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

Publication ,  Journal Article
Strope, PK; Skelly, DA; Kozmin, SG; Mahadevan, G; Stone, EA; Magwene, PM; Dietrich, FS; McCusker, JH
Published in: Genome Res
May 2015

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. cerevisiae is found in multiple environments-one of which is the human body-as an opportunistic pathogen. To aid in the understanding of the S. cerevisiae population 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. cerevisiae strains from multiple geographic and environmental origins, including many clinical origin strains. These 93 S. cerevisiae strains, 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 PDR5 was 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. cerevisiae population genetics, quantitative genetics, and the emergence of an opportunistic pathogen.

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

May 2015

Volume

25

Issue

5

Start / End Page

762 / 774

Location

United States

Related Subject Headings

  • Virulence
  • Sequence Alignment
  • Saccharomyces cerevisiae
  • Polymorphism, Genetic
  • Phylogeny
  • Phenotype
  • Genotype
  • Genome, Fungal
  • Contig Mapping
  • Bioinformatics
 

Citation

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Strope, P. K., Skelly, D. A., Kozmin, S. G., Mahadevan, G., Stone, E. A., Magwene, P. M., … McCusker, J. H. (2015). The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. Genome Res, 25(5), 762–774. https://doi.org/10.1101/gr.185538.114
Strope, Pooja K., Daniel A. Skelly, Stanislav G. Kozmin, Gayathri Mahadevan, Eric A. Stone, Paul M. Magwene, Fred S. Dietrich, and John H. McCusker. “The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen.Genome Res 25, no. 5 (May 2015): 762–74. https://doi.org/10.1101/gr.185538.114.
Strope PK, Skelly DA, Kozmin SG, Mahadevan G, Stone EA, Magwene PM, et al. The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. Genome Res. 2015 May;25(5):762–74.
Strope, Pooja K., et al. “The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen.Genome Res, vol. 25, no. 5, May 2015, pp. 762–74. Pubmed, doi:10.1101/gr.185538.114.
Strope PK, Skelly DA, Kozmin SG, Mahadevan G, Stone EA, Magwene PM, Dietrich FS, McCusker JH. The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. Genome Res. 2015 May;25(5):762–774.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

May 2015

Volume

25

Issue

5

Start / End Page

762 / 774

Location

United States

Related Subject Headings

  • Virulence
  • Sequence Alignment
  • Saccharomyces cerevisiae
  • Polymorphism, Genetic
  • Phylogeny
  • Phenotype
  • Genotype
  • Genome, Fungal
  • Contig Mapping
  • Bioinformatics