Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
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DOI：
10.1101/gr.089250.108
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发表时间：
2009-07-01
期刊：
影响因子：
7
通讯作者：
Stanhope, Michael J.
中科院分区：
文献类型：
--
作者：
Lefebure, Tristan;Stanhope, Michael J.
细菌基因组学中的一个悬而未决的问题是核心基因组的适应性进化在细菌物种的多样化和适应中所发挥的作用，以及占据不同环境条件的细菌群体之间的差异。弯曲杆菌属包括几种重要的人类和动物肠道病原体，有八个物种的基因组序列数据。我们估计弯曲杆菌核心基因组有 647 个基因，其中 92.5% 的非重组核心基因组位点在至少一个谱系中处于正选择状态，并且同一基因经常在多个谱系中处于正选择状态。提供的测试拒绝重组、饱和和密码子使用偏差的变化作为导致这种高水平选择的因素。我们认为这种全基因组适应性进化可能是红皇后宏观进化动态的结果，其中物种参与哺乳动物和/或脊椎动物胃肠道内资源的竞争。正如作者在早期工作中报道的那样，链球菌中明显的正选择水平大大降低，可能是因为这些类群栖息在物种丰富的栖息地和更独特的生态位中。尽管在多个弯曲杆菌谱系中存在正选择下的许多共同位点，但我们没有发现相同或相邻密码子甚至蛋白质结构域水平上分子适应性收敛的证据。总的来说，这些结果描述了细菌属的多样化，涉及几乎整个基因组中普遍存在的自然选择压力，尽管物种倾向于共同的胃肠道栖息地，但这种适应在不同的谱系中以不同的方式发生。
An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human and animal enteric pathogens, with genome sequence data available for eight species. We estimate the Campylobacter core genome at 647 genes, with 92.5% of the nonrecombinant core genome loci under positive selection in at least one lineage and the same gene frequently under positive selection in multiple lineages. Tests are provided that reject recombination, saturation, and variation in codon usage bias as factors contributing to this high level of selection. We suggest this genome-wide adaptive evolution may result from a Red Queen macroevolutionary dynamic, in which species are involved in competition for resources within the mammalian and/or vertebrate gastrointestinal tract. Much reduced levels of positive selection evident in Streptococcus, as reported by the authors in an earlier work, may be a consequence of these taxa inhabiting less species-rich habitats, and more unique niches. Despite many common loci under positive selection in multiple Campylobacter lineages, we found no evidence for molecular adaptive convergence at the level of the same or adjacent codons, or even protein domains. Taken collectively, these results describe the diversification of a bacterial genus that involves pervasive natural selection pressure across virtually the entire genome, with this adaptation occurring in different ways in different lineages, despite the species tendency toward a common gastrointestinal habitat.