sign in sign up
<<
Home , Dikarya, Exobasidiomycetes, Kickxellomycotina, Microsporidia, Mixiomycetes, Monoblepharidomycetes

Aphelidiomycota Rozellomycota Fungi Chytridiomyceta Monoblepharidomycota Zoopagomycota Entomophthoromycotina Glomeromycotina Mortierellomycotina Entorrhizomycota + Wallemiomycotina

Supplementary Figure 1. Current consensus of evolutionary relationships of major lineag- es within Fungi. Phyla not sampled in this study are shown in red font. 1 Full matrix Rogue_taxa_removal (1,672 taxa/290 (1,639 taxa) genes)

12

LB_taxa_removal 2 Subset_Dikarya_taxa (1,649 taxa) (540 taxa)

11

Top100_low Top100_DVMC Top100_long_length Top100 _low_LB Top_100 _low_RCFV Top100_slow evolving Top100_complete Top100_high_ABS saturation

3 4 5 6 7 8 9 10 Supplementary Fig. 2. Relationships between the 12 data matrices analyzed in this study. Data matrices with taxon-based ltering are in - purple boxes and those with gene-based ltering are in green boxes. The number for each data matrix corresponds to its number in the Methods - section. See Methods for further information on each data matrix and ltering strategy used to generate it. C

C

C

C

u

u

u

u

C

t

C t

t

C a

a t

a

C

u a

u

n

n

u n

t n

u

T t

e

e a

t 1 e a

e r a t

o

o n 1

a A o Xanthophyllomyces dend i n

o c n

t

t e 5

n t e

p r r h t e r

i s o r 4 i e s

o i i c c o i s A i o o c

K u t c 2

o

s

t h s

h N s t i r n s h t i t r p i I Holtermanniella nyarrowii h V I

i r t n A o s T r o i Holter o I n n I I p c a s o r i

a Solicoccozyma phenolica i c I Apiotrichum b i i d o I i M T c e c a akashimella koratensis o i l c s

i p s h A e e o s n s a c h

e i Phaeotremella skinneri T Apiot G t l G s

h m c r k a c i Spo h p a G t T e Solicoccozyma terricola p Filob C G o i g r i p h c n e l t p i o i r akashimella tepidaria r m o A p n o

s o c V c o V o r f t u o r s J l i o e T i Apiot s V n o a e v o V Pri i o i s o c t i l o e i i

e p h v i W o n s Spo e g f a r y m a c . p i i r r r a i t o i Basidioascus undulatus r o r n c s p a h t i Spo a l Phaeotremella fagi o o t i r t v i i o a i i o p t m r g mannia cornifo h o n o t r t p o t risorium iseilematisciliati c c t t Mrakia psychrophila o t p n d o u a r o i a n alle Pascua guehoae u m z t Pseudozyma hubeiensis e r e o Kalmanozyma brasiliensis llingera fragicola n t

a richum p n e V s o . o n g e o Naganishia albida i s i asidium wieringae m h h l Spo r c a t a o a

n a n e c r k e f m c t d a a l o f w a p l r l o r

r

anrija humic s i n n p Phaffia rhodozyma o risori u o f

Pseudozyma tsukubaensis o l g e g Pseudozyma sp. F8B2 i c a h r v i a i s c richum g a o s s i d o

o a o g j g c y o risorium graminicola n a p u s o s a n m s r s a W y l Moesziomyces antarcticus a n mia ichthyop u e e W h e c s n u e d a

e p s n e s h o a i r s

r e o o a n u s p c a i u s

s c n l m c h risorium reilianum o Moesziomyces sp. F16C1 u Mrakia blollopis u b b o s m m m a u t d u b p u s m

m u c ulajudae allemia mellicola m r n f r c u alle o c Moesziomyces sp. F5C1 e l a u v n u c c a n

z a o d c m o a c h g Mrakia frigida m e c a e c Moeszi i a u c vetiv c o i a c um scitamineum p e r a c u

a v o a l a Anthr t c o l c Ustilago xe r l e l r c a a l r e c n l l l c i i m o l Ustilago cynodontis a a l rassicae t o c l e l l c r g f t l c g l o e i e d n e i c v c l l o w d a o v r o V f y

a e o orosum g n e c n a i e mia hede o o p e e c o e o o o e i e a o r s n a o i Thecap Ustilago b m l b o i c r i Ustilago maydis e e i

i c pachydermatis i c a e e a i z c l

l a iolaceomyces palustris s t o c r l e z c h o t z r r i n Ustilago tr i s i h s r n Malassezia sympodialis i a i n o

e t n o amsii a n t o e c t d n i n o o e k n a

m l a t t s p o u m m s t o c a t u u t e a

l o t u p o

p a c o p t o rellus cibarius ia cornea c a i o p t acocystis flocculosa n e o u a n Pseud k t y p n o

u m e e Ustilago hordei o p c l p m h m

u p a T i i rorho h i i y a e Malass i i r p a y l a w p r r w omyces aph s m s s s e i s w s w y l ola s w w r y Malassezia yamatoensis rmis m e y o n r y esticularia cyperi i Malassezia capr e i r y gulare

