBank MB803721.

Basionym: Ulocladium obovoideum E.G. Simmons, Mycotaxon 37: 104. 1990.

Alternaria subcucurbitae (Yong Wang bis & X.G. Zhang) Woudenb. & Crous, comb. nov. MycoBank MB803722.

Basionym: Ulocladium subcucurbitae Yong Wang bis & X.G. Zhang, Mycologia 100: 456. 2008.

Alternaria terricola Woudenb. & Crous, nom. nov. MycoBank MB803725.

Basionym: Ulocladium tuberculatum E.G. Simmons, Mycologia 59: 83. 1967, non Alternaria tuberculata M. Zhang & T.Y. Zhang, 2006. Etymology: Name refers to soil from which it was originally isolated.

Section Ulocladium (Preuss) Woudenb. & Crous, comb. et stat. nov. MycoBank MB803747. Fig. 25.

Basionym: Ulocladium Preuss, Linnaea 24: 111. 1851.

Type species: Alternaria botrytis (Preuss) Woudenb. & Crous

Diagnosis: Section Ulocladium is characterised by simple conidiophores, or with one or two short, geniculate, sympodial proliferations, with (mostly) single, obovoid, non-beaked conidia with a narrow base.

Notes: Section Ulocladium resembles sect. Ulocladioides. The epitype of Ulocladium, U. botrytis CBS 197.67, and the isotype of U. oudemansii (CBS 114.07) cluster with the Sinomyces representative, as do many other strains stored as U. botrytis in the CBS collection (data not shown). Furthermore, a strain stored as A. capsici-annui (CBS 504.74) in the CBS collection clusters within the Sinomyces clade and displays identical morphological features.

Alternaria alternariae (Cooke) Woudenb. & Crous, comb. nov. MycoBank MB803716.

Basionym: Sporidesmium alternariae Cooke, Handb. Brit. Fungi 1: 1440. 1871.

≡ Stemphylium alternariae (Cooke) Sacc., Syll. Fungorum (Abellini) 4: 523. 1886.
≡ Ulocladium alternariae (Cooke) E.G. Simmons, Mycologia 59: 82. 1967.
≡ Sinomyces alternariae (Cooke) Yong Wang bis & X.G. Zhang, Fungal Biol. 115: 194. 2011.

Alternaria botrytis (Preuss) Woudenb. & Crous, comb. nov. MycoBank MB803718.

Basionym: Ulocladium botrytis Preuss, Linnaea 24: 111. 1851.

≡ Stemphylium botryosum var. ulocladium Sacc. (nom. nov.), Syll. Fungorum (Abellini) 4: 522. 1886.
≡ Stemphylium botryosum var. botrytis (Preuss) Lindau, Rabenhorst’s. Kryptog.-Fl., Edn 2 (Leipzig) 1(9): 219. 1908.

Alternaria capsici-annui Săvul. & Sandu, Hedwigia 75: 228. 1936.

Alternaria oudemansii (E.G. Simmons) Woudenb. & Crous, comb. nov. MycoBank MB803715.

Basionym: Ulocladium oudemansii E.G. Simmons, Mycologia 59: 86. 1967.

Section Undifilum (B.M. Pryor, Creamer, Shoemaker, McLain-Romero & Hambl.) Woudenb. & Crous, comb. et stat. nov. MycoBank MB803748. Fig. 26.

Basionym: Undifilum B.M. Pryor, Creamer, Shoemaker, McLain-Romero & Hambl., Botany 87: 190. 2009.

Type species: Alternaria bornmuelleri (Magnus) Woudenb. & Crous

Diagnosis: Section Undifilum is characterised by ovate to obclavate to long ellipsoid, straight to inequilateral, single, transseptate conidia; septa can be thick, dark and rigid, and form unique germ tubes, which are wavy or undulate until branching. Species of this section occur on Fabaceae and almost all produce the toxic compound swaisonine.

