Kvitek Daniel J, Will Jessica L, Gasch Audrey P
Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
PLoS Genet. 2008 Oct;4(10):e1000223. doi: 10.1371/journal.pgen.1000223. Epub 2008 Oct 17.
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.
生物体与其环境之间的相互作用会显著影响表型进化。理解这一过程的第一步是描述种群内部和种群之间的表型多样性。我们研究了从不同环境中收集的大量酿酒酵母菌株在应激敏感性和基因组表达方面的表型变异。我们测量了52个菌株对14种环境条件的敏感性，比较了18个菌株的基因组表达，并鉴定了其中6个分离株的基因拷贝数变异。我们的结果表明，应激敏感性和基因表达存在很大程度的表型变异。对这些数据集的分析揭示了来自相似生态位的菌株之间的关系，表明了酵母栖息地的共同和独特特征，并暗示了可变表达与抗逆性相关的基因。使用一个简单的指标来提示选择情况，我们发现从橡树渗出物中收集的菌株在表型上比基于其遗传多样性预期的更相似，而清酒和葡萄园分离株在中性模型下显示出比预期更多样化的表型。我们还表明，实验室菌株S288c在应激敏感性、基因表达、Ty拷贝数、线粒体含量和基因剂量控制方面在表型上与这里研究的所有其他菌株不同。这些结果突出了理解表型变异遗传基础的价值，并提醒人们在使用实验室菌株进行比较基因组学时要谨慎。
