Molecular reassessment of diaporthalean fungi associated with strawberry, including the leaf blight fungus, Paraphomopsis obscurans gen. et comb. nov. (Melanconiellaceae)

Udayanga, Dhanushka; Miriyagalla, Shaneya D.; Manamgoda, Dimuthu S.; Lewers, Kim S.; Gardiennet, Alain; Castlebury, Lisa A.

doi:10.1186/s43008-021-00069-9

Table 1 Isolates and DNA sequences used in this study

From: Molecular reassessment of diaporthalean fungi associated with strawberry, including the leaf blight fungus, Paraphomopsis obscurans gen. et comb. nov. (Melanconiellaceae)

Families in Diaporthales	Culture collection/Isolate	Species	Host	Country	GenBank Accessions
Families in Diaporthales	Culture collection/Isolate	Species	Host	Country	LSU	ITS	RPB2	TEF1
Apiosporopsidaceae	CBS 771.79	Apiosporopsis carpinea	Carpinus betulus	Switzerland	AF277130	–	–	–
Apoharknessiaceae	CBS 111377^*	Apoharknessia insueta	Eucalyptus pellita	Brazil	AY720814	JQ706083	–	MN271820
–	CBS 114575	Apoharknessia insueta	Eucalyptus sp.	Colombia	MN172370	MN172402	–	MN271821
Asterosporiaceae	MFLU 15–3555	Asterosporium asterospoermum	Fagus sylvatica	Italy	MF190062	–	–	–
Auratiopycnidiellaceae	CBS 132180^*/ CPC 16371	Auratiopycnidiella tristaniopsis	Tristaniopsis laurina	Australia: New South Wales	JQ685522	JQ685516	–	MN271825
–	CPC 16371	Auratiopycnidiella tristaniopsis	Tristaniopsis laurina	Australia: New South Wales	MN172374	MN172405	–	MN271826
Coryneaceae	D201	Coryneum umbonatum	Quercus robur	Austria	MH674329	MH674329	MH674333	MH674337
–	CFCC 52319/isolate 89–1^*	Coryneum gigasporum	Castanea mollissima	China	MH683557	MH683565	–	–
Cryphonectriaceae (subclade1)	ATCC 38755	Cryphonectria parasitica	Castanea dentata	USA	NG_027589	AY141856	DQ862017	EU222014
–	ATCC 48198/CMW7048	Cryphonectria parasitica	Quercus virginiana	USA	JN940858	JN942325	–	–
–	CFCC 52150	Cryphonectria parasitica	Castanea mollissima	China	MH514021	MG866018	–	MN271848
Cryphonectriaceae (subclade2)	CBS 112916^*/CMW62/CRY-98	Chrysoporthe australafricana	Eucalyptus grandis	South Africa	AY194097	AF292041	–	MN271832
–	CBS 118654^*	Chrysoporthe cubensis	Eucalyptus grandis	Cuba	MN172378	DQ368773	–	MN271834
Cytosporaceae	CFCC 89982^*	Cytospora chrysosperma	Ulmus pumila	China	KP310805	KP281261	KU710952	KP310848
–	CFCC 89633	Cytospora eleagni	Elaeagnus angustifolia	China	KF765693	KF765677	KU710956	KU710919
–	CBS 202.36^*	Cytospora viridistroma	Cercis canadensis	Georgia	MN172388	MN172408	–	MN271853
Diaporthaceae	AR 3405^*/CBS 135422	Diaporthe citri	Citrus sp.	USA	MT378365	KC843311	MT383081	KC843071
–	AR 4855	Diaporthe novem	Lactuca muralis	France	MT378366	MT378351	MT383082	MT383100
–	CBS 592.81^*	Diaporthe helianthi	Helianthus annuus	Serbia	MT378370	NR_103698	–	KC343841
–	CBS 138594/AR 5193^*	Diaporthe eres	Ulmus sp.	Germany	MT378367	KJ210529	MT383083	KJ210550
–	CBS 125529/AR 4658	Mazzantia galii	Galium aparine	France	MH875041	MH863563	–	MT383101
Diaporthosporellaceae	CBS 140348^*	Diaporthella cryptica	Corylus avellana	Italy	MN172390	MN172409	MN271800	MN271854
–	CFCC 51994^*	Diaporthosporella cercidicola	Cercis chinensis	China	KY852515	KY852492	–	MN271855
