Table S1. Fungal genomes used in trait analysis.

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Agaricus bisporus var.

bisporus Agabi_varbisH97_2 936046 Free-living filamentous (1)

Agaricus bisporus var.

burnettii Agabi_varbur_1 597362 Free-living filamentous (1)

Antonospora locustae Antlo1 1284279 Other (2, 3)

Armillaria mellea Armme1 1314977 Free-living filamentous (4)

Arthrobotrys oligospora Artol1 756982 Free-living filamentous (5)

Arthroderma benhamiae Artbe1 663331 Other (6)

Ascocoryne sarcoides Ascsa1 1016881 Other (7)

Ashbya gossypii Ashgo1 284811 Other (8, 9)

Aspergillus clavatus Aspcl1 344612 Free-living filamentous (10)

Aspergillus flavus Aspfl1 332952 Free-living filamentous (10, 11)

Aspergillus fumigatus Aspfu_A1163_1 451804 Other (12-15)

Aspergillus kawachii Aspka1_1 1033177 Free-living filamentous (16)

Aspergillus nidulans Aspnid1 162425 Free-living filamentous (10, 17)

Aspergillus niger Aspni5 380704 Free-living filamentous (18)

Aspergillus oryzae Aspor1 510516 Free-living filamentous (10)

Aspergillus terreus Aspte1 341663 Free-living filamentous (10)

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Aureobasidium pullulans

var. melanogenum Aurpu_var_mel1 1043003 Free-living filamentous (19)

Aureobasidium pullulans

var. namibiae Aurpu_var_nam1 1043004 Free-living filamentous (19)

Aureobasidium pullulans

var. pullulans Aurpu_var_pul1 1043002 Free-living filamentous (19)

Aureobasidium pullulans

var. subglaciale Aurpu_var_sub1 1043005 Free-living filamentous (19)

Baudoinia compniacensis Bauco1 717646 Free-living filamentous (20)

Beauveria bassiana Beaba1 655819 Other (21)

Bjerkandera adusta Bjead1_1 748444 Free-living filamentous (22)

Blumeria graminis Blugr1 546991 Other (23)

Botryobasidium

botryosum Botbo1 264124 n. a. (24)

Botryosphaeria dothidea Botdo1 55169 Other (25)

Botrytis cinerea Botci1 332648 Other (26, 27)

Candida tenuis Cante2 590646 Yeast (28)

Ceriporiopsis

subvermispora Cersu1 914234 Free-living filamentous (29)

Chaetomium globosum Chagl_1 306901 Other (30)

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Cladosporium fulvum Clafu1 5499 Other (20, 31)

Coccidioides immitis Cocim1 246410 Other (32)

Coccidioides posadasii Cocpo1 222929 Other (33)

Cochliobolus carbonum Cocca1 930089 Other (34)

Cochliobolus

heterostrophus CocheC4_1 665024 Other (20, 34)

Cochliobolus miyabeanus Cocmi1 930090 Other (34)

Cochliobolus sativus Cocsa1 665912 Other (20, 34)

Cochliobolus victoriae Cocvi1 930091 Other (34)

Colletotrichum

graminicola Colgr1 645133 Other (35)

Colletotrichum

higginsianum Colhi1 759273 Other (35)

Coniophora puteana Conpu1 741705 Free-living filamentous (36)

Coprinopsis cinerea Copci1 240176 Free-living filamentous (37)

Cordyceps militaris Cormi1 983644 Other (38)

Cryptococcus neoformans

var. grubii Cryne_H99_1 235443 Yeast (39)

Cryptococcus neoformans

var. neoformans Cryne_JEC21_1 214684 Yeast (40)

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Dacryopinax sp Dacsp1 745407 Free-living filamentous (36)

Debaryomyces hansenii Debha1 284592 Yeast (41)

Dekkera bruxellensis Dekbr2 747657 Yeast (42)

Dichomitus squalens Dicsq1 732165 Free-living filamentous (36)

Dothistroma septosporum Dotse1 675120 Other (20, 31)

Encephalitozoon cuniculi Enccu1 284813 Other (43, 44)

Encephalitozoon hellem Enche1 907965 Other (45)

Encephalitozoon

intestinalis Encin1 876142 Other (46)

Encephalitozoon romaleae Encro1 1178016 Other (45)

Enterocytozoon bieneusi Entbi1 481877 Other (47)

Eurotium rubrum Eurhe1 1388766 n. a. (48)

Eutypa lata Eutla1 1287681 Other (49)

