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

Handle URI:
http://hdl.handle.net/10754/346969
Title:
Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts
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 ( 0000-0001-7850-1743 ) ; Pai, Tun-Wen; Chen, Yu-Tin; Hwang, Chi-Chuan; Chiang, Tzen-Yuh
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.
KAUST Department:
Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts 2015, 16 (1) BMC Genomics
Publisher:
BioMed Central
Journal:
BMC Genomics
Issue Date:
15-Mar-2015
DOI:
10.1186/s12864-015-1369-8
PubMed ID:
25879893
PubMed Central ID:
PMC4372319
Type:
Article
ISSN:
1471-2164
Additional Links:
http://www.biomedcentral.com/1471-2164/16/188
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorHuang, Chao-Lien
dc.contributor.authorPu, Pei-Huaen
dc.contributor.authorHuang, Hao-Jenen
dc.contributor.authorSung, Huang-Moen
dc.contributor.authorLiaw, Hung-Jiunen
dc.contributor.authorChen, Yi-Minen
dc.contributor.authorChen, Chien-Mingen
dc.contributor.authorHuang, Ming-Banen
dc.contributor.authorOsada, Naokien
dc.contributor.authorGojobori, Takashien
dc.contributor.authorPai, Tun-Wenen
dc.contributor.authorChen, Yu-Tinen
dc.contributor.authorHwang, Chi-Chuanen
dc.contributor.authorChiang, Tzen-Yuhen
dc.date.accessioned2015-03-23T08:07:34Zen
dc.date.available2015-03-23T08:07:34Zen
dc.date.issued2015-03-15en
dc.identifier.citationEcological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts 2015, 16 (1) BMC Genomicsen
dc.identifier.issn1471-2164en
dc.identifier.pmid25879893en
dc.identifier.doi10.1186/s12864-015-1369-8en
dc.identifier.urihttp://hdl.handle.net/10754/346969en
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.en
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/16/188en
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.en
dc.titleEcological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shiftsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalBMC Genomicsen
dc.identifier.pmcidPMC4372319en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Life Sciences, National Cheng Kung University, Tainan 701, Taiwanen
dc.contributor.institutionInstitute of Biotechnology, National Cheng Kung University, Tainan 701, Taiwanen
dc.contributor.institutionDepartment of Computer Science and Engineering, National Taiwan Ocean University, Keelung 202, Taiwanen
dc.contributor.institutionNational Institute of Genetics, Mishima, Shizuoka 411-8540, Yata, Japanen
dc.contributor.institutionDepartment of Engineering Science and Supercomputing Research Center, National Cheng Kung University, Tainan 701, Taiwanen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorGojobori, Takashien

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