Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts
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Type
ArticleAuthors
Huang, Chao-LiPu, 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
KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
Computational Bioscience Research Center (CBRC)
Date
2015-03-15Online Publication Date
2015-03-15Print Publication Date
2015-12Permanent link to this record
http://hdl.handle.net/10754/346969
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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 GenomicsPublisher
Springer NatureJournal
BMC GenomicsPubMed ID
25879893PubMed Central ID
PMC4372319Additional Links
http://www.biomedcentral.com/1471-2164/16/188ae974a485f413a2113503eed53cd6c53
10.1186/s12864-015-1369-8
Scopus Count
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