Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates

• Published in: PLoS genetics 2008-10, Vol.4 (10), p.e1000223-e1000223
• Main Authors: Kvitek, Daniel J, Will, Jessica L, Gasch, Audrey P
• Format: Article
• Language: English
• Subjects: Biology; Ecosystem; Environment; Evolution & development; Gene Dosage; Gene Expression; Genetic Variation; Genetics and Genomics/Comparative Genomics; Genetics and Genomics/Functional Genomics; Genetics and Genomics/Gene Expression; Genetics and Genomics/Genomics; Genetics and Genomics/Microbial Evolution and Genomics; Genome, Fungal; Genomics; Hybridization; Microbiology; Phenotype; Phylogeny; Ratios; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - isolation & purification; Saccharomyces cerevisiae - physiology; Standard deviation; Studies; Wineries & vineyards; Yeast
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1000223

Interactions between an organism and its environment can significantly influence phenotypic evolution. A first step toward understanding this process is to characterize phenotypic diversity within and between populations. We explored the phenotypic variation in stress sensitivity and genomic expression in a large panel of Saccharomyces strains collected from diverse environments. We measured the sensitivity of 52 strains to 14 environmental conditions, compared genomic expression in 18 strains, and identified gene copy-number variations in six of these isolates. Our results demonstrate a large degree of phenotypic variation in stress sensitivity and gene expression. Analysis of these datasets reveals relationships between strains from similar niches, suggests common and unique features of yeast habitats, and implicates genes whose variable expression is linked to stress resistance. Using a simple metric to suggest cases of selection, we found that strains collected from oak exudates are phenotypically more similar than expected based on their genetic diversity, while sake and vineyard isolates display more diverse phenotypes than expected under a neutral model. We also show that the laboratory strain S288c is phenotypically distinct from all of the other strains studied here, in terms of stress sensitivity, gene expression, Ty copy number, mitochondrial content, and gene-dosage control. These results highlight the value of understanding the genetic basis of phenotypic variation and raise caution about using laboratory strains for comparative genomics.