title: Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan. clhuang65535@gmail.com.
authors: Chao-Li
authors: CL
authors: Huang
authors: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan. pph941027@yahoo.com.tw.
authors: Pei-Hua
authors: PH
authors: Pu
authors: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan. haojen@mail.ncku.edu.tw.
authors: Hao-Jen
authors: HJ
authors: Huang
authors: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan. hmsung@mail.ncku.edu.tw.
authors: Huang-Mo
authors: HM
authors: Sung
authors: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan. liawh@mail.ncku.edu.tw.
authors: Hung-Jiun
authors: HJ
authors: Liaw
authors: Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan. cohen@mail.ncku.edu.tw.
authors: Yi-Min
authors: YM
authors: Chen
authors: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 202, Taiwan. d98570003@mail.ntou.edu.tw.
authors: Chien-Ming
authors: CM
authors: Chen
authors: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan. h2o41040272@gmail.com.
authors: Ming-Ban
authors: MB
authors: Huang
authors: National Institute of Genetics, Mishima, Shizuoka, 411-8540, Yata, Japan. nosada@nig.ac.jp.
authors: Naoki
authors: N
authors: Osada
authors: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan. tgojobor@nig.ac.jp.|National Institute of Genetics, Mishima, Shizuoka, 411-8540, Yata, Japan. tgojobor@nig.ac.jp.|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. tgojobor@nig.ac.jp.
authors: Takashi
authors: T
authors: Gojobori
authors: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 202, Taiwan. twp@mail.ntou.edu.tw.
authors: Tun-Wen
authors: TW
authors: Pai
authors: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan. wytchen@gmail.com.
authors: Yu-Tin
authors: YT
authors: Chen
authors: Department of Engineering Science and Supercomputing Research Center, National Cheng Kung University, Tainan, 701, Taiwan. chchwang@mail.ncku.edu.tw.
authors: Chi-Chuan
authors: CC
authors: Hwang
authors: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan. tychiang@mail.ncku.edu.tw.
authors: Tzen-Yuh
authors: TY
authors: Chiang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D055669:Ecological and Environmental Phenomena; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D059765:Homologous Recombination / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D014974:Xanthomonas / Q000145:classification / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins