Table 1.
Isolates and DNA sequences used in this study
| Families in Diaporthales | Culture collection/Isolate | Species | Host | Country | GenBank Accessions | |||
|---|---|---|---|---|---|---|---|---|
| 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