Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli.
Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli.
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DOI：
10.1186/1471-2164-13-256
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发表时间：
2012-06-19
期刊：
影响因子：
4.4
通讯作者：
Darling AE
中科院分区：
文献类型：
--
作者：
Didelot X;Méric G;Falush D;Darling AE
大肠杆菌是一种重要的细菌，它可以作为无害的居民生活在许多动物的肠道中，作为病原体引起危及生命的疾病，或在非宿主环境中自由活动。这种生活方式的多样性使其成为遗传变异研究的一个特别关注的焦点，主要目的是了解共生生物如何成为致命的病原体。在过去的几年里，许多大肠杆菌的全基因组已经被完全测序，这为帮助理解这个重要物种是如何进化的提供了有用的数据。我们比较了27个全基因组，包括大肠杆菌的4个系统群（A、B1、B2和E）。从核心基因组中，我们确定了分离株之间的克隆关系以及同源重组在它们从共同祖先进化过程中所起的作用。我们发现了三个谱系（A+B1, B2， E）之间存在性隔离的有力证据，这可以用大肠杆菌的生态结构来解释，并可能代表正在进行的物种形成。我们发现了三个同源重组热点，其中一个以前没有被描述过，并且包含aroC基因，参与必要的莽草代谢途径。我们还描述了非同源重组在泛基因组中的作用，并表明这一过程是高度异质的。我们的分析特别表明，由于同源和非同源重组，B1系统群内的三种肠出血性（EHEC）菌株的基因组已经从最初分离的背景融合在一起。重组是塑造大肠杆菌基因组进化和多样化的重要力量，既可以通过用同源序列替换基因片段，也可以通过引入新基因。在这项研究中，发现了这些事件的几种非随机模式，这些模式与细菌生活方式的重要变化相关，因此为解释基因组变异与生态适应之间的关系提供了额外的证据。
Escherichia coli is an important species of bacteria that can live as a harmless inhabitant of the guts of many animals, as a pathogen causing life-threatening conditions or freely in the non-host environment. This diversity of lifestyles has made it a particular focus of interest for studies of genetic variation, mainly with the aim to understand how a commensal can become a deadly pathogen. Many whole genomes of E. coli have been fully sequenced in the past few years, which offer helpful data to help understand how this important species evolved. We compared 27 whole genomes encompassing four phylogroups of Escherichia coli (A, B1, B2 and E). From the core-genome we established the clonal relationships between the isolates as well as the role played by homologous recombination during their evolution from a common ancestor. We found strong evidence for sexual isolation between three lineages (A+B1, B2, E), which could be explained by the ecological structuring of E. coli and may represent on-going speciation. We identified three hotspots of homologous recombination, one of which had not been previously described and contains the aroC gene, involved in the essential shikimate metabolic pathway. We also described the role played by non-homologous recombination in the pan-genome, and showed that this process was highly heterogeneous. Our analyses revealed in particular that the genomes of three enterohaemorrhagic (EHEC) strains within phylogroup B1 have converged from originally separate backgrounds as a result of both homologous and non-homologous recombination. Recombination is an important force shaping the genomic evolution and diversification of E. coli, both by replacing fragments of genes with an homologous sequence and also by introducing new genes. In this study, several non-random patterns of these events were identified which correlated with important changes in the lifestyle of the bacteria, and therefore provide additional evidence to explain the relationship between genomic variation and ecological adaptation.
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影响因子：
3.3
作者：
Didelot, Xavier;Falush, Daniel
通讯作者：
Falush, Daniel
影响因子：
9.4
作者：
Boerlin, P;McEwen, SA;Gyles, CL
通讯作者：
Gyles, CL
影响因子：
9.8
作者：
Cadillo-Quiroz H;Didelot X;Held NL;Herrera A;Darling A;Reno ML;Krause DJ;Whitaker RJ
通讯作者：
Whitaker RJ
影响因子：
4.5
作者：
Didelot X;Bowden R;Street T;Golubchik T;Spencer C;McVean G;Sangal V;Anjum MF;Achtman M;Falush D;Donnelly P
通讯作者：
Donnelly P
影响因子：
4.4
作者：
Brennan, Fiona P.;Abram, Florence;O'Flaherty, Vincent
通讯作者：
O'Flaherty, Vincent