Notes: Section Undifilum shares morphological features with section Embellisia, but is characterised by the formation of a wavy germ tube upon germination (Pryor et al. 2009). Based on previous studies, the swaisonine producing species U. oxytropis (Pryor et al. 2009, Lawrence et al. 2012), U. fulvum and U. cinereum (Baucom et al. 2012) also belong to this section, although the type species, A. bornmuelleri, does not produce swaisonine.

Alternaria bornmuelleri (Magnus) Woudenb. & Crous, comb. nov. MycoBank MB803726.

Basionym: Helminthosporium bornmuelleri Magnus, Hedwigia 38 (Beibl.): 73. 1899.

≡ Undifilum bornmuelleri (Magnus) B.M. Pryor, Creamer, Shoemaker, McLain-Romero & Hambl., Botany 87: 190. 2009.

Alternaria cinerea (Baucom & Creamer) Woudenb. & Crous, comb. nov. MycoBank MB803731.

Basionym: Undifilum cinereum Baucom & Creamer, Botany 90: 872. 2012

Alternaria fulva (Baucom& Creamer) Woudenb. & Crous, comb. nov. MycoBank MB803732.

Basionym: Undifilum fulvum Baucom & Creamer, Botany 90: 871. 2012

Alternaria oxytropis (Q. Wang, Nagao & Kakish.) Woudenb. & Crous, comb. nov. MycoBank MB803727.

Basionym: Embellisia oxytropis Q. Wang, Nagao & Kakish., Mycotaxon 95: 257. 2006.

≡ Undifilum oxytropis (Q. Wang, Nagao & Kakish.) B.M. Pryor, Creamer, Shoemaker, McLain-Romero & Hambl., Botany 87: 191. 2009.

Monotypic lineages

The following six species are not assigned to one of the 24 above described Alternaria sections and are treated as separate, single species, lineages in this study. Future studies, including more and/or new Alternaria species, might eventually give rise to the formation of new sections, when these new species show to be closely related to one of these monotypic lineages.

Alternaria argyranthemi E.G. Simmons & C.F. Hill, Mycotaxon 65: 32. 1997.

Alternaria brassicae (Berk.) Sacc., Michelia 2(no. 6): 129. 1880.

Basionym: Macrosporium brassicae Berk., Engl. Fl., Fungi (Edn 2) (London) 5: 339. 1836.

Additional synonyms listed in Simmons (2007).

Alternaria dennisii M.B. Ellis, Mycol. Pap. 125: 27. 1971.

≡ Embellisia dennisii (M.B. Ellis) E.G. Simmons, Mycotaxon 38: 257. 1990.

Alternaria helianthiinficiens E.G. Simmons, Walcz & R.G. Roberts [as “helianthinficiens”], Mycotaxon 25: 204. 1986.

Alternaria soliaridae E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 374. 2007.

Alternaria thalictrigena K. Schub. & Crous, Fungal Planet No. 12: 2. 2007.

Paradendryphiella Woudenb. & Crous, gen. nov. MycoBank MB803750. Fig. 27.

Colonies on SNA effuse, entire, velvety, olivaceous. Reverse olivaceous-grey to iron-grey. Mycelium consisting of branched, septate hypha, (sub)hyaline, smooth. Conidiophores subhyaline, simple or branched, septate or not, straight or flexuous, often nodose with conspicuous, brown pigmentation at the apical region; at times reduced to conidiogenous cells. Conidiogenous cells terminal or lateral, with denticles aggregated at apex, with prominent conidial scars, thickened but not darkened; sometimes proliferating with a new head or a short, inconspicuous sympodial rachis. Conidia produced holoblastically, on narrow denticle, smooth, cylindrical to obclavate, straight or slightly flexuous, 1-7 transverse septa, pale to medium brown, often with dark septa (often constricted), and a darkened zone of pigmentation at the apex, and at the hilum, which is thickened, and somewhat protruding, with a minute marginal frill. Chlamydospores and sexual state not observed.