Fibroporia radiculosa Fibra1 1078123 Free-living filamentous (50)

Fomitiporia mediterranea Fomme1 694068 Free-living filamentous (36)

Fomitopsis pinicola Fompi3 743788 Free-living filamentous (36)

Fusarium fujikuroi Fusfu1 1279085 Other (51)

Fusarium graminearum Fusgr1 229533 Other (52)

Fusarium oxysporum Fusox1 426428 Other (53)

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Fusarium verticillioides Fusve1 334819 Other (52, 53)

Galerina marginata Galma1 685588 Free-living filamentous (24)

Ganoderma sp Gansp1 767862 Free-living filamentous (22)

Glarea lozoyensis Glalo1 1116229 Free-living filamentous (54)

Gloeophyllum trabeum Glotr1_1 670483 Free-living filamentous (36)

Grosmannia clavigera Grocl1 655863 Other (55)

Heterobasidion annosum Hetan2 747525 Other (56)

Histoplasma capsulatum Hisca1 339724 Other (32)

Hysterium pulicare Hyspu1 100027 Free-living filamentous (20)

Jaapia argillacea Jaaar1 933084 Free-living filamentous (24)

Kluyveromyces lactis Klula1 284590 Yeast (41)

Laccaria bicolor Lacbi2 29883 Mycorrhizal (57)

Leptosphaeria maculans Lepmu1 985895 Other (58)

Leucoagaricus

gongylophorus Leugo1 1258663 n. a. (59)

Macrophomina phaseolina Macph1 1126212 Other (60)

Magnaporthe grisea Maggr1 242507 Other (61)

Malassezia sympodialis Malsy1_1 1230383 Yeast (62)

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Melampsora laricis-

populina Mellp1 203908 Other (63)

Metarhizium acridum Metac1 655827 Other (64)

Metarhizium robertsii Metan1 655844 Other (64)

Microsporum canis Micca1 554155 Other (65)

Mixia osmundae Mixos1 764103 Yeast (66)

Monacrosporium

haptotylum Monha1 1284197 Free-living filamentous (67)

Moniliophthora perniciosa Monpe1_1 554373 Other (68)

Myceliophthora

thermophila Spoth2 573729 Free-living filamentous (69)

Mycosphaerella

graminicola Mycgr2 336722 Yeast (70)

Nectria haematococca Necha2 660122 Other (71)

Nematocida parisii Nempa1 881290 Other (72)

Neofusicoccum parvum Neopa1 1287680 Other (73)

Neosartorya fischeri Neofi1 331117 Other (10, 11)

Neurospora crassa Neucr2 367110 Free-living filamentous (74)

Neurospora tetrasperma Neute2 510952 Free-living filamentous (75)

Nosema ceranae Nosce1 578460 Other (76, 77)

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Omphalotus olearius Ompol1 1128401 Free-living filamentous (78)

Ophiostoma piceae Ophpc1 1262450 Free-living filamentous (79)

Orpinomyces sp. Orpsp1 1117330 n. a. (80)

Paracoccidioides

brasiliensis Parbr1 482561 Yeast (81)

Penicillium chrysogenum PenchWisc1_1 500485 Free-living filamentous (82)

Penicillium digitatum Pendi1 1170229 Other (83)

Penicillium oxalicum Penox1 933388 Free-living filamentous (84)

Phaeoacremonium

aleophilum Phaal1 1286976 Free-living filamentous (85)

Phanerochaete carnosa Phaca1 231932 Free-living filamentous (86)

Phanerochaete

chrysosporium Phchr2 5306 Free-living filamentous (87, 88)

Phlebia brevispora Phlbr1 747484 Free-living filamentous (22)

Phlebiopsis gigantea Phlgi1 745531 Free-living filamentous (89)

Pichia pastoris Picpa1 644223 Yeast (90)

Piriformospora indica Pirin1 1109443 Other (91)

Pleurotus ostreatus PleosPC15_2 5322 Free-living filamentous (24)

Pneumocystis jirovecii Pneji1 1209962 Yeast (92)

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Podospora anserina Podan2 515849 Free-living filamentous (93)

Postia placenta Pospl1 561896 Free-living filamentous (94)

Pseudozyma antarctica Psean1_1 84753 Yeast (95)

Pseudozyma hubeiensis Psehu1 1305764 Yeast (96)

Puccinia graminis f. sp

tritici Pucgr1 418459 Other (97)

Puccinia striiformis f.

sp tritici Pucst1 875184 Other (98)