Diaporthostomataceae	CFCC 52101	Diaporthostoma machili	Machilus leptophylla	China	MG682021	MG682081	MG682041	MG682061
–	CFCC 52100^*	Diaporthostoma machili	Machilus leptophylla	China	MG682020	MG682080	MG682040	MG682060
Dwiroopaceae	CBS 109755^*	Dwiroopa lythri	Lythrum salicaria	USA	MN172389	MN172410	MN271801	MN271859
–	CBS 143163^*	Dwiroopa punicae	Punica granatum var. azadi	USA:Minnesota	MK510686	MK510676	MK510692	–
Erythrogloeaceae	CBS 132185^*/CPC 18819	Erythrogloeum hymenaeae	Hymenaea courbaril	Brazil	JQ685525	JQ685519	–	–
–	CFCC 52106^*	Dendrostoma osmanthi	Osmanthus fragrans	China	MG682013	MG682073	MG682033	MG682053
Folicryphiaceae	CFCC 53025^*	Neocryphonectria chinensis	Carpinus turczaninowii	China	MN172397	MN172414	MN271812	MN271893
–	CFCC 53027^*/CFCC 53027	Neocryphonectria carpini	Carpinus turczaninowi	China	MN172396	MN172413	–	–
Gnomoniaceae	DMW 108/CBS 128442	Ophiognomonia rosae	Fragaria vesca	USA	MT378355	JF514851	MT383086	JF514824
–	CBS 851.79	Ophiognomonia rosae	Comarum palustre	Finland	MT378356	EU254930	MT383071	JQ414153
–	CBS 121226/AR4275^*	Gnomoniopsis fragariae	Fragaria vesca	USA	EU255115	EU254824	EU219250	EU221961
–	DMW 63	Gnomoniopsis fragariae	Fragaria × ananassa	USA	MT378357	MT378343	MT383072	MT383089
–	DMW 61	Gnomoniopsis fragariae	Fragaria sp.	USA	MT378358	MT378344	MT383073	MT383090
–	VPRI 15547	Gnomoniopsis fragariae	Fragaria × ananassa	Australia	MT378359	MT378345	MT383087	MT383091
–	CBS 275.51/ATCC 11430	Gnomoniopsis fragariae	Fragaria sp.	Canada:Ontario	MH868373	EU254829	MT383088	MT383092
–	CBS 208.34	Gnomoniopsis fragariae	Fragaria sp.	France	EU255116	EU254826	EU219284	EU221968
–	CBS 904.79	Gnomoniopsis tormentillae	Potentilla erecta	Switzerland	EU255133	EU254856	–	GU320795
–	CBS 806.79	Gnomoniopsis comari	Comarum palustre	Finland	EU255114	EU254821	–	GU320810
Harknessiaceae	CBS 120033^*/CFCC 53027	Harknessia gibbosa	Eucalyptus delegatensis	Tasmania	EF110615	EF110615	–	MN271868
–	CBS 120030^*	Harknessia ipereniae	Eucalyptus sp.	Western Australia	EF110614	EF110614	–	MN271870
Juglanconidaceae	MAFF 410216	Juglanconis oblonga	Juglans ailanthifolia	Japan	KY427153	KY427153	KY427203	KY427222
–	CBS 121083	Juglanconis juglandina	Juglans regia	Austria	KY427148	KY427148	KY427198	KY427217
–	MAFF 410079^*	Juglanconis pterocaryae	Pterocarya rhoifolia	Japan	KY427155	KY427155	KY427205	KY427224
Lamproconiaceae	MFLUCC 15–0870	Lamproconium desmazieri	Tilia tomentosa	Russia	KX430135	KX430134	MF377605	MF377591
–	MFLUCC 15–0872	Lamproconium desmazieri	Tilia cordata	Russia	KX430139	KX430138	–	MF377593
Macrohilaceae	CBS 140063^*	Macrohilum eucalypti	Eucalyptus piperita	Australia	NG_058183	NR_154184	MN271810	–
–	CPC 10945	Macrohilum eucalypti	Eucalyptus sp.	New Zealand	DQ195793	DQ195781	–	–
Mastigosporellaceae	VIC44383^*/COAD 2370	Mastigosporella pigmentata	Qualea parviflora	Brazil	MG587928	MG587929	–	–
–	CBS 136421^*	Mastigosporella anisophylleae	Anisophyllea sp.	Zambia	KF777221	KF779492	–	MN271892
Melanconidaceae	CFCC 50474	Melanconis itoana	Betula albosinensis	China	KT732974	KT732955	KT732987	KT733004