Type species: Paradendryphiella salina (G.K. Sutherl.) Woudenb. & Crous

Paradendryphiella salina (G.K. Sutherl.) Woudenb. & Crous, comb. nov. MycoBank MB803751.

Basionym: Cercospora salina G.K. Sutherl., New Phytol. 15: 43. 1916.

- ≡ Dendryphiella salina (G.K. Sutherl.) Pugh & Nicot, Trans. Brit. Mycol. Soc. 47(2): 266. 1964.
- ≡ Scolecobasidium salinum (G.K. Sutherl.) M.B. Ellis, More dematiaceous hyphomycetes (Kew): 192. 1976.
= Embellisia annulata de Hoog, Seigle-Mur., Steiman & K.-E. Erikss., Antonie van Leeuwenhoek J. Microbiol. Serol. 51: 409. 1985.

Paradendryphiella arenariae (Nicot) Woudenb. & Crous, comb. nov. MycoBank MB803752.

Basionym: Dendryphiella arenariae Nicot, [as “arenaria”] Rev. Mycol. (Paris) 23: 93. 1958.

≡ Scolecobasidium arenarium (Nicot) M.B. Ellis, More dematiaceous hyphomycetes (Kew): 194. 1976.

DISCUSSION

The well-supported node for the Alternaria clade obtained in the present study, and the low bootstrap support at the deeper nodes within the Alternaria complex is also consistently seen in previous phylogenetic studies published on these genera (Pryor & Bigelow 2003, Inderbitzin et al. 2006, Pryor et al. 2009, Runa et al. 2009, Wang et al. 2011, Lawrence et al. 2012). The only phylogenetic study which displays a second fully supported node is based on a five-gene combined dataset of GAPDH, Alt a 1, actin, plasma membrane ATPase and calmodulin (Lawrence et al. 2013). This node, called clade A by the authors, supports eight “asexual” Alternaria species-groups and an Ulocladium (sect. Ulocladioides in our phylogenies) clade. By resolving these eight asexual phylogenetic lineages of Alternaria together with Ulocladium, which is sister to the sexual A. infectoria species-group and other sexual genera, Lawrence et al. (2013) elevated the asexual species-groups to sections within Alternaria. If we take this node as cut-off for the genus Alternaria in our phylogenies, this would leave an Alternaria clade with 14 internal clades (sections) and three monotypic lineages. In order to create a stable phylogenetic taxonomy, seven new genera need to be described of which three would be monotypic; E. dennissii, A. argyranthemi and A. soliaridae. Embellisia species would be assigned to five different genera of which four would be new, leaving only E. allii, E. chlamydospora and E. tellustris in the genus Embellisia. The well-known (medical) A. infectoria species-group would also have to be transferred to a new genus. This node is not supported in our study (0.98 PP /65 ML Fig 1) and also the strict asexual/sexual division is not supported as two sexual morphs are found in section Panax. This approach would therefore give rise to multiple small genera, and would not end up in a logical and workable situation.

Based on our phylogenetic study on parts of the SSU, LSU, ITS, GAPDH, RPB2 and TEF1 gene regions of ex-type and reference strains of Alternaria species and all available allied genera, we resolved a Pleospora/Stemphylium-clade sister to Embellisia annulata, and a well-supported Alternaria clade. The Alternaria clade contains 24 internal clades and six monotypic lineages. In combination with a review of literature and morphology, the species within the Alternaria clade are all recognised here as Alternaria s. str. This puts the genera Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Lewia, Nimbya, Sinomyces, Teretispora, Ulocladium, Undifilum and Ybotromyces in synonymy with Alternaria.

The support values for the different sections described in this study are plotted in a heatmap per gene/gene combination and phylogenetic method used (Table 2). This shows that the Bayesian method provides greater support than the Maximum Likelihood bootstrap support values, which is in congruence with previous reports (e.g. Douady et al. 2003). The sections Cheiranthus, Eureka and Nimbya have the lowest support values. For sect. Eureka this is mainly caused by the position of A. cumini, which clusters within sect. Embellisioides based on its RPB2 sequence and as a monotypic lineage based on its TEF1 sequence. Section Cheiranthus and Nimbya are small sections, with relative long branches. Future studies, including more strains and/or species in these sections, are necessary to check the stability of these long branches.

