A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

Abstract

The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies.

Genomic Insights into the Saccharomyces sensu stricto Complex

“…Despite S. paradoxus displaying levels of genetic variation that are far greater than those observed for S. cerevisiae, there appears to be considerably less gene content variation within this species (Bergström et al 2014). This difference in SNP vs. gene content variation may reflect the different selective pressures observed between the natural ecological niches of S. paradoxus in contrast to the potentially sudden and disruptive pressures imposed upon S. cerevisiae during its transition toward "domestication."…”

The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

“…However, as with all species, there is more to S. cerevisiae than one strain. For example, array analyses McCusker 2009b, 2011;Schacherer et al 2009;Dunn et al 2012), low coverage sequencing (Liti et al 2009), and higher coverage sequencing (Wei et al 2007;Doniger et al 2008;Dowell et al 2010;Skelly et al 2013;Bergstrom et al 2014) of a limited number of additional S. cerevisiae strains identified extensive sequence variation. Studies of S. cerevisiae genetic variation and its influence on phenotypic variation have been limited by the modest number of high quality, complete, assembled, and annotated genome sequences.…”

Morphophysiological and molecular characterization of wild yeast isolates from industrial ethanol process

“…The dynamics involving mutations in populations depend on accumulation, natural selection, competition within the population itself and overall fitness (Lee and Marx, 2013;Bergström et al, 2014). Understanding native yeast population and evolution dynamics is important in order to comprehend how the stressing factors of the fermentation process impact the commercial yeast strains go through and how they interact with competitive invasive strains (Payen et al, 2014).…”

“…Mid-season isolates displayed predominantly smooth colony surface, differing from the end-season isolates, which displayed more rough morphotypes (Table 2). This can be caused by adaptive evolution, caused by the cell recycling process, among other stressing factors (Bergström et al, 2014).…”