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 nondomesticated 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 heavily domesticated microbe, and provide a foundation for understanding its origin and global colonization history.
23 24 Abstract 25 Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe 26 Baker's yeast (Saccharomyces cerevisiae), used in the food and biotechnology industry worldwide. Here, 27 we provide seven new, high quality long read genomes of non-domesticated yeast strains isolated from 28 primeval forests and other natural environments in China and Taiwan. In a comprehensive analysis of our new 29 genome assemblies, along with all long read Saccharomycetes genomes available to date, we show that the 30 newly sequenced East Asian strains are among the closest living relatives of the ancestors of the global diversity 31 of Baker's yeast, confirming predictions made from short read genomic data. Three of these strains (termed the 32 East Asian Clade IX Complex here) share a recent ancestry and evolutionary history suggesting an early 33 divergence from other S. cerevisiae strains prior to the larger radiation of the species. Our genomic analyses 34 reveal that the wild East Asian strains contain elevated levels of structural variations (balanced and unbalanced), 35 including large inversions and non-reciprocal chromosomal translocations. Two strains have severely reduced 36 genomes, due to the loss of exon content rather than coding genes. The new genomic resources provided 37 here contribute to our understanding of the natural diversity of S. cerevisiae, expand the intraspecific 38 genetic variation found in this this heavily domesticated microbe, and provide a foundation for 39 understanding its origin and global colonization history. 40 42 food technology. The sequencing of hundreds of Saccharomyces genomes has provided insight about the
Determining how adaptive possibilities do or do not become evolutionary realities is central to understanding the tempo and mode of evolutionary change. Some of the simplest evolutionary landscapes arise from underdominance at a single locus where the fitness valley consists of only one less-fit genotype. Despite their potential for rapid evolutionary change, few such examples have been investigated. We capitalized on an experimental system in which a significant evolutionary shift, the transition from uni-to-multicellularity, was observed in asexual diploid populations of Saccharomyces cerevisiae experimentally selected for increased settling rates. The multicellular phenotype results from recessive single-locus mutations that undergo loss-of-heterozygosity (LOH) events. By reconstructing the necessary heterozygous intermediate steps, we found that the evolution of multicellularity involves a decrease in size during the first steps. Heterozygous genotypes are 20% smaller in size than genotypes with functional alleles. Nevertheless, populations of heterozygotes give rise to multicellular genotypes more readily than unicellular genotypes with two functional alleles, by rapid LOH events. LOH drives adaptation that may enable rapid evolution in diploid yeast. Together these results show discordance between the phenotypic and genotypic multicellular transition. The evolutionary path to multicellularity, and the adaptive benefits of increased size, requires initial size reductions.
With increases in throughput and reductions in cost, long read sequencing has become the standard most genome assembly projects and has opened up new avenues for large-scale genomic research. While more amenable to assembly than short-read sequence data, long-read datasets tend to have higher error rates. To address this problem numerous tools have been developed to correct reads before assembly and polish assembled contigs. Although, numerous studies have been conducted to assess or benchmark these tools, few capture the real variance in long read sequence data that might affect tool performance much less full pipeline performance. To address these shortcomings, we compiled a dataset containing long-read sequences of 116 different strains of brewers yeast, S. cerevisiae, gathered largely from public databases and evaluated different assembly-related tools as well as their interactions. We found that pre-assembly short-read error correction of long reads combined with post-assembly short-read polishing provided the best assemblies. We also found that correction/polishing steps with uncorrected long reads often lead to degradation of assembly quality. Finally, we show which tools and pipelines work best with different types of input data.
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