Evolutionary Genomics of Salmonella enterica Subspecies.
Evolutionary Genomics of Salmonella enterica Subspecies.
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DOI：
10.1128/mbio.00579-12
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发表时间：
2013-03-05
期刊：
影响因子：
6.4
通讯作者：
McClelland M
中科院分区：
文献类型：
--
作者：
Desai PT;Porwollik S;Long F;Cheng P;Wollam A;Bhonagiri-Palsikar V;Hallsworth-Pepin K;Clifton SW;Weinstock GM;McClelland M
目前在肠沙门氏菌中发现了六个亚种。第一亚种（肠亚种）是人类和温血动物中几乎所有感染的罪魁祸首，而另外五个亚种主要是从冷血动物中分离出来的。我们对21株系统发育多样的菌株进行了测序，包括先前未测序的5个亚种中的两个代表菌株和11个不同的肠球菌亚种的新菌株，从进化的角度来研究该物种。亚种的系统发育在一定程度上被谱系之间大量的重组事件和亚种形成的相对较短的时间所掩盖。然而，各种不同的树构建方法给出了一致的亚种进化树拓扑结构。共有285个基因家族被招募到肠亚种中，其中大多数功能未知。在一个或多个亚种中发现了至少2807个基因家族，而这些基因家族在I亚种或bongori沙门氏菌中没有发现。这些基因家族中有13个新的候选效应子和7个新的候选毛簇。在salamae （II）两个亚种菌株中发现了第三个完整的III型分泌系统，该系统不存在于肠亚种(I)分离物中。一些基因家族具有复杂的分类，例如VI型分泌系统，这些系统来自6个亚种中的5个不同的谱系。对非同义到同义取代率的分析表明，肠球菌最近获得的区域比基因组的其他部分正在经历更快的固定率。最近获得的富含AT的区域通常编码毒力功能，正在进行选择以保持其高AT含量。我们已经对21个新的基因组进行了测序，这些基因组包含沙门氏菌的系统发育多样性，包括以前未测序的亚种arizonae， diarizonae, houtenae， salamae和indica菌株以及新的多样化亚种enterica菌株。我们已经推断出这种非常重要的人畜共患病原体可能走过的进化路径，并确定了在亚种i中没有发现的新的假定毒力因素。在肠亚种进化过程中获得的基因家族特别有趣，因为它们包括该亚种适应温血宿主的机制。
Six subspecies are currently recognized in Salmonella enterica. Subspecies I (subspecies enterica) is responsible for nearly all infections in humans and warm-blooded animals, while five other subspecies are isolated principally from cold-blooded animals. We sequenced 21 phylogenetically diverse strains, including two representatives from each of the previously unsequenced five subspecies and 11 diverse new strains from S. enterica subspecies enterica, to put this species into an evolutionary perspective. The phylogeny of the subspecies was partly obscured by abundant recombination events between lineages and a relatively short period of time within which subspeciation took place. Nevertheless, a variety of different tree-building methods gave congruent evolutionary tree topologies for subspeciation. A total of 285 gene families were identified that were recruited into subspecies enterica, and most of these are of unknown function. At least 2,807 gene families were identified in one or more of the other subspecies that are not found in subspecies I or Salmonella bongori. Among these gene families were 13 new candidate effectors and 7 new candidate fimbrial clusters. A third complete type III secretion system not present in subspecies enterica (I) isolates was found in both strains of subspecies salamae (II). Some gene families had complex taxonomies, such as the type VI secretion systems, which were recruited from four different lineages in five of six subspecies. Analysis of nonsynonymous-to-synonymous substitution rates indicated that the more-recently acquired regions in S. enterica are undergoing faster fixation rates than the rest of the genome. Recently acquired AT-rich regions, which often encode virulence functions, are under ongoing selection to maintain their high AT content. We have sequenced 21 new genomes which encompass the phylogenetic diversity of Salmonella, including strains of the previously unsequenced subspecies arizonae, diarizonae, houtenae, salamae, and indica as well as new diverse strains of subspecies enterica. We have deduced possible evolutionary paths traversed by this very important zoonotic pathogen and identified novel putative virulence factors that are not found in subspecies I. Gene families gained at the time of the evolution of subspecies enterica are of particular interest because they include mechanisms by which this subspecies adapted to warm-blooded hosts.