B P y l r T e i P T i D r a i D C K r S K ia sulphurascens K r i K r l orus baumii K K Malassezia vespe C C haga Cryptococcus sp. DSM 27421 a Malass Cryptococcus depauperatus C C C C u endipita vermifera hora thlaspeos C C Malassezia restricta Dacryopinax primogenitus Calocera viscosa C T T Malass Ceratobasidium theobromae rochlo rae Rhizoctonia solani Malass us Botryobasidium botryosum omicrostroma g lutescens illetiopsis washingtonensis Malass romiv Cantharellus appalachiensis Cantha Cantharellus cinnabarinus ogomphus rutilus n irre Ceraceosorus guamens Serendipita indica Ceraceosorus bombacis eriae Ser Malassezia obtusa ezia dermatis Exidia glandulosa itici Auricularia subglabra Auricular Malass linidium pouzarii Malassezia cuniculi Malassezia sp. Auricularia auric Auricularia heimSistotreuer mastrum suecicum Sistotremastrum niveocremeum Sphaerobolus stellatus huangp ezia equi Ramaria cf. rubripermanens Acaromyces ing Ramaria sp. MG151 Gomphus bonarii Gomphus sp. MG54 Mei ae Chro Quamba ezia glob ora ezia nana Rickenella melSchizolea pora paradoxa idis Phel ezia japonica Coniferipor Rhodotorula sp. CCFEE 5036 Phellinus lamaoensis Golubevi Mei Pyrrhoderma noxium Porodaedalea pini ra miltonrushii Sang ezia slooffiae Fomitiporia mediterranea Limonomyces culmigenus a sp. CONT Punctularia strigosozonata Jaapia argillacea ae Gloeophyllum trabeum Sal ra nashico Heliocybe sulcata Rhodotorula m T Neolentinus lepideus Jaminaea rosea Stereum hirsutum illetia controversa na Bondarzewia mesenterica sp. wahieum laria eucalypti rtilionis Heterobasidion parviporum lucosiph Heterobasidio Rhodotorula taiwanensis macisia buchloeana osa Heterobasidion annosum Albatrellus sp. MG142 ophor Rhodoto Albatrellus ellisii T a pallescens Pleurotus eryngii us sp. MG121 Rhodotorula sp. JG1b Dentipellis sp. KUC8613 T Dentipellis fragilis Microbotryum lychnidisSporidiobdioicaeolus salm Rhodotorula toruloides illetia ca Micr illetia T Hericium coralloides T T Hericium erinaceus Rhodotorula sp. FNED722Rhodotorula diobovata T Hericium alpestre Rhodotorula paludigeRhodotona rula graminis illetia walkeriilletia laevis oldii Peni Microbotryum silenesacaulis illetia indica Peniophora sp. CBMAI 1063 illetia h Lactarius trivialis la Lactarius indigo us echinatus urantiotincta Leucosporidium creatinivorum obotryum silenesd ilum Lactarius hatsudake ria ano Lactari Microbotryum saponariae rula kratochvilovae is Lactarius deliciosus Microbotryum interm Russula aff. compacta Russula foetens ries Russula virescens ucilaginosa Russula lepida Russula griseocarnosa orrida Russula abietina Lactari Lactifluus hygrophoroides mala Lactarius sp. MG50 Leucosporidium scottii Russula sp. MG48 Glaciozyma antarctica Lactarius piperatus Lactifluus rugatus Lactarius volemus Lactifluus pinguis Thelephora a Sarcodon aspratus Puccinia novopanici onicolor Sarcodon sp. MG97 Melampsora abietiscanadensis Lentinus polychrous MelampsorUroa aecidiomycesides viciaefabae Antrodiella citrinella MelamMelapsormapsor lariciap alliipopulionpulinaa Steccherinum ochraceum Puccinia Phlebia centrifuga Austropuccinia psidiiPuccinia horiana ioicae Pleurotus ostreatoroseus Melampsora occidentalis Irpex lacteus PuccinPuccinia triticinaia hordei Phlebiopsis gigantea Symmetrospora coprosmaeMelampsora medusae Phanerochaete Phanerochaete carnosa quercina Erythrobasidium yunnanense edium Gelatoporia subvermispora Obba rivulosa Sparassis latifolia Cystobasidiopsis lactophilus Sparassisaiwan crispaofungus camphoratus lea Cystobasidium pallidum sorghi T Cron Wolfiporia cocos Fibroporia radiculosa Hemileia vastatrix Postia placenta 91 Laetiporus sulphureus Fomitopsis rosea AH282 artium ribicola Daeda Fomitopsis pinicomlaetes cinnabarina Fomitopsis palustris 98 ra Mixia osmundae Grifola frondosa Muco T rametes coccineametes hirsuta circinelloides T rametes sanguinea T ra ChoanephorCokera cucurbitarParum Mucor ambiguus Actinomucor elegans T rametes polyzonametes versicolor T rametes pubescens r velutinosus T ra asitella parasitica T rametes villosa bertholletiae olopsis trogii omyces recurvatus T rametes sp. Mucor irregular T Lignosus rhinocerotis Cori azygospo Lentinus tigrinus rma lucidum Cunninghamella elegansRhizopus delemar Polyporus arcularius Rhizopus stoloniferMucor indicus Polyporus brumalis Graminctopomothelerellus lineata epimiltinus T Apop Hesseltinella vesiculosa Dichomitus squalens variabilis Ganoderma tsugae Ganode Apophysomyces elegans Ganoderma australe hysomyces trapeziformis Ganoderma sinense Thermomucor Phycoindicameseudaticyces blakeslae eeanusGongronella sp.Absid w5 ia glauca is 98 Ganoderma boninense oblongispora repe Ganoderma sp. BRIUMSc AM2018a Saksen Serpula lacrymans Coniophora puteana Suillus alpinus Syncephalastrum monosporum Auricularia polytricha rus Suillus pictus lus placidus Syncephalastrum racemosum Suillus luteus RhizoRhizomucor pusillusaea vasiformis Suillus sp. MG131 Suil Rhizopogon fuscorubens Jimgerdemannia flammicoronaLichtheimia ramosa ns Rhizopogon salebrosus mucor miehei 90 Rhizopogon vulgaris Rhizophagus sp. MUCLUmbelopsis isabellina Rhizopogon sp. EndogoneJimge sp. rFLAdemSF59071 68 Rhizopogon vesiculosus Bifiguratus adelaidae Rhizopogon vinicolor Rhizopogon parksii Rhizopogon rudus Rhizopogon villosulus 98 Rhizopogon hawkerae Rhizophagus irregul Scleroderma citrinum annia lactiflua 91 Pisolithus tinctorius Lobosporang Pisolithus microcarpus Phlebopus portentosus GlomusRhizop cerhebrifoagusOehlia rclame dirus Hydnomerulius pinastri Diversispora epigaea Paxillus rubicundulus Paxilylopilus involutuslus plumbeoviolaceoides T Basidiobolus heterosporus Xerocomus impolitus Basidiobolus meristosporusGigaspora rosea aphana 43196 Boletus sp. MG55 ium transversale Chiua virens Furculomyces booMortimerMortiaerellnguseMortirellae elongatarella alpina Boletus edulis Boletus bicolor aris 91 Caloboletus calopus Butyriboletus roseoflavus megazygSmittiuosporumm angustum Boletus speciosus a verticillata Retiboletus ornatipletuses magnificus Smittium mucr Pulveroboletus ravenelii Zancudomyces culisetae Boletus sp. MG95 98 Neoboletus brunneissimus Smittium culicis Neobo Capniomyces stellatus Boletus subvelutipes Plicaturopsis crispa Linde Smittium simulii Piloderma croceum neostramineus Dimargar Fibularhizoctonia sp. CBS 109695 EntomophthorCoemaa muscaensia reversa onatum Clavaria fumosa CochlonemaConid odiobolus coronatusrina pennispora Hygrophorus pudorinus Hygrophorus russula Pterula gracilis SyncepThamhalisnocepha pseudlopluis sphaemigalerosporaata is cristalligena Piptocephalis cylindrospora Agaricales sp. HM26F1 Zoopage sp. CT Pleurotus tuberregium AcaulZoophopageagus tetrac insiderosians Pleurotus