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

Chao-Li Huang, Pei Hua Pu, Hao-Jen Huang, Huang-Mo Sung, Hung-Jiun Liaw, Yi-Min Chen, Chien Ming Chen, Ming Ban Huang, Naoki Osada, Takashi Gojobori, Tun Wen Pai, Yu Tin Chen, Chi-Chuan Hwang, Tzen-Yuh Chiang

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish
Article number188
JournalBMC genomics
Volume16
Issue number1
DOIs
Publication statusPublished - 2015 Mar 15

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Xanthomonas
Homologous Recombination
Genomics
Genetic Selection
Genome
Xanthomonas campestris
Genes
Brassicaceae
Gene Flow
Host Specificity
Point Mutation
Bacteriophages
Cues
Alleles
DNA
Population

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Cite this

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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. 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.",
author = "Chao-Li Huang and Pu, {Pei Hua} and Hao-Jen Huang and Huang-Mo Sung and Hung-Jiun Liaw and Yi-Min Chen and Chen, {Chien Ming} and Huang, {Ming Ban} and Naoki Osada and Takashi Gojobori and Pai, {Tun Wen} and Chen, {Yu Tin} and Chi-Chuan Hwang and Tzen-Yuh Chiang",
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Ecological genomics in Xanthomonas : The nature of genetic adaptation with homologous recombination and host shifts. / 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; Pai, Tun Wen; Chen, Yu Tin; Hwang, Chi-Chuan; Chiang, Tzen-Yuh.

In: BMC genomics, Vol. 16, No. 1, 188, 15.03.2015.

Research output: Contribution to journalArticle

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T1 - Ecological genomics in Xanthomonas

T2 - The nature of genetic adaptation with homologous recombination and host shifts

AU - Huang, Chao-Li

AU - Pu, Pei Hua

AU - Huang, Hao-Jen

AU - Sung, Huang-Mo

AU - Liaw, Hung-Jiun

AU - Chen, Yi-Min

AU - Chen, Chien Ming

AU - Huang, Ming Ban

AU - Osada, Naoki

AU - Gojobori, Takashi

AU - Pai, Tun Wen

AU - Chen, Yu Tin

AU - Hwang, Chi-Chuan

AU - Chiang, Tzen-Yuh

PY - 2015/3/15

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N2 - 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.

AB - 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.

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