Abstract
Human intervention has subjected the yeast Saccharomyces cerevisiae to multiple rounds of independent domestication and thousands of generations of artificial selection. As a result, this species comprises a genetically diverse collection of natural isolates as well as domesticated strains that are used in specific industrial applications. However the scope of genetic diversity that was captured during the domesticated evolution of the industrial representatives of this important organism remains to be determined. To begin to address this, we have produced whole-genome assemblies of six commercial strains of S. cerevisiae (four wine and two brewing strains). These represent the first genome assemblies produced from S. cerevisiae strains in their industrially-used forms and the first high-quality assemblies for S. cerevisiae strains used in brewing. By comparing these sequences to six existing high-coverage S. cerevisiae genome assemblies, clear signatures were found that defined each industrial class of yeast. This genetic variation was comprised of both single nucleotide polymorphisms and large-scale insertions and deletions, with the latter often being associated with ORF heterogeneity between strains. This included the discovery of more than twenty probable genes that had not been identified previously in the S. cerevisiae genome. Comparison of this large number of S. cerevisiae strains also enabled the characterization of a cluster of five ORFs that have integrated into the genomes of the wine and bioethanol strains on multiple occasions and at diverse genomic locations via what appears to involve the resolution of a circular DNA intermediate. This work suggests that, despite the scrutiny that has been directed at the yeast genome, there remains a significant reservoir of ORFs and novel modes of genetic transmission that may have significant phenotypic impact in this important model and industrial species.
Highlights
During its long history of association with human activity, the genomic makeup of the yeast S. cerevisiae is thought to have been shaped through the action of multiple independent rounds of wild yeast domestication combined with thousands of generations of artificial selection
This has resulted in the species S. cerevisiae comprising a genetically diverse collection of individual strains that are often suited to very specific roles
In order to understand the genetic differences that underpin these diverse industrial characteristics, we have sequenced the genomes of six industrial strains of S. cerevisiae that comprise four strains used in commercial wine production and two strains used in beer brewing
Summary
During its long history of association with human activity, the genomic makeup of the yeast S. cerevisiae is thought to have been shaped through the action of multiple independent rounds of wild yeast domestication combined with thousands of generations of artificial selection. The study of industrial strains of S. cerevisiae provides an excellent model of how reproductive isolation and divergent selective pressures can shape the genomic content of a species Despite their diverse roles, industrial yeast strains all share the general ability to grow and function under the concerted influences of a multitude of environmental stressors, which include low pH, poor nutrient availability, high ethanol concentrations and fluctuating temperatures. Laboratory strains of S. cerevisiae, such as S288c, are unable to grow in the low pH and high osmolarity of most grape juices and cannot be used to make wine This is a clear difference between industrial and non-industrial strains of S. cerevisiae, there are numerous subtle differences between industrial strains, and between strains used within the same industry [4,5], highlighting the overall genetic diversity found in this species
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