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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: Interactions between an organism and its environment can significantly influence phenotypic evolution.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.

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 Saccharomycesstrains.The viability of 52 Saccharomyces strains and speciesgrown under 14 different environmental conditions was measured. Strainswere grown in at least duplicate on solid agar plates containing1–3 doses of each environmental variable, as described inMaterials and Methods. Each rowon the plot represents a different strain and each column indicates agiven environment. Colored boxes represent the average growth score ofeach strain grown in each environment, according to the key shown at thelower right. Strains and conditions were organized by hierarchicalclustering using the Pearson correlation as a similarity metric.
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pgen-1000223-g002: Phenotypic variation in diverse Saccharomycesstrains.The viability of 52 Saccharomyces strains and speciesgrown under 14 different environmental conditions was measured. Strainswere grown in at least duplicate on solid agar plates containing1–3 doses of each environmental variable, as described inMaterials and Methods. Each rowon the plot represents a different strain and each column indicates agiven environment. Colored boxes represent the average growth score ofeach strain grown in each environment, according to the key shown at thelower right. Strains and conditions were organized by hierarchicalclustering using the Pearson correlation as a similarity metric.

Mentions: The results reveal a tremendous amount of phenotypic diversity in environmentalsensitivity (Figure 2).Although there were similarities between strains, no two strains were exactlyalike in phenotypic profile. Each displayed a propensity for growth under atleast one environment and sensitivity to one or more conditions. Some strainswere generally tolerant to stressful environments across the board. For example,strain Y2, originally collected from a Trinidadian rum distillery, and clinicalisolates YJM454 and YJM440 were tolerant of most of these conditions, while theS. bayanus strain used in our study was sensitive to nearlyall stresses tested. Several strains, including commercial sake-producingstrains, showed a wide standard deviation of growth scores across the stresses,reflecting that they were either highly sensitive or highly resistant todifferent stresses. In contrast, most vineyard isolates grew moderately well inmost 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 Saccharomycesstrains.The viability of 52 Saccharomyces strains and speciesgrown under 14 different environmental conditions was measured. Strainswere grown in at least duplicate on solid agar plates containing1–3 doses of each environmental variable, as described inMaterials and Methods. Each rowon the plot represents a different strain and each column indicates agiven environment. Colored boxes represent the average growth score ofeach strain grown in each environment, according to the key shown at thelower right. Strains and conditions were organized by hierarchicalclustering using the Pearson correlation as a similarity metric.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000223-g002: Phenotypic variation in diverse Saccharomycesstrains.The viability of 52 Saccharomyces strains and speciesgrown under 14 different environmental conditions was measured. Strainswere grown in at least duplicate on solid agar plates containing1–3 doses of each environmental variable, as described inMaterials and Methods. Each rowon the plot represents a different strain and each column indicates agiven environment. Colored boxes represent the average growth score ofeach strain grown in each environment, according to the key shown at thelower right. Strains and conditions were organized by hierarchicalclustering using the Pearson correlation as a similarity metric.
Mentions: The results reveal a tremendous amount of phenotypic diversity in environmentalsensitivity (Figure 2).Although there were similarities between strains, no two strains were exactlyalike in phenotypic profile. Each displayed a propensity for growth under atleast one environment and sensitivity to one or more conditions. Some strainswere generally tolerant to stressful environments across the board. For example,strain Y2, originally collected from a Trinidadian rum distillery, and clinicalisolates YJM454 and YJM440 were tolerant of most of these conditions, while theS. bayanus strain used in our study was sensitive to nearlyall stresses tested. Several strains, including commercial sake-producingstrains, showed a wide standard deviation of growth scores across the stresses,reflecting that they were either highly sensitive or highly resistant todifferent stresses. In contrast, most vineyard isolates grew moderately well inmost of the environments examined (see Discussion).

Bottom Line: Interactions between an organism and its environment can significantly influence phenotypic evolution.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.

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