Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae
Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae
复制标题
DOI：
10.1073/pnas.0409159102
复制
发表时间：
2005-01-25
影响因子：
11.1
通讯作者：
Steinmetz, LM
中科院分区：
文献类型：
--
作者：
Gu, ZL;David, L;Steinmetz, LM
通过使用最大似然法，我们做了一个全基因组的进化率的比较，导致实验室菌株（S288 c）和野生菌株（YJM 789）的酿酒酵母的谱系，发现在实验室菌株的基因往往比在野生菌株进化得更快。这种进化升级的模式表明，选择强度的放松是主要的潜在原因，这与S。酿酒酵母实验室菌株群体。支持这一结论的是以下观察结果：（1）所有功能类别的基因的非同义进化率都增加;（h）S288 c的同义进化率增加大多发生在具有强密码子使用偏好的基因中;（iii）在较强的负选择下，基因的非同义进化率增加较大;和（iv）在实验室菌株中检测到更多具有适应性进化的基因，但它们并不占进化增加的大部分。目前的发现表明，实验室酵母菌株的实验和可能的工业操作可能对这种模式生物的遗传组成产生了强烈的影响。此外，它们暗示了实验室模式生物从野生生物进化而来，质疑了这些模式的相关性，特别是在实验室广泛培养的情况下。此外，这些结果揭示了人类驯化多年的牲畜和作物物种的进化。
By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces cerevisiae and found that genes in the laboratory strain tend to evolve faster than in the wild strain. The pattern of elevated evolution suggests that relaxation of selection intensity is the dominant underlying reason, which is consistent with recurrent bottlenecks in the S. cerevisiae laboratory strain population. Supporting this conclusion are the following observations: (1) the increases in nonsynonymous evolutionary rate occur for genes in all functional categories; (h) most of the synonymous evolutionary rate increases in S288c occur in genes with strong codon usage bias; (iii) genes under stronger negative selection have a larger increase in nonsynonymous evolutionary rate; and (iv) more genes with adaptive evolution were detected in the laboratory strain, but they do not account for the majority of the increased evolution. The present discoveries suggest that experimental and possible industrial manipulations of the laboratory strain of yeast could have had a strong effect on the genetic makeup of this model organism. Furthermore, they imply an evolution of laboratory model organisms away from their wild counterparts, questioning the relevancy of the models especially when extensive laboratory cultivation has occurred. In addition, these results shed light on the evolution of livestock and crop species that have been under human domestication for years.