Phylogenomic analysis of 3 genera to clarify species limits, identify domestication footprints, and characterize interspecific hybrids linked to wild-to-domesticate transitions.
We comprehensively surveyed the occurrence of hybridization events in three phylogenetically related yeast genera - Torulaspora, Zygotorulaspora and Zygosaccharomyces - using a dataset of 172 genomes, 123 of which were newly sequenced. We detected five new hybrids in Zygosaccharomyces, three in Torulaspora, and none in Zygotorulaspora. For most of the newly characterized hybrids we were able to identify their parental species. Moreover, we confirmed that Z. sapae is a triple hybrid that contains the contributions of Z. progenitor, Z. rouxii and Z. siamensis. One Torulaspora hybrid resulted from a hybridization event involving members of two very divergent populations of T. delbrueckii, which suggests that conventional mating is impaired and that one of the parental genomes might in fact represent a cryptic species. In general hybrid genomes maintained the chromosomal architecture of their parental species but in Zygosaccharomyces the MAT regions tended to be dynamic and variable, a situation also seen, but to a lesser degree, in non-hybrid genomes. Our results suggest that hybridization in Zygosaccharomyces is linked to the colonization of anthropic environments, as all cases of hybridization in this genus are linked to man-made environments. However, this pattern is not evident in Torulaspora. This study and the resources it provides pave the way for a better understanding of the mechanisms underlying hybridization in yeasts.