Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses

Detalhes bibliográficos
Autor(a) principal: Patané, José S. L.
Data de Publicação: 2019
Outros Autores: Martins, Joaquim, Rangel, Luiz Thiberio, Belasque, José, Digiampietri, Luciano A., Facincani, Agda Paula [UNESP], Ferreira, Rafael Marini [UNESP], Jaciani, Fabrício José, Zhang, Yunzeng, Varani, Alessandro M. [UNESP], Almeida, Nalvo F., Wang, Nian, Ferro, Jesus A. [UNESP], Moreira, Leandro M., Setubal, Joaõ C.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1186/s12864-019-6007-4
http://hdl.handle.net/11449/189733
Resumo: Background: Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A∗and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. Results: Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A∗strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence. Conclusions: Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.
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spelling Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analysesBiogeographyDivergence datingGenome evolutionPhylogenomicsRecombinationBackground: Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A∗and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. Results: Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A∗strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence. Conclusions: Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Departamento de Bioquímica Instituto de Química Universidade de Saõ PauloLaboratório Especial de Ciclo Celular Instituto ButantanDepartamento de Fitopatologia e Nematologia Escola Superior de Agricultura luiz de Queiroz Universidade de Saõ PauloEscola de Artes Ciências e Humanidades Universidade de Saõ PauloFaculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP)Departamento de Pesquisa e Desenvolvimento Fundo de Defesa da Citricultura (Fundecitrus)Citrus Research and Education Center Department of Microbiology and Cell Science University of FloridaFaculdade de Computacaõ Universidade Federal de Mato Grosso Do sulNúcleo de Pesquisas em Ciências Biológicas Universidade Federal de Ouro PretoBiocomplexity Institute of Virginia TechFaculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP)Universidade de Saõ PauloInstituto ButantanUniversidade Estadual Paulista (Unesp)Fundo de Defesa da Citricultura (Fundecitrus)University of FloridaUniversidade Federal de Mato Grosso do Sul (UFMS)Universidade Federal de Ouro PretoBiocomplexity Institute of Virginia TechPatané, José S. L.Martins, JoaquimRangel, Luiz ThiberioBelasque, JoséDigiampietri, Luciano A.Facincani, Agda Paula [UNESP]Ferreira, Rafael Marini [UNESP]Jaciani, Fabrício JoséZhang, YunzengVarani, Alessandro M. [UNESP]Almeida, Nalvo F.Wang, NianFerro, Jesus A. [UNESP]Moreira, Leandro M.Setubal, Joaõ C.2019-10-06T16:50:25Z2019-10-06T16:50:25Z2019-09-09info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/s12864-019-6007-4BMC Genomics, v. 20, n. 1, 2019.1471-2164http://hdl.handle.net/11449/18973310.1186/s12864-019-6007-42-s2.0-85071971805Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Genomicsinfo:eu-repo/semantics/openAccess2021-10-23T05:17:38Zoai:repositorio.unesp.br:11449/189733Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:15:24.233358Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
title Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
spellingShingle Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
Patané, José S. L.
Biogeography
Divergence dating
Genome evolution
Phylogenomics
Recombination
title_short Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
title_full Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
title_fullStr Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
title_full_unstemmed Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
title_sort Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
author Patané, José S. L.
author_facet Patané, José S. L.
Martins, Joaquim
Rangel, Luiz Thiberio
Belasque, José
Digiampietri, Luciano A.
Facincani, Agda Paula [UNESP]
Ferreira, Rafael Marini [UNESP]
Jaciani, Fabrício José
Zhang, Yunzeng
Varani, Alessandro M. [UNESP]
Almeida, Nalvo F.
Wang, Nian
Ferro, Jesus A. [UNESP]
Moreira, Leandro M.
Setubal, Joaõ C.
author_role author
author2 Martins, Joaquim
Rangel, Luiz Thiberio
Belasque, José
Digiampietri, Luciano A.
Facincani, Agda Paula [UNESP]
Ferreira, Rafael Marini [UNESP]
Jaciani, Fabrício José
Zhang, Yunzeng
Varani, Alessandro M. [UNESP]
Almeida, Nalvo F.
Wang, Nian
Ferro, Jesus A. [UNESP]
Moreira, Leandro M.
Setubal, Joaõ C.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade de Saõ Paulo
Instituto Butantan
Universidade Estadual Paulista (Unesp)
Fundo de Defesa da Citricultura (Fundecitrus)
University of Florida
Universidade Federal de Mato Grosso do Sul (UFMS)
Universidade Federal de Ouro Preto
Biocomplexity Institute of Virginia Tech
dc.contributor.author.fl_str_mv Patané, José S. L.
Martins, Joaquim
Rangel, Luiz Thiberio
Belasque, José
Digiampietri, Luciano A.
Facincani, Agda Paula [UNESP]
Ferreira, Rafael Marini [UNESP]
Jaciani, Fabrício José
Zhang, Yunzeng
Varani, Alessandro M. [UNESP]
Almeida, Nalvo F.
Wang, Nian
Ferro, Jesus A. [UNESP]
Moreira, Leandro M.
Setubal, Joaõ C.
dc.subject.por.fl_str_mv Biogeography
Divergence dating
Genome evolution
Phylogenomics
Recombination
topic Biogeography
Divergence dating
Genome evolution
Phylogenomics
Recombination
description Background: Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A∗and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. Results: Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A∗strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence. Conclusions: Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.
publishDate 2019
dc.date.none.fl_str_mv 2019-10-06T16:50:25Z
2019-10-06T16:50:25Z
2019-09-09
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1186/s12864-019-6007-4
BMC Genomics, v. 20, n. 1, 2019.
1471-2164
http://hdl.handle.net/11449/189733
10.1186/s12864-019-6007-4
2-s2.0-85071971805
url http://dx.doi.org/10.1186/s12864-019-6007-4
http://hdl.handle.net/11449/189733
identifier_str_mv BMC Genomics, v. 20, n. 1, 2019.
1471-2164
10.1186/s12864-019-6007-4
2-s2.0-85071971805
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv BMC Genomics
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
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instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
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