Huang Chao-Li, Pu Pei-Hua, Huang Hao-Jen, Sung Huang-Mo, Liaw Hung-Jiun, Chen Yi-Min, Chen Chien-Ming, Huang Ming-Ban, Osada Naoki, Gojobori Takashi, Pai Tun-Wen, Chen Yu-Tin, Hwang Chi-Chuan, Chiang Tzen-Yuh
Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan.
BMC Genomics. 2015 Mar 15;16(1):188. doi: 10.1186/s12864-015-1369-8.
Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants.
Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting.
Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification.
比较基因组学为细菌物种的多样化提供了见解。细菌物种形成通常伴随着持续的同源重组发生，同源重组不仅作为一种凝聚力作用于分化的谱系之间，还带来受自然选择青睐的有利等位基因，并导致生态上不同的物种形成，例如，对多种植物致病的黄单胞菌属中频繁的宿主转移。
我们使用全基因组序列研究了感染十字花科植物的野油菜黄单胞菌以及宿主范围更广的柑橘溃疡病菌的遗传分化。柑橘溃疡病菌芒果致病变种两个初始小种之间的遗传分化归因于噬菌体引入的一个DNA片段。与基因组的大多数部分因点突变积累而在亚种间具有几乎相同水平的遗传分化不同，同源重组相关的核心基因组的10%促成了黄单胞菌属的多样化，这一点通过同源重组与基因组分化之间的相关性得以揭示。有趣的是，有179个基因受到正选择；其中98个（54.7%）基因参与同源重组，这表明外来遗传片段可能导致了适应性多样化，尤其是在营养转换的谱系中。同源重组可能为自然选择提供了遗传物质，宿主转移可能触发了黄单胞菌属的生态适应。在一定程度上，我们观察到正选择促成了超出宿主转移的生态分化。
总之，在持续的基因流介导下，黄单胞菌属的物种形成可能受自然选择支配，自然选择在帮助偏离群体开拓新生态位（宿主）或响应环境线索方面发挥了关键作用，随后引发了物种多样化。