The sexual genus Crivellia with its Brachycladium asexual morph was described by Inderbitzin et al. (2006) with Crivellia papaveraceae (asexual morph Brachycladium penicillatum) as type species and B. papaveris, with an unnamed sexual morph, as second species. The genus Brachycladium, which was synonymised with Dendryphion (Ellis 1971), was resurrected for the non-sexual stage based on polyphyly within Dendryphion and morphological distinction from its type species, D. comosum. The type species of Brachycladium, B. penicillatum, resides in Alternaria sect. Crivellia, which places Brachycladium in synonymy with Alternaria instead of Dendryphion.

The genus Chalastospora was established by Simmons (2007) based on Chalastospora cetera, formerly Alternaria cetera. Two new Chalastospora species, C. ellipsoidea and C. obclavata, and A. malorum as C. gossypii were later added to the genus, based on sequence data of the ITS and LSU regions (Crous et al. 2009c). The genus is characterised by conidia which are almost always narrowly ellipsoid to narrowly ovoid with 1-6 transverse eusepta, generally lacking oblique or longitudinal septa (Crous et al. 2009c). Our study shows that Alternaria armoraciae and Embellisia abundans also belong to this clade. Juvenile conidia of A. armoraciae are ovoid, but vary from being narrow to broadly ovoid and ellipsoid, with 3-5 transverse septa and a single longitudinal septum in up to four of the transverse segments (Simmons 2007). Embellisia abundans was already mentioned as part of the Chalastospora clade (Andersen et al. 2009, Lawrence et al. 2012), and has long ovoid or obclavate conidia with 3-6 transverse septa and rarely any longitudinal septa (Simmons 1983). The description of sect. Chalastospora does therefore not completely follow the original description of the genus Chalastospora.

The genus Embellisia is characterised by the thick, dark, rigid conidial septa and the scarcity of longitudinal septa (Simmons 2007). It was first described by Simmons (1971), with Embellisia allii as type and E. chlamydospora as second species. Multiple Embellisia species followed after the description of the genus, which was later linked to the sexual genus Allewia (Simmons 1990). The latest molecular-based revision was performed based on sequences of the GAPDH, ITS and Alt a 1 genes (Lawrence et al. 2012). They found that Embellisia split into four clades and multiple species, which clustered individually amidst Alternaria, Ulocladium or Stemphylium spp. Our results mostly support these data, but with the inclusion of more ex-type/representative strains of Alternaria some additions were made to the different Embellisia groups mentioned by Lawrence et al. (2012). Group I (sect. Embellisia) and III (sect. Embellisioides) are identical to the treatment of Lawrence et al. (2012) but group II (section Phragmosporae) and IV (section Eureka) are both expanded with four Alternaria species. As not all species from group II and IV display the typical morphological characters of Embellisia, we chose to name these Alternaria sections based on the oldest species residing in the respective sections. Embellisia abundans was already mentioned as being part of the Chalastospora-clade and E. indefessa formed a clade close to Ulocladium, which we now assign to sect. Cheiranthus. Embellisia dennisii also forms a separate lineage in our phylogenies; therefore the old name Alternaria dennissii is resurrected. Furthermore, the clustering of E. conoidea within the A. brassicicola species-group and E. annulata close to Stemphylium, now assigned as Paradendryphiella gen. nov., is confirmed by our phylogenetic data. The morphological character of thick, dark, rigid septa seems to have evolved multiple times and does not appear to be a valid character for taxonomic distinction at generic level.