–	CFCC 50475^*	Melanconis stilbostoma	Betula platyphylla	China	KT732975	KT732956	KT732988	KT733005
–	CFCC 50471	Melanconis betulae	Betula albosinensis	China	KT732971	KT732952	KT732984	KT733001
Melanconiellaceae	AU01	Greeneria uvicola	Vitis vinifera	Australia	JN547720	–	–	–
–	OH35	Greeneria uvicola	Vitis labrusca	Ohio	AF362570	–	–	–
–	AR 3457	Melanconiella spodiaea	Carpinus betulus	Austria	AF408369	MT378352	MT383074	MT383093
–	AR 3462	Melanconiella spodiaea	Carpinus betulus	Austria	AF408370	MT378353	MT383075	MT383094
–	AR 3830/CBS 131494	Melanconiella elegans	Carpinus caroliniana	USA	JQ926264	JQ926264	JQ926335	JQ926401
–	CBS 125597	Melanconiella chrysodiscosporina	Carpinus betulus	Austria	MH875191	MH863730	–	–
–	BPI 878343	Melanconiella ellisii	Carpinus caroliniana	USA	JQ926271	JQ926271	JQ926339	JQ926406
–	MFLU 15–1112^*	Microascospora rubi	Rubus ulmifolius	Italy	MF190099	MF190154	MF377611	MF377582
–	MFLU 17–0883	Microascospora rubi	Rubus ulmifolius	Italy	MF190098	MF190153	–	MF377581
–	M1261/DS016	Paraphomopsis obscurans	Fragaria × ananassa	USA	MT378360	MT378346	MT383076	MT383095
–	CBS 143829/M1262/DS020^*	Paraphomopsis obscurans	Fragaria × ananassa	USA	MT378361	MT378347	MT383077	MT383096
–	M1259/DS013	Paraphomopsis obscurans	Fragaria × ananassa	USA	MT378362	MT378348	MT383078	MT383097
–	M1333/DS133	Paraphomopsis obscurans	Fragaria × ananassa	USA	MT378363	MT378349	MT383079	MT383098
–	M1278/DS055	Paraphomopsis obscurans	Fragaria × ananassa	USA	MT378364	MT378350	MT383080	MT383099
–	strain 1–1	Paraphomopsis obscurans (as. Sphaeronaemella fragariae)	Fragaria sp.	China	–	HM854850	–	–
–	strain 1–3	Paraphomopsis obscurans (as. Sphaeronaemella fragariae)	Fragaria sp.	China	–	HM854852	–	–
–	strain 12	Paraphomopsis obscurans (as. Sphaeronaemella fragariae)	Fragaria sp.	China	–	HM854849	–	–
Phaeoappendicosporaceae	MFLUCC 13–0161^*/MFLU 12–2131	Phaeoappendicospora thailandensis	Quercus sp.	Italy	MF190102	MF190157	–	–
Prosopidicolaceae	CBS 113529^*	Prosopidicola mexicana	Prosopis glandulosa	USA	KX228354	AY720709	–	–
–	CBS 141298/CPC 27478^*	Prosopidiocola albizziae	Albizzia falcataria	Malaysia	KX228325	KX228274	–	–
Pseudomelanconidaceae	CFCC 52787^*	Neopseudomelanconis castaneae	Castanea mollissima	China	MH469164	MH469162	–	–
–	CFCC 52110^*	Pseudomelanconis caryae	Carya cathayensis	China	MG682022	MG682082	MG682042	MG682062
Pseudoplagiostomaceae	CBS 115722/CMW 6674	Pseudoplagiostoma oldii	Eucalyptus camaldulensis	Australia	GU973610	GU973535	–	GU973565
–	CPC 14161	Pseudoplagiostoma eucalypti	Eucalyptus camaldulensis	Vietnam	GU973604	GU973510	–	GU973540
Schizoparmaceae	CBS 112640^*/STE-U 3904	Coniella eucalyptorum	Eucalyptus grandis × tereticornis	Queensland	AY339290	AY339338	KX833452	KX833637
–	CBS 110394^*	Coneilla peruensis	soil in rain forest	Peru	KJ710441	KJ710463	KX833499	KX833695
Stilbosporaceae	CBS 122529^*	Stilbospora longicornuta	Carpinus betulus	Austria	KF570164	KF570164	KF570194	KF570232
–	CBS 117025^*	Stegonsporium acerophilum	Acer saccharum	USA: Tennessee	EU039993	EU039982	KF570173	EU040027
Sydowiellaceae	AR 3809	Chapeckia nigrospora	Betula sp.	USA	EU683068	–	–	–