citrinopileatus Pleurotus salmo Pleurotus tuoliensis SpizeSpizellomycesllomyces sp. pa pulustrisnctatus ontosperma Pleurotus ostreatus Batrachochytrium salamandrivorans Pleurotus platypus Batrachochytrium dendrobatidis Fistulina hepatica 88 Schizophyllum commune Powellomyces hirtus All Auriculariopsis ampla Blyttiomyces helicus 90 Crepidotus sp. BD2015 95 Mycena citricolor Homo Rhizophlyctis rosea Mycena chlorophos Rhizocl Baeospora myosura Chytriomyces confervae Megacollybia marginata Synchytrium endlaphlyctiobioticums Chondrostereum purpureum Cauloc 88 Gloeostereum incarnatum Synchytrosmatium globosum Moniliophthora roreri Dendrothele bispora Pecoramyces ruminati es hytrium protostelio Omphalotus olearius ip Neocal polyrhiza Lentinula edodes ium microbalum 88 Gymnopus luxuriansfusc Cylindrobasidium torrendii limastix cal 96 Flammulina velutipes Anaeromyces robustus Hymenopellis chiangmaiae Piromyces finnis Piromyces sp. E2 36 Hymenopellis radicata AllomGonapodyyces macrogynus Armillamillariar ia ostoyae Encephalitozoon romaleae Ar iforniaeides EncephalitozooCatenan intestinalis Armillaria solidipes Encephalitozoon hellem um Armillaria cepistipes Armillaria gallica Encephalitozoon cuniculiria angua prolifera Macrocystidia cucumis Collybrichioaloma sp. MG36 terreum 89 T Tricholoma sp. MG99 Ordospo illulae richoloma matsutake moreus T richoloma bakamatsutakear T T ubulinosema ratisbonensis Tricholoma saponaceum V ceranae richoloma sp. MG77 EnterittaformaNosem corneaera collia apis T Tricholoma flavumovirens decastes tvaeAntonosrminnporaensis loc Trachipleistophora ohosporaminis ca Lepista sordida gata Hypsizygus m yophyll hizus Hamiltosporidium m L r Lyophyllum shimeji V Termitomyces sp. J132 avrai nceri ermitomyces sp. MG145 Spr T Termitomyces sp. JCM 13351 aguea loa culicisustae ermitomyces heimii Nematoc T Edhazardia a 94 Termitomyces sp. MG148 Par Amphiamblys sp. NematocWS ida parisii Termitomyces eur amicrosporidiumNematoc saccaidam oebaedisplodereagnivoraphii Termitomyces sp. MG16 sp.ida E sp. 1 Metchnik Pluteus cervinus Volvariella volvjacksoniiacea edis a like sp SCN 57 25 Amanita thiersii R Amanita inopinata ovella inc Tm5 Amanit Rozell BS20 Amanitan polypyita brunramisnescens Amanita pseudoporphyria urvata Ama Octopus bimaculoidesa allomyc 06 93 Fonticul Amanita bisporigera Lottia giga 99 Amanita phalloides Coprinus comatus bisporus is DrosophilaHelob m Lingudellal aro anatinabustaa alba Lepiota venenata Macrolepiota dolichaula Capitel ntea Agaricus Leucoagaricus sp. SymC.cos 98 Leucoagaricus gongylophorus IxodesDaphn scapulelanogia pulexla teleta Bra Strigamia Floccularia luteovirens Strongylocentr Crucibulum laeve nchiostomCionaa lanceol i atum aster Laccaria bicolor Laccaria amethystina Mus muscmaulusritima Coprinellus micaceus AmphimedNematosteon queenslandicantestinalisaris otus purpuratus 88 Psathyrella aberdarensis Trichoplax adhaerens Coprinopsis marcescibilis Coprinopsis strossmayeri Monosiga brev lla vectensis Coprinopsis cinerea Mnemiopsis leidyi Panaeolus cyanescens Salp Agrocybe cylindracea Sphaeroforma arctica Psilocybe cyanescens ingoeca rosetta CreolSphaimax efraroforgrantissimaicollis sirkkama M Galerina marginata CapsaspoIchthyosporra owczarzaki Gymnopilus dilepis Cora Ichthyophonus hoferi X1 Hebeloma cylindrosporum llochytrium limacispor Pholiota ea sp. XGB 2017a Hypholoma sublateritium Stropharia rugosoannulata compces llactucaeicata debilis 83 irregularis ATCC 30864 65 Protomy aphrinaina popu flavorlinaubra um 97 T 65 Taphr deformans Pneumocystis murina 89 Pneumocystis carinii 98 japonicus Schizosaccharomyces pombe Schizosaccharomyces cryophilus Schizosaccharomyces octosporus 98 japonicus Lipomyces lipofer Lipomyces oligophaga Lipomyces suomiensis 97 Lipomyces doorenjongii 94 92 Lipomyces kononenkoae Lipomyces starkeyi 74 Lipomyces arxii Lipomyces mesembrius Trigonopsis variabilis Trigonopsis vinaria . fulvescens Botryozyma nematodophila . elongata Tortispora starmeri Tortispora ganteri 98 98 Tortispora caseinolytica Nadsonia fulvescens var Nadsonia fulvescens var 96 hispaniensis Yarrowia bubula ungensis 96 Yarrowia divulgata Yarrowia deformans Yarrowia keel Yarrowia lipolytica Middelhovenusiomycesomyces tetr atepaespermus Magnrochaete clavata Sap 89 geniculatus Dipodascus albidus 90 Deakozyma indianensis 95 Candida incommunis rcqiae Wickerhamiella cacticola Wickerhamiella infanticola ickerhamiella versatilis W la bombicola Wickerhamiella dome Starmerel Starmerella apicola Epichloe typhina Groenewaldozyma salmanticensis Epichloe sylvatica Zygoascus meyerae Epichloe aotearoae Zygoascus ofunaensis Epichloe brachyelytri Sugiyamaella lignohabitans Epichloe bromicola Diddensiella caesifluorescens Spencermartinsiella europaea EpichlEpichoe amaloer illaelymins Blastobotrys muscicola Epichloe baconii Blastobotrys mokoenaii Epich Blastobotrys proliferans loe sp. Epichloe festucae Blastobotrys nivea Epichloe glyce AL99riae Blastobotrys serpentis Epich 24 Blastobotrys adeninivorans Claviceloeps gansu fusiformis Blastobotrys raffinosifermentans Claviceps purpuernsisea Blastobotrys americana Claviceps paspali Blastobotrys peorermiiensisaa lactativora quercuum Aciculosporium take Alloarscoideaopachyd hylecoeti Atkinsonella texensis Spo Sporopachydermi Bala Atkinsonellan siahypoxy obtectalon Saccharomycopsis capsularis Periglandula ipomoeae Saccharomycopsis malanga Ustilaginoidea virens Ascoidea asiatica Hypocr Ascoidea rubescens Candida ponderosae Moelelllaerie siallam libeensisra na Metarhizium robertsii Starmera quercuum Metarhizium anisopliae Candida stellimalicola Metarhizium brunneum 94 Starmera amethioni Metar Wickerhamomyces ciferrii hizium guizhouense Wickerhamomyces anomalus Metarhizium majus Wickerhamomyces hampshirensis Metarhizium acridum Candida freyschussiira xylosilytica Metar Cyberlindne OphiocordycepsPocho sp. campniaMetar chlaonoti-lhhiziumizium a rlbumileyi Cyberlindnera fabianii Ophiocordyceps polyrhachis-furcata Cyberlindnera petersonii Ophiocordyceps sp. camponoti-samydospoundersiria Candida mycetangii lens Ophiocordyceps camponoti- eonardi Cyberlindnera americana Cyberlindnera mrakii Ophiocordyceps unilateralis Cyberlindnera suaveo Cordyceps sp. RAO-20rufiped17is Cyberlindnera saturnus Cyberlindnera jadinii is Hirsutella thompsonii Candida vartiovaarae Hirsutella minnesotensis Cyberlindnelindnerraa maclmisuumraeaiens Cyber Ophiocordyceps australis Wickerhamomyces alni TolypocladiumTolypocl sp. Sadiumalcha iM Wickerhamomyces canadensis T Wickerhamomyces sp. NRRL YB-2243 olypocladium sp. Sup5 nPDAflatum ickerhamomyces bovis Tolypocladium ophioglossoides W EA-2 Barnettozyma californica Tolypocl -1 Barnettozyma populi