The sexual morphs Lewia (Simmons 1986) and Allewia (Simmons 1990) were linked to Alternaria and Embellisia respectively, with the only difference between these genera being the morphology of their asexual morphs. Lewia chlamidosporiformans and L. sauropodis are transferred to the genus Leptosphaerulina (Simmons 2007), which leaves 11 Lewia species with a known Alternaria anamorph. Most of them (9/11) reside in sect. Infectoriae, the others are found in sect. Panax. Allewia only contains two species of which one resides in sect. Eureka and one in sect. Embellisioides. With the establishment of the new International Code of Nomenclature for algae, fungi and plants (ICN), the dual nomenclature system for sexual and asexual fungal morphs was abandoned and replaced by a single-name nomenclature (Hawksworth et al. 2011, Norvell 2011). In order to implement the new rules of the ICN, we synonymised Lewia and Allewia with Alternaria.

Although multiple molecular studies included Nimbya isolates in their phylogenies (Chou & Wu 2002, Pryor & Bigelow 2003, Hong et al. 2005, Inderbitzin et al. 2006, Pryor et al. 2009), a more extensive molecular-based study was recently published by Lawrence et al. (2012). Based on sequences of the GAPDH, ITS and Alt a 1 genes, the authors found a Nimbya clade which contained the type species N. scirpicola together with N. scirpinfestans, N. scirpivora and N. caricis. The N. scirpicola isolate which we included in our study, was assigned to this genus by Simmons (1989) based on morphological characters, as is the one used in other molecular studies (Pryor & Bigelow 2003, Hong et al. 2005, Lawrence et al. 2012). The sequences of the ITS, GAPDH and Alt a 1 genes of these isolates are however not identical, but do cluster in the same clade in the two phylogenies (data not shown), together with the isolate of N. caricis. The N. gomphrenae isolate we included in our phylogeny was not representative of the name. Simmons mentioned in 1989 that Togashi (1926) described two different fungi and deposited the small-spored species in the CBS collection, instead of the large-spored N. gomphrenae isolate. Nimbya gomphrenae CBS 108.27, which does not sporulate anymore, will therefore be treated as “Alternaria sp.”, and resides in sect. Alternata. The ITS sequence of N. gomphrenae from Chou & Wu (2002) actually clusters within sect. Alternantherae. This section was described by Lawrence et al. (2012) and consists of three Nimbya species, which they renamed to Alternaria based on the position of the clade amidst the Alternaria species-groups. Based on the data from Chou & Wu (2002), the name Alternaria gomphrenae is resurrected and placed in sect. Alternantherae.

The genus Sinomyces was described in by Wang et al. (2011) to accommodate Ulocladium alternariae and two new species from China, S. obovoideus and S. fusoides (type). The genus was differentiated from Ulocladium based on its simple conidiophores with a single apical pore or 1-2 short, uniperforate, geniculate sympodial proliferations. Unfortunately, our DNA sequence analyses of the ex-type cultures of the two new species from China (CBS 124114 and CBS 123375) were not congruent with the GAPDH (both species) and Alt a 1 (S. obovoideus) sequences deposited in GenBank (data not shown), leading us to doubt the authenticity of these strains. This matter could not be resolved in spite of contacting the original depositors. The ex-type strain of S. alternariae (CBS 126989) was therefore included as representative of the genus Sinomyces. The presence of the epitype of Ulocladium, U. botrytis CBS 197.67, in this section resulted in us rejecting the name Sinomyces, and calling this sect. Ulocladium. In addition, the presence of U. oudemansii in this section, with conidiophores with 1-5 uniperforate geniculations (Simmons 1967), also disagrees with the mentioned differentiation of Sinomyces from Ulocladium.

