Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Baker’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 all long read Saccharomycetes genomes available to date, we show that the newly sequenced East Asian strains are among the closest living relatives of the ancestors of the global diversity of Baker'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 prior to the larger radiation of the species. Our genomic analyses reveal that the wild East Asian strains contain elevated levels of structural variations (balanced and unbalanced), including large inversions and non-reciprocal chromosomal translocations. Two strains have severely reduced genomes, due to the loss of exon content rather than coding genes. 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.
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