Tolypocl adium capitatum Barnettozyma hawaiiensis adium paradoxum Albophoma yamanashiensis Barnettozyma salicaria Barnettozyma pratensis Purpureoc da montana Drechmeriilliua coniospom lilacinurma Candi Trichoderma koningii Phaffomyces antillensis Trich Phaffomyces opuntiae oderma longi Trichoder brachiatum Phaffomyces thermotolerans ma parareesei Candida orba Trichoder Trichoder ma reesei osmophila Trichodermma aguizho citrinovuenseiride Hanseniaspora vineae Hanseniaspora valbyensis Trichoder iaspora singularis T ma virens Hansen richoderma harzianum Kloeckera hatyaiensis Trichoder Trichoderma arunmdainaceum pleuroti Hanseniaspora pseudoguilliermondii Trichoderma brevicompactum Hanseniaspora uvarum Hanseniaspora clermontiae nus Trichoderma gamsii 99 Kluyveromyces aestuarii Trichoderma koningiopsis Kluyveromyces moarxiabzhanskii Trichoderma atroviride Kluyveromyces d Trichoderma hamatum Kluyveromyces lactis Trichoderma asperellum coryli Escovopsis sp. Eremothecium sinecaudum Escovopsis sp. Ae720 Eremothecium cymbalariae Escovopsis sp. Ae724 Escovopsis sp.Ae733 Ashbya aceri Escovopsis weberiAC Lachancea kluyveri Escovopsis sp. TC Lachancea fermentati Lachancea cidri Cordyceps tenuipes Cordyceps cicadae Lachancea mirantina Cordyceps fumoso Lachancea waltii Cordyceps pruiroseanosa Cordyceps militaris Lachancea quebecensis Beauveria bassiana Lachancea nothofagi Lachancea dasiensis Beauveria rudraprayagi Cordyceps brongniartii Lachancea meyersii Beauveria pseudobassiana Lachancea lanzarotensis ud Lachancea fantastica nom n Cordyceps farinosa Zygosaccharomyces rouxii Paecilomyces hepiali Zygosaccharomyces kombuchaensis Cordyceps confragosa Zygosaccharomyces bailii Lecanicillium psalliotae 93 Zygosaccharomyces bisporus Lecanicillium fungicola Torulaspora microellipsoides Lecanicillium sp. LEC01 Zygotorulaspora florentina Lecanicillium sp. MT-2017a Zygotorulaspora mrakii Torrubiella hemipterigena Torulaspora maleeae Stachybotrys chartarum 99 Torulaspora delbrueckii Stachybotrys chlorohalonata Torulaspora franciscae Memnoniella echinata Torulaspora pretoriensis Paramyrothecium roridum Tetrapisispora blattae Geosmithia flava Yueomyces sinensis Geosmithia morbida Vanderwaltozyma polyspora Geosmithia putterillii Outgroups Pucciniomycotina Tetrapisispora iriomotensis Acremonium chrysogenum Tetrapisispora phaffii Clonostachys rosea Tetrapisispora namnaonensis Gliomastix tumulicola Tetrapisispora fleetii Trichothecium sympodiale Candida castellii Trichothecium ovalisporum Nakaseomyces bacillisporus Trichothecium roseum 99 Sarocladium oryzae Sarocladium strictum Nakaseomyces delphensis sp. Na10 Fonticula Candida nivariensis Ustilaginomycotina Saccharomyces uvarum Fusarium circinatum Saccharomyces eubayanus Fusarium pininemorale Saccharomyces arbor Fusarium temperatum Saccharomyces kudriavzevicola ii Fusarium fracticaudum ium agapanthi Saccharomyces mikatae Fusar Saccharomyces paradoxus Fusarium nygamai Fusarium verticillioides ium udum Naumovozyma dairene Fusar Naumovozyma castelliinsis Fusarium fujikuroi Opisthosporidia Agaricomycotina+ Kazachstania viticola Fusarium proliferatum Kazachstania africana Fusarium mangiferae Kazachstania spencerorum Fusarium oxysporum Kazachstania rosi Fusarium commune Kazachstania kunashnii irensis Fusarium hostae Kazachsta Fusarium algeriense Kazachstanniaia maturicensis Fusarium burgessii Wallemiomycotina Kazachstania intestinartiniae Fusarium beomiforme Kazachstania bromeliaclisearum Blastocladiomycota Kazachstania naganishii Fusarium graminearum Fusarium asiaticridionualem Kazachstania taianensis Fusarium me Kazachstania yakushimaensis Fusarium culmorum Kazachstania transva Kazachstania siamensisalensis Fusarium pseudograminearum Kazachstania unispora Fusarium praegramineaoridesum Taphrinomycotina Kazachstania aerobia Fusarium spoiumr otrichilangsethiae Kazachsta Fusar nia solico Fusarium venenatum Pachysolen tannop la ium sambucinum Chytridiomycota Peterozyma xylosa hilus Fusar Fusarium gpoaeipes Peterozyma toletana Fusarium lon Nakazawaea holstii 96 Nakazawaea peltata Fusarium sp. FIESC 12 Fusarium equiseti Komagataella pseudop ium sp. FIESC 28 Komagataell Fusar ium sp. JS626 Pezizomycotina Komagataellaa phaffiipopuli astoris Fusar Citero Fusarium avenaceum Citeromycesyces matrsiamitensisensis Fusarium tricinctum 82 Citero Fusarium phaseoli Zoopagomycota myces hawaiiensis Kuraishia og Fusarium cuneirostrum Kuraishia m atae Fusarium tucumasilienseaniae Kuraishia capsolischiaulatana Fusarium br me Candida boidi Fusarium azukicguliforola Ogataea methynliiivora Fusarium vir Saccharomycotina Ogataea ramenticola Nectria haematococca Candida succiphila Fusarium solani Ogataea nag Fusarium euwalsp. FSlaceaeSC 6 Ogataea pilisensisanishii Mucoromycota Ogataea nitratoaversa Fusarium Candi Fusarium sp. JS103rae0 da arab Neonectria punicea 83 Ogataea treh inofer Neonectria hede Ogataea methaalophinolicalma entans Neonectria ditissima Ogataea trehaloabstin Nectria sp. B-13 Ogataea populialbae Ogataea zsoltii Corinectria fuckeliana Ogataea gluc ens Ilyonectria morsa destructans-panacis Ogataea hen Ilyonectri rodidyma ozyma Ogataea pini ricii Dactylonectria mac Ogataea nonfe Calonectria naviculata Ogataea minuta Ogataea koda rmenta CalonectriaCalon pseuectriadonavicu leucothoeslata Ogataea philodend ns Ogataea parapolymaemorpha Calonectrianectria pseu pedoreteanicillioidesudii Aqua nicola Ogataea polymorpha Pseudonectria foliicola Ambrosiozyma maleeriae Colletotrichum grami 64 Ambrosiozyma kashinagacola Colletotrichumrichum su falcblineoatumla Ambrosiozy Colletot Amb ma pseudov Colletotrichum incanum Amb rosiozy Amb rosiozymmaa monos vandepora Colletotrichum tofieldiae rosiozy anderk Amb rkliftii liftii ColletotrichumColletot hrigginsiichuma lnumentis Ambrrosiozyosiozymmaa amb oreg mmondsiiae onensis mphae custersianus Colletotrichum coccuotatumdes Brettanomycesma ano philerosiae Colletotrichum nysi fioriniae 64 Brettanomyces br ntoma Colletot Kre Colletotrichum ac odetiae gervanrija delftensis Colletotrichum 99 Kre malus Martigervanrija fluxuumxellensis Colletotrichum g hyti Colletotrichumrchido saphilumlicis Saturnnisporiozyma mendo Saturnispor a abiesophila richum chlorop Saturnispora saitoi Colletotrichum o a silvae ColletotColletotrichum musae Saturnispora zaruensisncae Saturnispora dispora Colletotrichum fructicola 83 Saturnispor Satur are nterricoisporaala serrahagledrocipensi is ColletotColletotrichumrichum gloeospo sansevierrioideiaes Colletotrichum truncatumS-367 83 Candi Pichia membda sorboxy acii ColletotColletotrichumr ichumichumlindem sp.ourthianumbicul J Pichi Pichi a occidentalislosa ColletotVerticillium klebahnii ranifaciens