The type species of Ulocladium, U. botrytis, was typified by two representative strains QM 7878 (CBS 197.67) and QM 8619 (CBS 198.67) (Simmons 1967). Molecular studies performed afterwards showed that these strains are not identical (de Hoog & Horré 2002). Most molecular studies performed used CBS 198.67 as representative of U. botrytis (Pryor & Gilbertson 2000, Pryor & Bigelow 2003, Hong et al. 2005, Xue & Zhang 2007, Pryor et al. 2009, Runa et al. 2009, Wang et al. 2010, Wang et al. 2011, Lawrence et al. 2012), which clusters in section Ulocladioides. However, de Hoog & Horré (2002) epitypified U. botrytis with CBS 197.67, which clusters with Sinomyces strains, as does Ulocladium oudemansii, now named sect. Ulocladium. Extended phylogenetic analyses on all U. botrytis strains present in the CBS culture collection (16 isolates) also highlight this issue as they cluster either within sect. Ulocladium or sect. Ulocladioides (data not shown), both with one of the representative strains described by Simmons (1967). The suggestion to synonymise Ulocladium with Alternaria has been made several times in the past (Pryor & Gilbertson 2000, Chou & Wu 2002). The latest systematic revision of the genus Ulocladium (Runa et al. 2009) based on sequences from the ITS, GAPDH and Alt a 1 genes supported previous findings of poly- and paraphyletic relationships of Ulocladium among Alternaria, Embellisia and Stemphylium spp. (de Hoog & Horré 2002, Pryor & Bigelow 2003, Hong et al. 2005). Ulocladium alternariae and U. oudemansii, now known as sect. Ulocladium, cluster separately. The core Ulocladium clade, containing the two sister clades now called sect. Ulocladioides and sect. Pseudoulocladium, was confirmed by later studies (Wang et al. 2010, Lawrence et al. 2012). Alternaria cheiranthi and Embellisia indefessa have been linked to Ulocladium (Pryor & Gilbertson 2000, Pryor & Bigelow 2003, Hong et al. 2005, Pryor et al. 2009, Runa et al. 2009, Lawrence et al. 2012), but missed the diagnostic feature of Ulocladium. Our study showed that they form a sister section, sect. Cheiranthus, to sect. Ulocladioides. The confusing taxonomy in this genus strengthens our decision to reduce Ulocladium to synonymy with Alternaria. The characteristics of the former genus Ulocladium are added to the new broader Alternaria generic circumscription.

The genus Undifilum was described by Pryor et al. (2009) to accommodate the species U. oxytropis and U. bornmuelleri. It shares the morphological feature of thick, dark and rigid septa with the genus Embellisia, but was characterised by the formation of a wavy germ-tube upon germination (Pryor et al. 2009). A recent study on fungal endophytes in locoweeds in the US described two new Undifilum species (Baucom et al. 2012). Both new species produce the toxic compound swaisonine, which is also produced by U. oxytropis. Swaisonine is the cause of a neurological disease, locism, of grazing animals, resulting in economic losses in livestock (James & Panter 1989). The production of swaisonine seems to be related to this section, although the type-species, U. bornmuelleri, does not produce this toxin.

The genus Ybotromyces contains one species, Y. caespitosus (originally Botryomyces caespitosus), which was isolated from a skin lesion of a human patient (de Hoog & Rubio 1982). De Hoog et al. (1997) discovered a high similarity to Alternaria spp. based on restriction patterns of the ITS and SSU rDNA. A phylogeny study of melanised meristematic fungi based on their SSU and ITS rDNA sequences (Sterflinger et al. 1999) placed Y. caespitosus within the Pleosporales together with Alternaria and Pleospora. De Hoog & Horré (2002) hypothesized that the ex-type strain of Y. caespitosus, CBS 177.80, is likely a synanamorph of a yet undescribed Alternaria species. Our phylogeny supports this hypothesis, and places the genus in sect. Infectoriae.

Chmelia slovaca, described from dermatic lesions of a human (Svobodová 1966), also clusters with sect. Infectoriae as was shown previously (de Hoog & Horré 2002). The genus produces different types of chlamydospores and sporadically blastospores, but no conidia or conidiophores, which makes it difficult to identify based on morphology. De Hoog & Horré (2002) were confident that Chmelia is a sterile member of A. infectoria, which is in agreement with our results.

