Genomic evidence of an early evolutionary divergence event in wild Saccharomyces cerevisiae

Abstract Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Brewer’s yeast ( Saccharomyces cerevisiae ), used in the food and biotechnology industry worldwide. Here, we provide seven new, high quality long read genomes of non-domesticated yeast strains isolated from primeval forests and other natural environments in China and Taiwan. In a comprehensive analysis of our new genome assemblies, along with other long read Saccharomycetes genomes available, we show that the newly sequenced East Asian strains are among the closest living relatives of the ancestors of the global diversity of Brewer’s yeast, confirming predictions made from short read genomic data. Three of these strains (termed the East Asian Clade IX Complex here) share a recent ancestry and evolutionary history suggesting an early divergence from other S. cerevisiae strains before the larger radiation of the species, and prior to its domestication. Our genomic analyses reveal that the wild East Asian strains contain elevated levels of structural variations. The new genomic resources provided here contribute to our understanding of the natural diversity of S. cerevisiae , expand the intraspecific genetic variation found in this this heavily domesticated microbe, and provide a foundation for understanding its origin and global colonization history. Significance statement Brewer’s yeast ( Saccharomyces cerevisiae ) is a domesticated microbe and research model organism with a global distribution, and suspected origin in East Asia. So far only limited genomic resources are available from non-domesticated lineages. This study provides seven new, high quality long read genomes of strains isolated from primeval forests and other natural environments in China and Taiwan. Comparative genomics reveal elevated levels of structural variation in this group, and early phylogenetic branching prior to the global radiation of the species. These new genomic resources expand our understanding of the evolutionary history of Brewer’s yeast, and illustrate what the ancestors of this highly successful microbe may have looked like.