Verticillium isa Pichi a kudriavz erticillium tricorpus Pichiaa exigua norvegensis V Pichia heedii evii Pichia nakasei VerticilVliumerticil zaerticilliumregams laliumbo-atr ialfaanumulfaem Babjeviella inositovora V hliae Cephaloascus alb Verticillium nonalfalfaebilum Cephaloascus fragrans Candi VerticilVlerticilium loliumngispo darum m furcatum Kurtz da schatavii idus Verticillium nu Candimaniella cleridarum Acremoniu Candiddaa ascalap fragi Candi Reticulascus tulasneorum Candi da gorg Y CeratocystisCeratocystis eucalypticola fimbriata amaddaazyma tamma scolytiasii hidar Yamadazyma tenuis um Ceratocystis manginecansngtonii Yamadazyma philogaeaniensis Ceratocystis platani Yamadazyma nakazawae Ceratocystis cacaofunesta Candida athensensis Ceratocystis albifundus Meyerozyma guilliermondii Ceratocystisphora harri paoricicolonicala Candida carpophila rescens Chalaornidioopsisp thiehoralavioid l es Meye niella vi Mill rozyma caribbica Endoc Debaerozym EndocDavidsoonidio Deba ryomycesa acaciae m Thielaviopsis ethacetica Deba ryomyces nepalensis Thielaviopsis musarumensis Deba ryomyces ha Thielaviopsisla savannae euricoi aviopsis punctulata Deba ryomyces fabryiaramus Deba Thiel Huntiel ryomyces p Pric ryomyces subglobosusnsenii Huntiella oman Priceeomycesomyces m caediusrsonii Huntiella decipiens Priceomyces ha rosopid Huntiella bhutanensis Pric is Huntiella moniliformis Wickerheomycesamia fluo castillae Ambrosiella xylebori 85 Teunomyces gatunensis Ceratocystis adiposa Teuno plophilus Bretziella fagacearum Teuno Suhomycesmyces pyra kruisiilidae Knoxdaviesia proteae myces cretensisrescens m apiospedehoormumgii Suhomyces tanzawaensis Knoxdaviesia capensisntiacum Suhomyces emberor Scedosporium boydii Suhomyces canberraensis Scedosporiu Aciculoconidium aculeatum Koda Scedosporium rasiliensis ntospora prolificans llida Candi maea la Scedosporium aura oh Lome Sporrothrixothrix b schenckii lmi Scheffersda restingae um etipori Spo Sporothrixrothrix gl opabosa Scheffersomyces lignosus Spo Spathaspora hagerdaliae a novo-uicomis omycesmeri stipitis Ophiostoma piceae Spathaspora gorwiae rus Spathaspora passalidarum Ophiostoms brev a ips Ophiostom Spathaspora arborariae Spathaspora gi 90 Candi Lodde CeratocystiCeratocystiopsi opsis minuta Candida dparaa corydapsilosisli rothrix insectorum Candida rorthopsomycesilosis e Candi rioi FragSpoosphaeria purpurea 90 HawksworthiomycRaffaeleaes lignivo quercivora gera Candi rum Candida dsojaea dubli longisp RaffaeleaEsteya su verlphurmicolaea Candida dtropicaa albicalis nnia clavi Hyphopichia burtoniiniensis orus Raffaelea quercus-mongomlicae proce Hyphopichia ho Danie ns LeptogGrosmaraphiuraphium lundbergii C Candian da lrhagozymaii onta di LeptogGrosmaRaffaeleannia pen laicillatauricola Hyphop da Candida aurisg milentoma Raffaelea sp. RL272 ot Candida heveicolaoi RaffaeleaRaffaelea ambrosiae arxii Candi ichia hei rioens Raffaelea albimanens Candi Clavisp da oregonensismii is Graphiaporthelbum sp.frag MG03rans Candida dintera fructusmedia Candi ora lusita Magn aporthe sp. MG07 Candi Magnaporthe sp. MG12 gena Candida dgoluba blattaeevii MagnMagnaporthe oryzae Metschnikda wanche Candida hawaiiana niae kipukae Magnaporthea sp.penniseti MG08 MagnMagnaportheaporthe sp. MG05 grisea Metschnikowia hibisci Metschnikowia abeowia bicusrniae ryzae Metschnikowia shivo PyricMagnulariaporthiopsis poae Metschnikowia drakensbe Metschnikowia pr pidata va Metschnikowia ar Magnaporthiopsis rhizophila ensis Metschnik GaeumanFalcipnomyceshora tr oitici Magnaporthinnomycesopsis Nakataeaincr sp.ustans JS- 464oryzae Metschnikowia dekortorum is Metschnikowia bow rdeen r. bicuspidata uterocub ola Metschnikowia kamakouana Gaeuma Metschnik owia sim gae iae Metschnikowia haw oteae 98 izonensis Pseudohalonectria lignicolalla lustric Metschnikowia hamakuensis Ophioceportheras dolichde ostomum Metschnik ilis rgensis Metschnikowia boorwiaealis ma ChrysoportheConie cubensis Metschnikowia loch ChrysoChrysoportheCryph austonectriaroafrica radicalna acearum Metschnikowia matae var lesiae Metschnikowia mataowiae vaipo uinuia JuglancJuglanconiso ujuglnisgland aoblondinanga Metschnikowia contin rthe longicolla Metschnikowia cerradonensis aiiensis a maydis na Metschnikowia santaceciliae moeae Diapo Drechslerella stenobrocha Juglanconis sp. DMW523rpell alsa mali Diaporthe ampelinaV 99 Arthrobotrys oligospora Diaporthe helianthi 99 Dactylell headii a clavigignenti-j Pyronema omphalodes StenocaDiaporthe aspalathi Morc mophila Morchella eximia ina haptotyla . matae omoni Tube hella septimelata entalisr. maris erina Tuber borchii T r calosporum Chaetomium globosum T ube Ophiogn T ube PhaeoacreChaetomoniummiumThiel mini cochamviauml iodesterrestris ube r magnatum pora ans Arthonia rrad umbiliataicatum Cryo r melan Madurella mycetomatisospora terricola Sphaceloma murrayae Elsinoe austral Podos africana myces antarcticus Thermothelomyces therNeur iaria Aur Chaetomium thermophilum 86 Aureobasidium subglacialeosporum eobasidium sp. FSWF8-4 Neurospora pannonica Aureobasid Aureobasid Neurospora crassa Aur Neurospora sublineohlataaeta lign NeurosporaNeur tetrodsporariaasper amacrospma ora Leptoxyphium fumago Peltasteer obasidfructicola is Sor haeta hoffmannii Rachicladospo Conioc 83 Cladosporium sphaerosperiumm naummibiae n sp. EC38 Clados ium me ium pul Conioc Cladosporium sp. SL-16 Hypoxylon pulicicidum JS573 99 Preussia sp. BSL10 . Microcyclospora pomic Hypoxylon sp. E7406B 401 poriu lanogenum HypoxyloHypoxylon sp. CO27-5 Micr lulans Acidomyces richmondensis ria sp rium sp. CCFEE 5018 Daldinia sp. EC12 Baud ocyclospo m cladosp Daldinia eschscholtzii SB201 Ramic AnnulohypoxylonXyla stygium morpha Ramularia endophylla Hypoxylon sp. CI-4A Ramularia coolinialo-cyg panniame Zymose hlori KretzschmariXylaa deustaria longipes Zymoseptoria pseudotritici ra tardicrescens orioides Rosellinia necatrEutypaix lata Zymose Zymoseptoria tritici dium luteum Xylaria poly Zymose ptoria pass Xylaria sp. MSU Lecanosticta acicola ola Mycosphaerelloides m ricana Micr ptoria a DidymobotryuPestalotim rigiduompsis fici Zasmidium angulare Microdochium bolleyi ptoria brevis m agropyri iae 83 Zasmidium citri-gr Exutisph ocyclosporella m ina Mycosphaerella arachidis rdabil erinii Passalora fulva Dothistro Dothistroma septosporum iae PestalotiPseudoRhynchospsisomassa sp. JCMrpiellaoriu 9685 mvex secalisata Nothoph aerella laric la subalp Pseudocercospora fijiensis Cadophoraonina ma colorumronar Pseudocercospora pin RhynchosRhynchosporiupmoriu commHelotiauneles sp. F229 99 Pseudocercosp ides Cadophora sp. DSE1049 Mycosphaerella eumusaema pini iseum ali adeirae Marssonina brunnea Mycosphaerella