Genera unrelated to Alternaria

The placement of the sexual genus Pleospora (1863) with Stemphylium (1833) asexual morphs as basal sister clade to the Alternaria complex is well-documented in multiple molecular studies (Chou & Wu 2002, Pryor & Bigelow 2003, Hong et al. 2005, Pryor et al. 2009, Lawrence et al. 2012). Therefore, we only included the type species of both genera in our phylogenies and used them as outgroup in the Alternaria phylogeny. Pleospora herbarum with its Stemphylium herbarum (CBS 191.86) asexual morph is the type species of the genus Pleospora. Stemphylium botryosum with its Pleospora tarda (CBS 714.68) sexual morph is the type species of the genus Stemphylium.

Embellisia annulata proved to be identical to the marine species Dendryphiella salina, and forms a well-supported clade in the Pleosporaceae together with D. arenariae. Several DNA-based studies (dela Cruz 2006, Jones et al. 2008, Zhang et al. 2009) concluded that the marine Dendryphiella species, D. arenariae and D. salina, belonged to the Pleosporaceae as sister clade to the Pleospora/Stemphylium complex. Furthermore, they showed the type species of Dendryphiella, D. vinosa, to be only distantly related, based on sequences of the ITS, SSU, LSU (Jones et al. 2008) and ITS, TEF1, RPB2 (dela Cruz 2006) gene regions. The transfer of the marine Dendryphiella species to Scolecobasidium (Ellis 1976), was also disputed. Scolecobasidium does not belong to the Pleosporales based on ITS, TEF1, and RPB2 sequences (dela Cruz 2006) and the morphology of the two Dendryphiella species does not fit the generic circumscription of Scolecobasidium (dela Cruz 2006, Jones et al. 2008). Ellis (1976) described denticles on the conidiogenous cells when the conidia become detached. However other observers describe a marginal basal frill on the conidia after detachment, leaving a scar on the conidiophore. We propose to place the two species in the new genus Paradendryphiella as C. arenariae and C. salina. The need for a new genus to accommodate the two species was already suggested by Jones et al. (2008).

A recent study on Diademaceae, a family which is characterised by a flat circular operculum and bitunicate asci (Shoemaker & Babcock 1992), excluded the sexual genera Comoclathris and Clathrospora, and (provisionally) placed them in the Pleosporaceae with alternaria-like asexual morphs (Zhang et al. 2011). Molecular data of two strains (Dong et al. 1998, Schoch et al. 2009) placed them within the Pleosporaceae. A confusing factor is that Dong et al. (1998) use the name Comoclathris baccata in their paper for strain CBS 175.52, but submitted their sequences under the name Clathrospora diplospora to GenBank. Shoemaker & Babcock (1992) synonymised Clathrospora diplospora with Comoclathris baccata, which renders Comoclathris as the correct generic name. The confusion around these genera is illustrated by the fact that the CBS collection currently harbours six strains named as Clathrospora species of which four were renamed by Shoemaker & Babcock in 1992 based on morphological studies, and three of these four strains were even transferred to the genus Comoclathris. The type species of Clathrospora, C. elynae is represented by two strains of which one, CBS 196.54, was also studied morphologically by Shoemaker and Babcock (1992). They form a well-supported clade, located basal to the Pleosporaceae (Fig. 2), outside the Alternaria complex. The type species of Comoclathris, Comoclathris lanata, was not available to us, but the two Comoclathris compressa strains cluster together in a well-supported clade within the Pleosporaceae, also outside the Alternaria complex, which we believe to be the correct phylogenetic placement of the genus. Two other strains, named Comoclathris magna (CBS 174.52) and Clathrospora heterospora (CBS 175.52) by Shoemaker and Babcock (1992), cluster amidst sect. Alternata. Culture studies performed by Simmons (1952) showed the presence of alternaria-like conidia in these cultures and no (mature) ascospore formation. Presumably the species observed by Shoemaker and Babcock (1992) on plant material were lost during cultivation and became replaced by A. alternata species-group isolates. Both strains will be treated as “Alternaria sp.”

