Abstract
Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report the whole-genome sequencing and phenotyping of 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture of the genomic variants that shape the species-wide phenotypic landscape of this yeast. Genomic analyses support a single ‘out-of-China’ origin for this species, followed by several independent domestication events. Although domesticated isolates exhibit high variation in ploidy, aneuploidy and genome content, genome evolution in wild isolates is mainly driven by the accumulation of single nucleotide polymorphisms. A common feature is the extensive loss of heterozygosity, which represents an essential source of inter-individual variation in this mainly asexual species. Most of the single nucleotide polymorphisms, including experimentally identified functional polymorphisms, are present at very low frequencies. The largest numbers of variants identified by genome-wide association are copy-number changes, which have a greater phenotypic effect than do single nucleotide polymorphisms. This resource will guide future population genomics and genotype–phenotype studies in this classic model system.
Highlights
Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations
S. cerevisiae has recently emerged as a model in population genomics[3,4,5], because it can be found worldwide in a broad array of human-associated and wild biotopes
Species-wide genetic and phenotypic diversity We assembled a collection of 1,011 S. cerevisiae isolates that maximized the breadth of their ecological and geographical origins (Supplementary Fig. 1a, b and Supplementary Table 1)
Summary
Together, these introgression and HGT events with distinct population frequency distributions (Fig. 4c) correspond to important evolutionary processes that have shaped the S. cerevisiae species genome. Genetic diversity and evolution by subpopulation The comparison of genome content variation and levels of SNPs in domesticated and wild clades (Supplementary Fig. 28) shows higher SNP density (median 0.55% versus 0.41%) and lower genome content variation (median 115 ORFs that are not shared, versus 161 shared ORFs) in wild versus domesticated clades, respectively (Supplementary Fig. 28 and Supplementary Tables 9, 10) These findings suggest a shift in evolutionary mechanisms during the domestication process. The effect of the domestication event on the sake genomes is very similar These genomes have low levels of genetic diversity, low heterozygosity and extensive LOH regions.
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