Whole-genome sequencing of a laboratory-evolved yeast strain.
Whole-genome sequencing of a laboratory-evolved yeast strain.
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DOI：
10.1186/1471-2164-11-88
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发表时间：
2010-02-03
期刊：
影响因子：
4.4
通讯作者：
Fields S
中科院分区：
文献类型：
--
作者：
Araya CL;Payen C;Dunham MJ;Fields S
微生物种群的实验进化提供了一个独特的机会，研究进化适应控制选择压力。然而，直到最近，在全基因组范围内确定适应的精确遗传变化一直很困难。新的DNA测序技术现在可以快速确定微生物的亲本和进化菌株的基因组。我们对实验室进化的酿酒酵母菌株及其祖先的>93.5%的基因组进行了测序，深度>28×。单核苷酸多态性和拷贝数扩增都被发现，与以前用于分析这些基因组的基于阵列的方法相比有特定的收获。应用分割算法来量化结构变化，我们确定了5×基因扩增的近似基因组边界。这些边界引导断点序列的恢复，这提供了对复杂基因组重排的性质的见解。这项研究表明，全基因组测序可以提供一种快速的方法来揭示进化适应的遗传基础，并进一步应用于实验室选择和诱变筛选的研究。此外，我们还展示了单端短读测序数据如何提供有关结构重排的详细信息，并生成有关基因组可塑性基础的基因组特征和过程的预测。
Experimental evolution of microbial populations provides a unique opportunity to study evolutionary adaptation in response to controlled selective pressures. However, until recently it has been difficult to identify the precise genetic changes underlying adaptation at a genome-wide scale. New DNA sequencing technologies now allow the genome of parental and evolved strains of microorganisms to be rapidly determined. We sequenced >93.5% of the genome of a laboratory-evolved strain of the yeast Saccharomyces cerevisiae and its ancestor at >28× depth. Both single nucleotide polymorphisms and copy number amplifications were found, with specific gains over array-based methodologies previously used to analyze these genomes. Applying a segmentation algorithm to quantify structural changes, we determined the approximate genomic boundaries of a 5× gene amplification. These boundaries guided the recovery of breakpoint sequences, which provide insights into the nature of a complex genomic rearrangement. This study suggests that whole-genome sequencing can provide a rapid approach to uncover the genetic basis of evolutionary adaptations, with further applications in the study of laboratory selections and mutagenesis screens. In addition, we show how single-end, short read sequencing data can provide detailed information about structural rearrangements, and generate predictions about the genomic features and processes that underlie genome plasticity.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
56.9
作者：
Shendure, J;Porreca, GJ;Church, GM
通讯作者：
Church, GM
影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard
DOI：
10.1073/pnas.0803466105
发表时间：
2008-07-08
影响因子：
11.1
作者：
Lynch, Michael;Sung, Way;Thomas, W. Kelley
通讯作者：
Thomas, W. Kelley
影响因子：
7
作者：
Smith, Douglas R.;Quinlan, Aaron R.;Richardson, Paul M.
通讯作者：
Richardson, Paul M.