1. The 100-genomes strains, an S. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen
- Author
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Strope, Pooja K., Skelly, Daniel A., Kozmin, Stanislav G., Mahadevan, Gayathri, Stone, Eric A., Magwene, Paul M., Dietrich, Fred S., and McCusker, John H.
- Abstract
Saccharomyces cerevisiae, a well-established model for species as diverse as humans and pathogenic fungi, is more recently a model for population and quantitative genetics. S. cerevisiaeis found in multiple environments—one of which is the human body—as an opportunistic pathogen. To aid in the understanding of the S. cerevisiaepopulation and quantitative genetics, as well as its emergence as an opportunistic pathogen, we sequenced, de novo assembled, and extensively manually edited and annotated the genomes of 93 S. cerevisiaestrains from multiple geographic and environmental origins, including many clinical origin strains. These 93 S. cerevisiaestrains, the genomes of which are near-reference quality, together with seven previously sequenced strains, constitute a novel genetic resource, the “100-genomes” strains. Our sequencing coverage, high-quality assemblies, and annotation provide unprecedented opportunities for detailed interrogation of complex genomic loci, examples of which we demonstrate. We found most phenotypic variation to be quantitative and identified population, genotype, and phenotype associations. Importantly, we identified clinical origin associations. For example, we found that an introgressed PDR5was present exclusively in clinical origin mosaic group strains; that the mosaic group was significantly enriched for clinical origin strains; and that clinical origin strains were much more copper resistant, suggesting that copper resistance contributes to fitness in the human host. The 100-genomes strains are a novel, multipurpose resource to advance the study of S. cerevisiaepopulation genetics, quantitative genetics, and the emergence of an opportunistic pathogen.
- Published
- 2015
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