Punctularia strigosozonata Punst1 741275 Free-living filamentous (36)

Pyrenophora teres f. teres Pyrtt1 861557 Other (99)

Pyrenophora tritici-

repentis Pyrtr1 45151 Other (100)

Pyronema confluens Pyrco1 1076935 Free-living filamentous (101)

Rhizoctonia solani Rhiso1 1108050 Other (102)

Rhizophagus Gloin1 747089 Mycorrhizal (103)

Rhizopus microsporus var.

chinensis Rhich1 1271458 Free-living filamentous (104)

Rhizopus oryzae Rhior3 246409 Free-living filamentous (105)

Rhytidhysteron rufulum Rhyru1 37885 Other (20)

Rozella allomycis Rozal1_1 988480 Other (106)

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Saccharomyces cerevisiae SacceM3707_1 1149757 Yeast (107)

Schizophyllum commune Schco2 578458 Free-living filamentous (108)

Schizosaccharomyces

cryophilus Schcy1 653667 Yeast (109)

Schizosaccharomyces

japonicus Schja1 402676 Yeast (109)

Schizosaccharomyces

octosporus Schoc1 483514 Yeast (109)

Schizosaccharomyces

pombe Schpo1 4896 Yeast (110, 111)

Sclerotinia sclerotiorum Sclsc1 665079 Other (27)

Serpula lacrymans SerlaS7_3_2 936435 Free-living filamentous (112)

Setosphaeria turcica Settu1 671987 Other (20, 34)

Spathaspora passalidarum Spapa2 619300 Yeast (28)

Sporisorium reilianum Spore1 999809 Other (113)

Stagonospora nodorum Stano2 321614 Other (114)

Stereum hirsutum Stehi1 721885 Free-living filamentous (36)

Taphrina deformans Tapde1_1 1097556 Yeast (115)

Thielavia terrestris Thite2 35720 Free-living filamentous (69)

Trametes versicolor Trave1 717944 Free-living filamentous (36)

Taxon JGI ID

NCBI

Taxonomic

ID

Morphological Group* Source

Tremella mesenterica Treme1 578456 Other (36)

Trichoderma atroviride Triat2 452589 Free-living filamentous (116)

Trichoderma reesei TrireRUTC30_1 1344414 Free-living filamentous (117)

Trichophyton rubrum Triru1 559305 Other (65)

Trichophyton verrucosum Triver1 663202 Other (6)

Tuber melanosporum Tubme1 656061 Mycorrhizal (118)

Uncinocarpus reesii Uncre1 336963 n. a. (32)

Ustilago maydis Ustma1 559306 Yeast (119)

Verticillium alfalfae Veral1 27335 Other (120)

Verticillium dahliae Verda1 27337 Other (120)

Volvariella volvacea Volvo1 706473 Free-living filamentous (121)

Wolfiporia cocos Wolco1 742152 Other (36)

Yarrowia lipolytica Yarli1 284591 Yeast (41)

*Only free-living filamentous fungi, mycorrhizal fungi, and yeasts were included in the comparison of morphological groups. n. a. = not available

Table S2. Significant pairwise relationships between traits among 157 whole genomes of fungi.

Trait Trait Independent contrast r Spearman ρ

Amino acid permease Ammonium transporter 0.23** 0.47***

Amino acid permease RNA helicase 0.20* 0.36***

β1,3-glucan synthase Ammonium transporter 0.26** 0.23**

β1,3-glucan synthase RNA helicase 0.51*** 0.35***

β1,3-glucan synthase Trehalase 0.37*** 0.32***

Cellulase GH7 Cellulase AA9 0.47*** 0.84***

Cellulase GH7 Lignin peroxidase 0.23** 0.52***

Cellulase GH7 Phosphate transporter 0.24** 0.30***

Lignin peroxidase Cellulase AA9 0.33*** 0.63***

Phosphatase Ammonium transporter 0.41*** 0.27**

Phosphatase Phosphate transporter 0.25** 0.26**

Phosphatase RNA helicase 0.40*** 0.20*

RNA helicase Ammonium transporter 0.47*** 0.33***

RNA helicase Trehalase 0.50*** 0.34***

RNA helicase Cellulase GH7 0.03 NS -0.41***

RNA helicase Cellulase AA9 0.04 NS -0.45***

RNA helicase Lignin peroxidase 0.13 NS -0.43***

β1,3-glucan synthase Cellulase GH7 0.05 NS -0.13†

†P < 0.10, *P < 0.05, **P < 0.01, ***P < 0.001, NS = not significant

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