–	F129/P3/1^*	Paragnomonia fragariae	Fragaria × ananassa	Latvia	MK524447	MK524430	–	MK524466
–	GF300/M1530	Paragnomonia fragariae	Fragaria sp.	France	MT378368	–	MT383084	MT383102
–	GF301/M1531	Paragnomonia fragariae	Fragaria sp.	France	MT378369	–	MT383085	MT383103
–	MFLU 16–2864^*	Sillia karstenii	Centaurea sp.	Italy	KY523500	KY523482	KY501636	–
Synnemasporellaceae	CFCC 52094	Synnemasporella aculeans	Rhus chinensis	China	MG682026	MG682086	MG682046	MG682066
–	CFCC 52097^*	Synnemasporella toxicodendri	Toxicodendron sylvestre	China	MG682029	MG682089	MG682049	MG682069
Tirisporellaceae	BCC 00018	Thailandiomyces bisetulosus	Licuala longicalycata	Thailand	EF622230	–	–	–
–	BCC 38312	Tirisporella beccariana	Nypa fruticans	Thailand	JQ655449	–	–	–
Tubakiaceae	CBS 129012^*	Tubakia iowensis	Quercus macrocarpa	USA	MG591971	JF704194	–	MG603576
–	CBS 127490^*	Tubakia seoraksanensis	Quercus mongolica	South Korea	KP260499	MG591907	–	MG592094
–	CBS 114386	Tubakia dryina	Quercus robur	New Zealand	JF704188	MG591852	–	MG592040
–	CPC 13806	Racheliella wingfieldiana	Syzygium guineense	South Africa	MG592006	MG591911	MG976487	MG592100
–	CBS 189.71^*	Oblongisporothyrium castanopsidis	Castanopsis cuspidata	Japan	MG591943	MG591850	–	MG592038
–	CBS 124732	Oblongisporothyrium castanopsidis	Castanopsis cuspidata	Japan	MG591942	MG591849	MG976453	MG592037
–	MUCC 2293^*	Paratubakia subglobosoides	Quercus glauca	Japan	MG592010	MG591915	MG976491	MG592104
–	CBS 193.71^*	Paratubakia subglobosa	Quercus glauca	Japan	MG592009	MG591914	MG976490	MG592103
–	CPC 31361	Sphaerosporithyrium mexicanum	Quercus eduardii	Mexico	MG591988	MG591894	–	MG592081
–	CPC 33021^*	Sphaerosporithyrium mexicanum	Quercus eduardii	Mexico	MG591990	MG591896	MG976473	MG592083
–	MUCC 2304^*	Involutiscutellula rubra	Quercus phillyraeoides	Japan	MG591995	MG591901	MG976478	MG592088
–	CBS 192.71^*	Involutiscutellula rubra	Quercus phillyraeoides	Japan	MG591993	MG591899	MG976476	MG592086
Outgroup (Magnaporthales)	MFLU 18–2323^*/MFLUCC 18–1337	Ceratosphaeria aquatica	submerged wood	China	MK835812	MK828612	MN156509	MN194065
–	CG-4/M83^*	Pyricularia grisea	Digitaria sp.	USA	JX134683	JX134671	–	JX134697

Abbreviations of the culture collections: ATCC: American Type Culture collection; CMW:FABI fungal culture collection; CBS:CBS-KNAW culture collection, Westerdijk Fungal Biodiversity Institute; MFLU: Mae Fah Luang University Herbarium; MFLUCC: Mae Fah Luang University Culture Collection; CFCC: China Forestry Culture Collection Center; STE-U: culture collection of the Department of Plant Pathology at the University of Stellenbosch; AR, M, DMW: Cultures housed at MNGDBL, USDA-ARS, Beltsville, Maryland; CPC: Culture collection of Pedro Crous, housed at Westerdijk Fungal Biodiversity Institute; MUCC: Murdoch University Culture Collection; BCC: BIOTEC Culture Collection, Bangkok, Thailand; VPRI: Victoria Plant Pathology Herbarium. *Ex-type/epitype/neotype cultures or specimens are indicated by asterisks. Newly generated sequences in this study are bold

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ISSN: 2210-6359

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