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dc.contributor.authorHuang, Chao-Li
dc.contributor.authorPu, Pei-Hua
dc.contributor.authorHuang, Hao-Jen
dc.contributor.authorSung, Huang-Mo
dc.contributor.authorLiaw, Hung-Jiun
dc.contributor.authorChen, Yi-Min
dc.contributor.authorChen, Chien-Ming
dc.contributor.authorHuang, Ming-Ban
dc.contributor.authorOsada, Naoki
dc.contributor.authorGojobori, Takashi
dc.contributor.authorPai, Tun-Wen
dc.contributor.authorChen, Yu-Tin
dc.contributor.authorHwang, Chi-Chuan
dc.contributor.authorChiang, Tzen-Yuh
dc.date.accessioned2015-03-23T08:07:34Z
dc.date.available2015-03-23T08:07:34Z
dc.date.issued2015-03-15
dc.identifier.citationEcological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts 2015, 16 (1) BMC Genomics
dc.identifier.issn1471-2164
dc.identifier.pmid25879893
dc.identifier.doi10.1186/s12864-015-1369-8
dc.identifier.urihttp://hdl.handle.net/10754/346969
dc.description.abstractBackground: 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.
dc.publisherSpringer Nature
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/16/188
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.titleEcological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.identifier.journalBMC Genomics
dc.identifier.pmcidPMC4372319
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDepartment of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
dc.contributor.institutionInstitute of Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
dc.contributor.institutionDepartment of Computer Science and Engineering, National Taiwan Ocean University, Keelung 202, Taiwan
dc.contributor.institutionNational Institute of Genetics, Mishima, Shizuoka 411-8540, Yata, Japan
dc.contributor.institutionDepartment of Engineering Science and Supercomputing Research Center, National Cheng Kung University, Tainan 701, Taiwan
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personGojobori, Takashi
refterms.dateFOA2018-06-13T16:19:31Z


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