Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

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• 作者：Chao-Li Huang (1)
  Pei-Hua Pu (1)
  Hao-Jen Huang (1)
  Huang-Mo Sung (1)
  Hung-Jiun Liaw (1)
  Yi-Min Chen (2)
  Chien-Ming Chen (3)
  Ming-Ban Huang (1)
  Naoki Osada (4)
  Takashi Gojobori (1) (4) (5)
  Tun-Wen Pai (3)
  Yu-Tin Chen (1)
  Chi-Chuan Hwang (6)
  Tzen-Yuh Chiang (1)
  
  1. Department of Life Sciences ; National Cheng Kung University ; Tainan ; 701 ; Taiwan
  2. Institute of Biotechnology ; National Cheng Kung University ; Tainan ; 701 ; Taiwan
  3. Department of Computer Science and Engineering ; National Taiwan Ocean University ; Keelung ; 202 ; Taiwan
  4. National Institute of Genetics ; Mishima ; Shizuoka ; 411-8540 ; Yata ; Japan
  5. Computational Bioscience Research Center ; Biological and Environmental Sciences and Engineering Division ; King Abdullah University of Science and Technology ; Thuwal ; 23955-6900 ; Kingdom of Saudi Arabia
  6. Department of Engineering Science and Supercomputing Research Center ; National Cheng Kung University ; Tainan ; 701 ; Taiwan
  
• 关键词：Xanthomonas ; Adaptive diversification ; Host shift ; Parapatric speciation ; Homologous recombination ; Comparative genomics
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：1,499 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background 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. Results 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. Conclusion 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.