Data from: Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution.

Most laboratory evolution studies that characterize evolutionary adaptation genomically focus on genetically simple traits that can be altered by one or few mutations. Such traits are important, but they are few compared with complex, polygenic traits influenced by many genes. We know much less about complex traits, and about the changes that occur in the genome and in gene expression during their evolutionary adaptation. Salt stress tolerance is such a trait. It is especially attractive for evolutionary studies, because the physiological response to salt stress is well-characterized on the molecular and transcriptome level. This provides a unique opportunity to compare evolutionary adaptation and physiological adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good model system to study salt stress tolerance, because it contains several highly conserved pathways that mediate the salt stress response. We evolved three replicate lines of yeast under continuous salt (NaCl) stress for 300 generations. All three lines evolved faster growth rate in high salt conditions than their ancestor. In these lines, we studied gene expression changes through microarray analysis and genetic changes through next generation population sequencing. We found two principal kinds of gene expression changes, changes in basal expression (82 genes) and changes in regulation (62 genes). The genes that change their expression involve several well-known physiological stress-response genes, including CTT1, MSN4 and HLR1. Next generation sequencing revealed only one high-frequency single-nucleotide change, in the gene MOT2, that caused increased fitness when introduced into the ancestral strain. Analysis of DNA content per cell revealed ploidy increases in all the three lines. Our observations suggest that evolutionary adaptation of yeast to salt stress is associated with genome size increase and modest expression changes in several genes.

绝大多数从基因组层面解析进化适应性的实验室进化研究，均聚焦于可通过单个或少数突变即可改变的遗传简单性状。这类性状固然重要，但相较于受众多基因调控的复杂多基因性状而言，其数量仍相对稀少。目前学界对复杂性状，以及其在进化适应过程中基因组与基因表达层面发生的变化，所知仍较为有限。盐胁迫耐受性正是这类复杂性状之一。该性状尤其适合进化研究，因为盐胁迫的生理响应在分子与转录组层面已有较为充分的解析，这为对比盐胁迫下的进化适应与生理适应提供了绝佳契机。酿酒酵母（Saccharomyces cerevisiae）是研究盐胁迫耐受性的优良模式生物，其体内存在多条介导盐胁迫响应的高度保守通路。本研究将酿酒酵母置于持续氯化钠（NaCl）盐胁迫环境中进行传代培养，共获得3个独立重复进化株系，时长达300代。三个株系在高盐环境下的生长速率均显著高于其祖先菌株。针对这些进化株系，本研究通过微阵列分析（microarray）检测基因表达变化，并通过下一代群体测序（next generation population sequencing）解析遗传变异。本研究共发现两类主要的基因表达变化：基础表达水平改变（涉及82个基因）与调控模式改变（涉及62个基因）。表达发生改变的基因涵盖多个经典生理胁迫响应基因，如CTT1、MSN4与HLR1。下一代群体测序结果显示，仅存在1个高频单核苷酸变异位点，位于MOT2基因内；将该变异引入祖先菌株后，可显著提升菌株的适合度。对细胞DNA含量的分析显示，三个进化株系均发生了倍性增加。本研究结果表明，酿酒酵母对盐胁迫的进化适应，与基因组大小增加及多个基因的适度表达变化密切相关。