The genus Alternariaster was first described by Simmons (2007) with Alternariaster helianthi, formerly Alternaria helianthi or Helminthosporium helianthi, as type and only species. It is distinct from Alternaria by the lack of a pigmented conspicuous internal, circumhilar ring in its conidia and conidiophores. Our study showed that this genus is clearly not part of the Alternaria complex and belongs to the Leptosphaeriaceae (Fig. 2) (Alves et al. 2013).

In the recently published book “The genera of Hyphomycetes” (Seifert et al. 2011) three more genera are linked to Alternaria, namely Pantospora, Briansuttonia and Rhexoprolifer. A recent study on Pantospora included ITS and LSU sequence data of the type species Pantospora guazumae, which placed the genus in Mycosphaerellaceae (Minnis et al. 2011). This refutes the link with Alternaria. The genus Rhexoprolifer was described in 1996 by Matsushima with R. variabilis as type and only species, isolated from South Africa. Rhexoprolifer variabilis has rhexolytic conidial liberation and proliferating conidiophores with both phragmosporous and dictyosporous conidia. Briansuttonia was described in 2004 to accommodate Corynespora alternarioides (Castañeda Ruiz et al. 2004). The distoseptate muriform conidia of Briansuttonia do resemble Alternaria and Stemphylium, but the conidiogenous loci and euseptate conidia of Alternaria and holoblastic conidial ontogeny and euseptate muriform conidia of Stemphylium were enough for the authors to regard their taxon as a different genus. Both asexual genera presently lack molecular data, and we were unable to obtain any living specimens of these taxa. It would be valuable to include both genera in a future study to resolve the connection among genera with muriform conidia and Alternaria.

The description of Alternaria s. str. in the present study is supported by i) a well-supported phylogenetic node in multiple analyses, ii) high similarity of clades within Alternaria based on SSU, LSU and ITS data, and iii) variation in the order of the clades between the different gene phylogenies, which is in congruence with low support values at these deeper nodes. We follow the precedence introduced by Lawrence et al. (2013) to assign the taxonomic status of sections of Alternaria for the different clades found, thus allowing us to retain the former generic names but associated with a different taxonomic status. For end-users, this also results in a more stable and understandable taxonomy and nomenclature.

DEDICATION

We would like to dedicate this manuscript to the late Dr E.G. Simmons, who spent over 50 years of his life researching the systematics of the genus Alternaria. Without the time EGS spent on characterising the species included in this study, and his impeccable strain collection, which he placed in CBS for preservation and further study, the present study would not have been possible.

Acknowledgments

Mrs M. Vermaas is thanked for preparing the photoplates, Mrs J. Bloem for assisting with the molecular work, and Prof. dr B.M. Pryor for sending us the Undifilum isolate. This research was supported by the Dutch Ministry of Education, Culture and Science through an endowment of the FES programme “Making the tree of life work”.

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PERMALINK

Alternaria redefined

JHC Woudenberg

JZ Groenewald

M Binder

PW Crous

Abstract

Taxonomic novelties:

INTRODUCTION

MATERIAL AND METHODS

Isolates

Table 1.

Taxonomy

PCR and sequencing

Phylogenetic analyses

RESULTS

Phylogeny

Table 2.

Table 3.

Fig. 1.

Fig. 2.

Taxonomy

ALTERNARIA SECTIONS

Fig. 3.

Fig. 4.

Fig. 5.

Fig. 6.

Fig. 7.

Fig. 8.

Fig. 9.

Fig. 10.

Fig. 11.

Fig. 12.

Fig. 13.

Fig. 14.

Fig. 15.

Fig. 16.

Fig. 17.

Fig. 18.

Fig. 19.

Fig. 20.

Fig. 21.

Fig. 22.

Fig. 23.

Fig. 24.

Fig. 25.

Fig. 26.

Monotypic lineages

Fig. 27.

DISCUSSION

Genera unrelated to Alternaria

DEDICATION

Acknowledgments

REFERENCES

ACTIONS

PERMALINK

RESOURCES

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