sp. Ston1aeocrypto Marss locepha Erysiphe pisi Spha Erysiphe pulchra icae Spha ina locephala scopiformis Mycosphaerella sp. PB-2012b Phia 94 Cercospora can Erysiphe necator rum erulina populicola ryne sarco Cercos eruli PhiaArticulospora tetracladiaBlumeria graminisoma er Cercos Cercospora soj pus gaeumannii Cercos na musiva ora mus niomyces variabilis Cercospora nicotianae Ascoco Pezol Cercospora beticola pora zeina pora berteroae Ochroconis constricta i-densiflorae Meli Meliniomyces bicolor V V err pora cf ae Cairneyella variabilis 5553 V Calycina herba enturi escens lozoyensis V enturi uconis gallopava V enturi 87 Phyllenturiostictaa pyrinacapitalensis ina Phyllosticta citricarpa a effusa . Hymenoscyphus infarciens Neofusicoccum parvuma carpop sigesbeckiae ndron maius ae Neoscytali a inaequ Glarea Macr Hymenoscyphus scutula HymenHymenoscyphusoscyphus fructig salicenusellus linia laxa Botryos Hymenoscyphus linearis Lasiodiplodi iaeana Diplo rphotheca resinae Diplo ophomina phase Hymenoscyphus fraxiOidiodeneus linia Monifructigena Diplodia sapinea hila Diplo alis Coniosporium apollinis phaer dium dimidiatum HymenoscyphusAmo repandus melliae dia corticola MoniMonilinia polystroma Lepidopterella palustrdiais K4 Cenococcum geop Gamarada debralockiaeMonilinia fructicola Gloniu dia scrobiculata Rhytidhyste seriata a theobroia dothidea Phialophora cf. hyalina BP Hysterium pulica Monilinia aucupari rinia ca Clohesy Nigr osclerotinia dur ns Beve m stellatum Sclerotinia borrealisotinia glacialis Corynespora cassiicola Cibo 017a WR Paraphaeosphaeria sporulosa olina osclerotinia curreyana rmis Per ogran Myri Botrytis cinerea Myriosclerotinia scirpicola Botrytis paeoniae Helminthosporium solrwykella pulmonaria mae Scle Ascochyta rabiei omyces aquaticus Myri Phoma herb iconia macrospinosa ron ruful Sclerotinia sclerotiorum Stagonosporo Epicoccum sorg a mackinn Epicoccum nig 89 Shiraia sp. slf14 hilum Par re Lanzia echinophila -2642 Par Pleos ria aeruginasce um mia sp. NJR-2 22 Stagon aphoma sp. B47-9 Pyrenochaeta sp.astagonosp DS3sA ora nodorum 3629 07 Pyrenochaeta sp. UM 256 Clarireedia homoeocarpaphoma craterifo F Pseudopyrenochaeta lycopersici onii Rutstroemia sydowiana -28 arum Pezicula radicicola Leptosph porales sp. UM rocibo phoma cylindrospora -26 Leptosphaeria maculans W -1-I1 Pyre psis tanaceti Scytalidium lignicola 41 Pyre ospora sp. S -2643 RutstroeRutstroemia sp. NJR-2017a BColeoBW Pyre -2644 A rum hinum Chlo -22 Alter Rutstroemia sp. NJR-2017a BVV2 -928 ani Coleo Alternaria solt nophora seminiperda Alternaria a e nophora tritici-repentis W nopho sp. 05NY08 Alternaria a r aeria biglobosa -3775 Stemphylium lycopersici n VKM F-4519 FW ascus destructans -929 Exserohilum turcicum naria brassicico -969 Curvu a ascus sp. WS W Curvularia g r -4518 FW W Curvu ia Curvularia papendorfii ra teres ogymnoascus sp. 03VT05 Bipolaris cookei c RC1lsM3a Pseudogymnoascus verrucosus Bipo 1110 2012 ogymno VKM F is Bipo o Bipolaris o laria sp. IFB-Z10 n Pseudogymnoascus sp. 24MN13ogymno Bipo PseudogymnoaPseudscus sp.ogymno VKM aFscus-103 sp. 04NY16 Bipolaris zeicola s ogymno ascus sp. BL549 laria lunata rbor lani ascus sp. ogymnoascusVKM sp. F BL308 VKM F-3557 Symb laris maydis lternata o Pseud Xylon laris sorokiniana r ascus pannorum Umbi t Y3a Pseud Umbilicari i Lasall laris victo escens a ingensis Gyalolechia flavorubescens l Pseud Rama eniculata i KM F-4514 F s Pseud Ramalina intermedia iotaphr la Pseud Evernia prunastri a heveae ogymno Pseud licaria muehlenbergii ogymno Cetradonia linearis ryzae rgillus luchuensis bericus Cladonia uncialis awamori rgillus neoniger Cladonia metaco ia hispan ascus sp. ascus sp. Cladonia macilenta Aspergillus kaAspewachiirgillus piperis rasiliensis Phaeomoniella chlamydospora lina pe Pseudogymnoascus sp.ogymno 23342ascus sp. VKM F-4246 Endoc rgillus vadensis iensis Herpotrichie a pustulata riae rgillus eucalypticola rbonarius Knufia p ina buchn Pseud Pseud Aspe rgillus tub sp. everni Aspe Cyphel Aspergillus niger Phia Pseudogymno rgillus phoenicis Exophiala mesophila rgillus costaricaens enus Exoph Exoph Pseud ascus sp. VKM F-4516 F Aspe Exoph ruviana ogymno Aspe oviolaceus Capr arpon pusillum ica Aspe Capronia epimyces rgillus welwitschiae 6037 Exophiala sideris lophora attae Pseudogymnoascus sp. VKM F-4517 F orphus Exoph a furfuracea ogymnoascus sp. VKM F-4513 F Aspe rgillus fij Exophiala xeno Pseudogymnoascus sp. VKM F-4515 FW Pseudogymnoascus sp. Aspe Exophiala spin Aspergillus i Rhinoc lopho etricola Exophiala alca Aspergillus lacticoffeatus Phialophora verr iala aquamar eri jae Phialophora ame onia cor iala calicioides Pseudogymno Aspergillus b rgillus sclerotioniger runne Clado iala dermatitidis Aspe Cladophialophora yegresii llaceae sp. U Pseudogymnoascus sp. VKM F-4520 FW Pseud rgillus aculeatus Cladophialophora b Pseudogymnoascus sp. VKM F-3808 Aspergillus ellipticus Clado Aspe Clado Pseudogymnoascus sp. VKM F-4281 FW omom icola ii Fonsecaea erecta iala oli Pseud Aspergillus ca Fonseca ra europaea rallifera Fonsecaea nubica rgillus sp. Z5 m Fonsecaea monophora Ascosph ladiella mackenziei u Aspe ersii Polytoly rgillus indolog r Helicoc phialo Aspe Par arasiticus Par rgillus versicolor Emmonsia crescens Pseudogymnoascus sp. V Aspergillus aculeatinus Aspergillus uvarum o Aspergillus japonicus rgillus nidulans Emergomyc phialo onata Pseudogymno ombycis i Emmonsia sp. CAC-2015a rgillus so ancockii Emergomyces pasteurianus phialophora immun Aspergillus heteromorphus t Histoplasma capsul Blasto gosper rgillus sp. MA Aspe Blasto Aspergillus sclerotiicarbonarius o Blastomyces Blastogilchristii acoccidioides lutzii rgillus h r Blastomyces dermatitidis acoccidioides brasiliensis rgillus oryzae ri Malbranchea cinnamomea Aspe Aspergillus sydowii Ophidio Uncinocarpus reesii Aspergillus ustus e immitis Aspe Coccidioides posa ea multi phora carrio ina Aspergillus violaceofuscus l Ama ifera biotica rgillus mulundensis Ama Aspergillus b Aspe Chrysosporium queens Aspe rgillus p c Onygena corvinaByssoonygena ceratinophila arpus g pa hystricis lophila canis aera apis phora ps M238 Nannizzia gypsea Aspe T rgillus steyn T s T T T T AspergillusAspe saccharolyticus T richophyton interdigitale myces parvus Aspergillus rambellii 6038 T richophyton mentagrophytes myces sp. MA-2018 ucosa Aspe E T richophyton tonsurans ma Aspergillus flavus rgillus tanneri R richophyton equinum rgillus h T richophyton verrucosum myces percursus s 6039 T T rich T r ricana Aspergillus calidoustus eudoterreus T T T rich T r uroascus n T uroascus mutatus T T T l i T T T P B alaromyces piceae h u P B Aspe B a a m 6 e a i m a a c i a Aspergillus nomius l s i a m s a a c r i a

l m l s a a

a Aspe s rgillus candidus a m e s s h s u 3 m e l myces ophi i 1 y h m l l e y u y l m p n m l Aspergillus p m l Aspe u u l h m a i a k l es orientalis l e a l u a morphosa u l a ense l

l u u l a a 6040 n a r i e ophyton benhamiae n s a 0 u s n g e s u 0 a o n a t a a h u u ophyton soudanense

e r rgillus ruber u x antiana n o n c r Aspergillus b u r l m riseus r b r r Aspe c r Aspe i e r l s m m biforme e s r r h s r e r o Aspergillus arachid n 6 n i o p s r i c i r a r o c r o

S o

rgillus fumigatus o o

e a r o p n e c

c o i m l u e t o ammo o o p o o o i o e o Aspergillus ochraceoroseus p l o t b n a a m o s n m h l r m m m p m rgillus turcosus i i s g p u h i r i m p rgillus glaucus u c S m m

A m l m Aspe Aspergillus terreus m c m s c l t l c n o a t nii m italicum p o m o y e a m rubens r l

u s i l i o i

o p y s rgillus udagawae s m i y r s y

i i y Y h y h illium solitum h y y Aspergillus fischeri z x o y Aspergillus westerdijkiae u t r

o y v b a rgillus ps M a s p y y c y i y n Aspe h y t e m r u c o m camemberti p p c y u c c A t b c Aspergillus campestris l c l t l o o m c r B m c Aspergillus lentulus r x u c m p s a

u c a a a c

. c Aspe c i c e e c e u e a c e n o e da n e a r r e m roqueforti n i n Penicillium freii l u e a . e c

u e p s e u s e m e m e m p m iger i l m s e Aspergillus clavatus m fuscoglaucum e atum Aspe m flavigenum i c s s Aspergillus wentii c s s phila s Aspe a l l s b b c s l a s m u p s i o v

p i e s s l s u s s e l j illium sp. HKF2 u s r d Aspergillus taichungensis s

a m sp. MA m nalgiov s i i Aspe r s y i i y Aspergillus neoellipticus Aspergillus cristatus y u w s i u a m s g u i l c Penicilliu c c

b m m l odiicola s dasii Aspe s m Penic a Aspergillus chevalie i o

l i c a m n u p m l v l s c c s m s u s i l l m i z

y i c t m griseofulvum u e r b i o u t o m l l a

m s m i c l n c d m e r u o i e i u i i a a c a p m l u o e a u n i c i i l n y s p r n s o illiu i n r u i r Penicilliu l y n i i t Aspergillus novofumigatus l r Penicilliu l u l s

e m p c u r i l l i r n n u l l b Penicillium nordicum m i i t u l n a r c e i e i u c p l o l l p M i e l r r n i s l i i i Penicillium digitatum n m u n l l i a u s Penicillium polonicum i o r t c l v l d u m P Penicilliu c l u o e u m o i a n Penic e s i n s i e p a c l .

i r e c P i e i e P c e g e o c i n l i e i Penicillium carneum l l Penicillium sp. CF05 i i landicum c c n s u i a o t a t i c t t e n A Penicillium verrucosum l c h t Penicilliu c c a i c n e s l s i i c o f a P i t a n o i n a u Penicilliu n P Penicilliu u e n n i i m n l f n

a t e y u i s t e P n F c h y c n X l e c i a l e n e s u Penicilliu Penic i l u o e n k i e u n

n Eurotiomycetes sp. MA M u s Penicillium chrysogenum o u e P c t

0 e Eurotiomycetes sp. MA e P i b e m s i i P n s s P e s i P u s P c a s s o Penicilliu i P 0 u i o P u e P

l

s u P u s e r

i

1 s

s s

P s s s a

l

y

a

B Supplementary Fig. 3. The -scale phylogeny ofT 1,644 in the fungal kingdom. The tree of the 1,644 fungal species and 28 outgroups was reconstructed from the maximum likelihood concatenation analysis of 290 single-copy BUSCO genes under a single LG+G4 model (lnL = -78287339.984). All internal branches were supported with 100% bootstrap value unless otherwise noted. See also Figure 3A and Supplementary Table 1. 1 Full (1) top100_ABS (10) top100_complete (9) 0.98 top100_DVMC (3) top100_LB (5) 0.95 top100_longest (4) top100_RCFV (6) concatenation-based single model top100_saturation (7) 0.92 top100_slow_evolving (8) top100_ABS (10) top100_complete (9) 0.9 top100_DVMC (3) top100_LB (5) 0.88 top100_longest (4) top100_RCFV (6) top100_saturation (7) 0.85 concatenation-based data-partioning top100_slow_evolving (8) Full (1) 0.82 top100_ABS (10) top100_complete (9)

top100_DVMC (3) 0.8 top100_LB (5) top100_longest (4) top100_RCFV (6) 0.78 Coalescent-based top100_saturation (7) top100_slow_evolving (8) 0.75

