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

Kvitek DJ, Will JL, Gasch AP - PLoS Genet. (2008)

Bottom Line: Our results demonstrate a large degree of phenotypic variation in stress sensitivity and gene expression.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.These results highlight the value of understanding the genetic basis of phenotypic variation and raise caution about using laboratory strains for comparative genomics.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

ABSTRACT
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.

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Phenotypic variation in diverse Saccharomyces                            strains.The viability of 52 Saccharomyces strains and species                            grown under 14 different environmental conditions was measured. Strains                            were grown in at least duplicate on solid agar plates containing                            1–3 doses of each environmental variable, as described in                                Materials and Methods. Each row                            on the plot represents a different strain and each column indicates a                            given environment. Colored boxes represent the average growth score of                            each strain grown in each environment, according to the key shown at the                            lower right. Strains and conditions were organized by hierarchical                            clustering using the Pearson correlation as a similarity metric.
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pgen-1000223-g002: Phenotypic variation in diverse Saccharomyces strains.The viability of 52 Saccharomyces strains and species grown under 14 different environmental conditions was measured. Strains were grown in at least duplicate on solid agar plates containing 1–3 doses of each environmental variable, as described in Materials and Methods. Each row on the plot represents a different strain and each column indicates a given environment. Colored boxes represent the average growth score of each strain grown in each environment, according to the key shown at the lower right. Strains and conditions were organized by hierarchical clustering using the Pearson correlation as a similarity metric.

Mentions: The results reveal a tremendous amount of phenotypic diversity in environmental sensitivity (Figure 2). Although there were similarities between strains, no two strains were exactly alike in phenotypic profile. Each displayed a propensity for growth under at least one environment and sensitivity to one or more conditions. Some strains were generally tolerant to stressful environments across the board. For example, strain Y2, originally collected from a Trinidadian rum distillery, and clinical isolates YJM454 and YJM440 were tolerant of most of these conditions, while the S. bayanus strain used in our study was sensitive to nearly all stresses tested. Several strains, including commercial sake-producing strains, showed a wide standard deviation of growth scores across the stresses, reflecting that they were either highly sensitive or highly resistant to different stresses. In contrast, most vineyard isolates grew moderately well in most of the environments examined (see Discussion).


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

Kvitek DJ, Will JL, Gasch AP - PLoS Genet. (2008)

Phenotypic variation in diverse Saccharomyces                            strains.The viability of 52 Saccharomyces strains and species                            grown under 14 different environmental conditions was measured. Strains                            were grown in at least duplicate on solid agar plates containing                            1–3 doses of each environmental variable, as described in                                Materials and Methods. Each row                            on the plot represents a different strain and each column indicates a                            given environment. Colored boxes represent the average growth score of                            each strain grown in each environment, according to the key shown at the                            lower right. Strains and conditions were organized by hierarchical                            clustering using the Pearson correlation as a similarity metric.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2562515&req=5

pgen-1000223-g002: Phenotypic variation in diverse Saccharomyces strains.The viability of 52 Saccharomyces strains and species grown under 14 different environmental conditions was measured. Strains were grown in at least duplicate on solid agar plates containing 1–3 doses of each environmental variable, as described in Materials and Methods. Each row on the plot represents a different strain and each column indicates a given environment. Colored boxes represent the average growth score of each strain grown in each environment, according to the key shown at the lower right. Strains and conditions were organized by hierarchical clustering using the Pearson correlation as a similarity metric.
Mentions: The results reveal a tremendous amount of phenotypic diversity in environmental sensitivity (Figure 2). Although there were similarities between strains, no two strains were exactly alike in phenotypic profile. Each displayed a propensity for growth under at least one environment and sensitivity to one or more conditions. Some strains were generally tolerant to stressful environments across the board. For example, strain Y2, originally collected from a Trinidadian rum distillery, and clinical isolates YJM454 and YJM440 were tolerant of most of these conditions, while the S. bayanus strain used in our study was sensitive to nearly all stresses tested. Several strains, including commercial sake-producing strains, showed a wide standard deviation of growth scores across the stresses, reflecting that they were either highly sensitive or highly resistant to different stresses. In contrast, most vineyard isolates grew moderately well in most of the environments examined (see Discussion).

Bottom Line: Our results demonstrate a large degree of phenotypic variation in stress sensitivity and gene expression.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.These results highlight the value of understanding the genetic basis of phenotypic variation and raise caution about using laboratory strains for comparative genomics.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus