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

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    Type
    Article
    Authors
    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 cc
    Pai, Tun-Wen
    Chen, Yu-Tin
    Hwang, Chi-Chuan
    Chiang, Tzen-Yuh
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Computational Bioscience Research Center (CBRC)
    Date
    2015-03-15
    Online Publication Date
    2015-03-15
    Print Publication Date
    2015-12
    Permanent link to this record
    http://hdl.handle.net/10754/346969
    
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    Show full item record
    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. 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. © Huang et al.
    Citation
    Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts 2015, 16 (1) BMC Genomics
    Publisher
    Springer Nature
    Journal
    BMC Genomics
    DOI
    10.1186/s12864-015-1369-8
    PubMed ID
    25879893
    PubMed Central ID
    PMC4372319
    Additional Links
    http://www.biomedcentral.com/1471-2164/16/188
    ae974a485f413a2113503eed53cd6c53
    10.1186/s12864-015-1369-8
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC)

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