V (6)

V (6)

V (6)

LB (5)

est (4)

LB (5)

MC (3)

est (4)

lete (9) LB (5)

Full (1)

MC (3)

est (4)

lete (9)

Full (1)

MC (3)

lete (9)

CF

ation (7)

V

CF

ABS (10)

ation (7)

V

CF

ABS (10)

ation (7)

V

ABS (10)

olving (8) olving (8)

D

R

D

R

long olving (8)

v v

D

R

long

omp 100_

long

omp 100_

v

e e

omp 100_

c

c

e

c

satur

satur

100_

top

satur

100_

top

100_

w_ w_

top 100_

100_

100_

100_

100_

w_

100_

100_

100_

100_

top

top 100_

100_ top

slo slo

top

top

100_

100_ top

top

slo

top

100_ top

top

top

100_

top

top

top

top

top

top

top

100_ 100_

100_

top top

top

concatenation-based concatenation-based Coalescent-based single model data-partioning Supplementary Fig. 4. Heatmap of topological similarities for all pairwise comparisons among the phylogenies reconstructed from analyses of 12 di er- ent data matrices using three di erent approaches (concatenation under a single partition, concatenation under gene-based partitioning, and coales- cence). The topological congruence between each pair of phylogenies was calculated using Gotree. The size and color of the squares represents the degree of congruence as measured by percentage. Results from data matrices 2, 11, and 12 are not shown here since they have di erent sets of taxa that have been removed. Outgroups outgroup (26)

Fonticula (2) Fonticula Opisthosporidia Paramicrosporidium Microsporidia (23) Blastocladiomycota

Blastocladiomycete (2) Chytridiomyceta (13) Zoopagomycota (1) 96 Neocallimastigomycetes (5) Mucoromycota

Zoopagomycetes (7) Pucciniomycotina Entomophthoromycetes (2) Ustilaginomycotina Dimargaritomycetes (1) Harpellomycetes (8) Agaricomycotina+ Wallemiomycotina Kickxellomycetes (2) Taphrinomycotina

Mortierellomycete (3) Pezizomycotina 99 Glomeromycetes (7) Saccharomycotina 98 Endogonomycetes_clade1 (3) Endogonomycetes_clade2 (1) 97 Umbelopsidomycetes (1) Mucoromycetes (33)

Microbotryomycetes (20) 87 (15)

Cystobasidiomycetes (3) (1) (1) Geminibasidiomycetes (1) (3)

Tremellomycetes (63)

Agaricomycetes (246)

99 (3) Moniliellomycetes (1) Exobasidiomycetes_clade_1 (7)

Exobasidiomycetes_clade_2 (10)

Ustilaginomycetes (24)

Malasseziomycetes (15) 87 Neolectomycetes (2) 89 (5)

Pneumocystidomycetes (3)

Schizosaccharomycetes (4)

Pezizomycetes (8)

Orbiliomycetes (3)

Sordariomycetes (322)

Leotiomycetes (80) (1) (117)

Xylonomycetes (2)

Lecanoromycetes (12)

Eurotiomycetes (196)

Lipomycetacea (8)

Trigonopsidaceae (6)

Dipodascaceae/ (37) Alloascoideaceae (1) Sporopachydermia clade (2)

CUG-Ser1 (94)

Pichiaceae (60)

CUG-Ala (5)

CUG-Ser2 (4)

Phaffomycetaceae (34)

Saccharomycetaceae (71)

Saccharomycodaceae (8)

Supplementary Fig. 5. Phylogeny of 1,639 fungal species from the Rogue_taxa_removal data matrix. The topology shown was obtained from maximum likelihood analysis of a concatenated data matrix of 290 genes under a single LG+G4 model (lnL = -76877622.807). All internal branches were supported with 100% bootstrap values unless otherwise noted. Each tip corresponds to the -level ranking derived from NCBI (except for Saccharomycotina, where each tip corresponds to each one of the 12 major clades to re ect the current understanding of Saccharomycotina phylogeny21). outgroup (26) Outgroups Fonticula (2) Fonticula Rozella Opisthosporidia Paramicrosporidium Blastocladiomycota Microsporidia (23) Chytridiomyceta Blastocladiomycete (2) Zoopagomycota Neocallimastigomycete (5) Mucoromycota Monoblepharidomycetes (1) Chytridiomycetes (13) Pucciniomycotina (2) Ustilaginomycotina 28 Agaricomycotina+ Zoopagomycetes (7) Wallemiomycotina Entomophthoromycetes (2) Taphrinomycotina Dimargaritomycetes (1) Pezizomycotina Harpellomycetes (8) Saccharomycotina Kickxellomycetes (2) Glomeromycetes (7) 97 Mortierellomycetes (3) 92 97 Endogonomycetes (4) Umbelopsidomycetes (1) Mucoromycetes (33) Pucciniomycetes (15) (20) (3) 28 Agaricostilbomycetes (1) Mixiomycetes (1) 89 +Moniliellomycetes (19) (24) Malasseziomycetes (15) Geminibasidiomycetes (1) Wallemiomycetes (3) (65) Dacrymycetes (3) (253) Neolectomycete_clade_1 (1) Neolectomycete_clade_2 (1) Taphrinomycetes (5) (4) (3) (8) Orbiliomycetes (3) 98 (327) (83) Arthoniomycetes (1) Dothideomycetes (118) Xylonomycetes (2) Eurotiomycetes (204) (12) (9) Trigonopsidaceae (6) /Trichomonascaceae (37) Sporopachydermia clade (2) Alloascoideaceae (1) CUG-Ser2 (4) Phaffomycetaceae (34) (71) (8) CUG-Ser1 (94) CUG-Ala (5) (61) Supplementary Fig. 6. Phylogeny of 1,672 fungal species from the Top100_slow_evolving data matrix under a single LG+G4 model. The topology shown was obtained from maximum likelihood analysis of a concatenated data matrix of 290 genes under a single LG+G4 model (lnL = -13426586.414). All internal branches were supported with 100% bootstrap values unless otherwise noted. Each tip corresponds to the class-level ranking derived from NCBI taxonomy (except for subphylum Saccharomycotina, where each tip corresponds to each one of the 12 major clades to re ect the current understanding of Saccharomycotina phylogeny21). 1.00

0.75

result −monophyly−strong−signal

0.50 Zygomycota−monophyly−weak−signal

Proportion Zygomycota−−weak−signal Zygomycota−paraphyly−strong−signal

0.25

0.00

Spatafora2016_46taxa_192genes Subset_Dikarya matrix Supplementary Fig. 7 . Distribution of phylogenetic signal for two alternative hypotheses on the Zygomycota lineage. The two alternative hypotheses are: Mucoromycota is sister to Zoopagomycota (Zygomycota-monophyly; T1 Orange), Mucoromycota is sister to Dikarya (Zygomycota-paraphyly; T2 Green). Proportions of genes supporting each of two alternative hypotheses in the Spatafo- ra2016_46taxa_192genes and Subset_Dikaya data matrices. The GLS values for each gene in each data matrix are provided in Supple- mentary Table 5. We considered a gene with an absolute value of log-likelihood di erence of two as a gene with strong (|ΔlnL| > 2) or weak (|ΔlnL| < 2) phylogenetic signal.