The speciation and hybridization history of the genus Salmonella
The speciation and hybridization history of the genus Salmonella
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DOI：
10.1099/mgen.0.000284
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发表时间：
2019-08-01
影响因子：
3.9
通讯作者：
Brisse, Sylvain
中科院分区：
文献类型：
--
作者：
Criscuolo, Alexis;Issenhuth-Jeanjean, Sylvie;Brisse, Sylvain
细菌和古细菌构成了自然多样性的大部分，但原核生物物种起源和维持的机制却知之甚少。我们研究了沙门氏菌属的物种形成历史，这是一个生态多样化的细菌谱系，其中肠沙门氏菌亚种。肠杆菌是重要的人类食源性感染的原因。我们使用多位点序列分型对大量参考资料进行了多样性调查，随后对不同谱系进行了基因组测序。我们确定了11个不同的系统群，其中3个以前未被描述过。归属于肠链球菌亚种的菌株。salamae是多种的，有两个不同的谱系，我们称之为salamae A和b。salamae亚种的菌株被细分为两组，houtenae A和b，都与Selander的第七组有关。我们称之为VIII的种群以前是未知的。一个简单的物种形成的二元裂变模型不能解释观察到的序列多样性模式。在最近的过去，发生了大规模的杂交事件，涉及一个未采样的祖先谱系和该属的三个远亲谱系，这些谱系产生了Houtenae A， Houtenae B和VII。我们没有发现其他八个谱系中存在杂交的证据，但发现了古代重组事件的微妙信号。我们无法完全解决该属的物种形成历史，这可能涉及额外的物种杂交或多路物种形成事件。我们的结果表明，传统的由二元裂变和分化形成的物种模型不足以解释沙门氏菌的进化。
Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella, an ecologically diverse bacterial lineage, within which S. enterica subsp. enterica is responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified 11 distinct phylogroups, 3 of which were previously undescribed. Strains assigned to S. enterica subsp. salamae are polyphyletic, with two distinct lineages that we designate Salamae A and B. Strains of the subspecies houtenae are subdivided into two groups, Houtenae A and B. and are both related to Selander's group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large-scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages, but detected subtler signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence are not sufficient to account for Salmonella evolution.