Supplementary table 1: Examples of polyploid fungal species described in the literature

Supplementary table 1: Examples of polyploid fungal species described in the literature

Species	References	Comments
Rhizopus oryzae	[1]	Paleopolyploid
Phycomyces blakesleeanus	[2]	Paleopolyploid
Allomyces macrogynus	[3]	Haploid, diploid, tetraploid
Allomyces arbuscula	[4, 5]	Haploid, diploid, triploid, tetraploid
Allomyces javanicus	[5]	Putative allopolyploid whose progenitors may be A. arbuscula & A. macrogynus
Glomus etunicatum	[6]
Cyathus stercoreus	[7, 8]	Tetraploid, possibly allotetraploid
Agaricus campestris	[9]
Coprinellus micaceus	[10]
Coprinopsis atramentaria	[10]
Botrytis alli	[11]	Allotetraploid whose progenitors may be B. byssoidea and B. aclada
Phyllactinia sp.	[12]	Autopolyploid and allopolyploid
Xylaria curta	[13]	Multivalent at meiosis
Stephensia shanori	[14]
Zygosaccharomyces rouxii	[15]	Allopolyploid whose progenitors may be Z. rouxii and Z. pseudorouxii
Saccharomyces genus	[16-18]	paleotetraploid
Saccharomyces cerevisiae	[19-24]	Autotetraploid, allotetraploid
Saccharomyces pastorianus	[25, 26]	Allotetraploid (in the curse of diploidization) whose progenitors may be S. cerevisiae and S. eubayanus
Candida utilis	[27]	Ploidy status unclear, possibly tetraploid

Supplementary table 2: Examples of natural intra- and inter-specific fungal hybrids

Species	References	Comments
Melampsora medusa-populina	[28]	Interspecific hybrids whose progenitors are M. medusa and M. larici-populina
Melampsora x columbiana	[29]	Interspecific hybrids whose progenitors are M. medusa and M.occidentalis
Epichloe sp.	[30]
Verticillium dahliae	[31]	Interspecific hybrid
Agaricus bisporus	[32]	Interspecific hybrid
Flammulina genus	[33]	Interspecific hybrid whose progenitors are F.velutipes and F. rossica
Dekkera bruxellensis	[34]	Interspecific origin or/and duplications

Supplementary table 3: Factors affecting genome size in Fungi.

Species	References	Factors	Comments
Candida albicans	[35]	Abiotic	Chromosome loss associated with heat shock
Candida glabrata	[36]	Abiotic	Chromosome duplications and rearrangements associated with antifungal drug resistance
Dictyostelium discoideum	[37]	Abiotic	Ploidy increase associated with fungicides
Saccharomyces cerevisiae	[38]	Abiotic	Ploidy increase associated with saline stress during lab evolution
Saccharomyces cerevisiae	[39-45]	Genetic	Ploidy increase associated with , esp1, spa1, cdc31, kar1, ndc1, chc1, mps1, mps2 mutants
Saccharomyces cerevisiae	[46]	Genetic	Aneuploidy associated with Hsp90 stress.
Schizosaccharomyces pombe	[47]	Genetic	Ploidy increase associated with bub1 mutant
Armillaria mellea	[48]	Development	Ploidy associated with cellular differentiation
Aspergillus nidulans	[49-51]	Development	Frequent aneuploidy that increases with tissue age
Didymium iridis	[52]	Development	Polyploidy, chromosome loss and aneuploidy
Helicobasidium mompa	[53]	Development	Haploid, diploid and tetraploid cells
Macrophomina phaseoli	[54]	Development	Ploidy variation associated with development
Mucor hiemalis	[55]	Development	Ploidy variations associated with life cycle, including haploid, diploid, and aneuploid cells
Neurospora crassa	[56]	Development	Unreduced gametes, frequent aneuploidy
Phymatotrichum omnivorum	[57]	Development	Ploidy variations associated with life cycle, including haploids, diploids, and aneuploids
Pleurotus ostreatus	[58]	Development	Variation of genome size and chromosome number
Ajellomyces capsulatus	[59]		Formerly Histoplasma capsulatem, possible aneuploidy
Septoria tritici	[60]		Chromosome polymorphism
Nectrla haematococca	[61]	Biotic	Chromosome polymorphism associated with pathogenicity
Fusarium oxysporum	[62]	Biotic	Chromosome polymorphism associated with pathogenicity

Supplementary table 4: Examples of polyploid species belonging to the Chromalveolata eukaryotic supergroup

Species	References	Comments
Phytophthora infestans	[63]	Triploid & tetraploid
Phytophthora megasperma	[64]
Phytophthora alni	[65]	Autotetraploid, allotriploid
Phytophthora meadii	[66]	Tetraploid
Phytophthora genus	[67]	Paleopolyploid
Achlya racemosa	[68-70]
Saprolegnia multispora	[68-70]
Ascophyllum nodosum	[71]
Cystoseira nodicaulis	[71]
Macrocystis angustifolia	[71]
Dickieia ulvacea	[72]
Seminavis sp.	[73]
Paramecium tetraurelia	[74-78]	Paleopolyploid

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