Figure 4

Encephalitozoon cuniculi Phycomyces blakesleeanus 1.0 Rhizopus oryzae Mucor circinelloides Schizosaccharomyces pombe Tuber melanosporum Verticillium dahliae 1.0 1.0 Colletotrichum graminicola Colletotrichum sublineola 1.0 Hypocrea atroviridis 1.0 1.0 Hypocrea jecorina 1.0 Hypocrea virens Nectria haematococca 1.0 1.0 Fusarium oxysporum Gibberella zeae 1.0 1.0 Thielavia heterothallica 1.0 1.0 Neurospora crassa 1.0 1.0 1.0 Neurospora tetrasperma 1.0 Magnaporthe grisea Cryphonectria parasitica Blumeria graminis 1.0 1.0 Sclerotinia sclerotiorum Botryotinia fuckeliana Talaromyces stipitatus 1.0 1.0 Penicillium rubens 1.0 Penicillium chrysogenum 1.0 Eurotium herbariorum Aspergillus clavatus 1.0 1.0 Neosartorya fumigata 1.0 1.0 Neosartorya fischeri 1.0 Aspergillus terreus Aspergillus oryzae 0.955 1.0 1.0 Aspergillus flavus 1.0 Aspergillus aculeatus Emericella nidulans 1.0 Emericella nidulans 1.0 1.0 Phaeosphaeria nodorum 1.0 Phaeosphaeria nodorum Leptosphaeria maculans Cochliobolus lunatus 1.0 1.0 Aureobasidium pullulans 1.0 Passalora fulva 1.0 Zymoseptoria tritici Yarrowia lipolytica Zygosaccharomyces rouxii 1.0 Candida glabrata 1.0 1.0 Saccharomyces cerevisiae 1.0 Ashbya gossypii Kluyveromyces lactis 1.0 1.0 Candida tenuis Debaryomyces hansenii 1.0 Spathaspora passalidarum 1.0 Lodderomyces elongisporus 1.0 Candida albicans 1.0 1.0 1.0 Scheffersomyces stipitis Dekkera bruxellensis Komagataella pastoris 1.0 1.0 Ustilago hordei Ustilago maydis 0.637 Wallemia sebi Tremella mesenterica 1.0 1.0 1.0 Cryptococcus gattii Cryptococcus neoformans 1.0 Piriformospora indica Auricularia subglabra Fomitiporia mediterranea 1.0 1.0 Punctularia strigosozonata Gloeophyllum trabeum 1.0 1.0 Heterobasidion annosum Stereum hirsutum 1.0 1.0 Phanerochaete chrysosporium 0.963 0.790 Phlebiopsis gigantea 1.0 1.0 Dichomitus squalens 0.999 1.0 Trametes versicolor Fomitopsis pinicola 1.0 Postia placenta 0.840 Wolfiporia cocos Coniophora puteana 1.0 Schizophyllum commune 1.0 Agaricus bisporus 1.0 Coprinopsis cinerea 1.0 Laccaria bicolor Puccinia graminis 1.0 Puccinia graminis Mixia osmundae Batrachochytrium dendrobatidis Batrachochytrium dendrobatidis Spizellomyces punctatus

1.0

1.0

1.0

0.2 subst. per site 1.0

Supplementary figure 1: Fungi tree inferred from 100 orthologous groups exported using the new “marker gene export” function. The tree, which could be computed within 40 minutes on a single CPU, is highly congruent with, but considerably more resolved than the NCBI taxonomy.