Supporting data for "Clonality, inbreeding, and hybridization in two extremotolerant black yeasts"

The great diversity of lifestyles and survival strategies observed in fungi is reflected in the many ways in which they reproduce and recombine. Although truly asexual fungi are rare, population genomic data support the clonality of two extremotolerant black yeasts from Dothideomycetes: <i>Hortaea werneckii</i> and <i>Aureobasidium melanogenum</i>. Thus, the discovery of a number of diploid strains of these species could not be explained as the product of conventional sexual reproduction. <br>Genome sequencing revealed that the ratio of diploid to haploid strains in both <i>H. werneckii</i> and <i>A. melanogenum</i> is approximately 2:1. Linkage disequilibrium between pairs of polymorphic loci and a high degree of concordance between the phylogenies of different genomic regions confirmed that both species are clonal. Heterozygosity of diploid strains is high, with several hybridizing genome pairs reaching the intergenomic distances typically seen between different fungal species. The origin of diploid strains collected worldwide can be traced to a handful of hybridization events that produced diploids, which were stable over long periods of time and distributed over large geographic areas. <br>Our results, based on the genomes of over 100 strains of two black yeasts, show that although they are asexual, they occasionally form stable and highly heterozygous diploid hybrids. The mechanism of these apparently rare hybridization events, which are not followed by meiosis or haploidisation, remains unknown. Both extremotolerant yeasts, <i>H. werneckii</i> and even more so <i>A. melanogenum</i>, a close relative of the intensely recombining and biotechnologically relevant <i>Aureobasidium pullulans</i>, provide an attractive model for studying the role of clonality and ploidy in extremotolerant fungi.