Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses

Autores
Patané, José S.L.; Martins Jr, Joaquim; Castelão, Ana Beatriz C.; Nishibe, Christiane; Montera, Luciana; Bigi, Fabiana; Zumarraga, Martin Jose; Cataldi, Angel Adrian; Fonseca Junior, Antônio; Roxo, Eliana; Osório, Ana Luiza Alves Rosa; Jorge, Klaudia dos Santos Goncalves; Thacker, Tyler C.; Almeida, Nalvo Franco; Araujo, Flabio Ribeiro de; Setubal, Joâo C.
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from the United Kingdom, South Korea, Brazil, and the United States revealed four novel large-scale structural variations of at least 2,000 bp. A comparative phylogenomic study including 2,483 core genes of 38 taxa from eight countries showed conflicting phylogenetic signal among sites. By minimizing this effect, we obtained a tree that better agrees with sampling locality. Results supported a relatively basal position of African strains (all isolated from Homo sapiens), confirming that Africa was an important region for early diversification and that humans were one of the earliest hosts. Selection analyses revealed that functional categories such as “Lipid transport and metabolism,” “Cell cycle control, cell division, chromosome partitioning” and “Cell motility” were significant for the evolution of the group, besides other categories previously described, showing importance of genes associated with virulence and cholesterol metabolism in the evolution of M. bovis. PE/PPE genes, many of which are known to be associated with virulence, were major targets for large-scale polymorphisms, homologous recombination, and positive selection, evincing for the first time a plethora of evolutionary forces possibly contributing to differential adaptability in M. bovis. By assuming different priors, US strains originated and started to diversify around 150–5,210 ya. By further analyzing the largest set of US genomes to date (76 in total), obtained from 14 host species, we detected that hosts were not clustered in clades (except for a few cases), with some faster-evolving strains being detected, suggesting fast and ongoing reinfections across host species, and therefore, the possibility of new bovine tuberculosis outbreaks.
Instituto de Biotecnología
Fil: Patané, José S. L. Universidade de São Paulo. Instituto de Química. Departamento de Bioquímica; Brasil
Fil: Martins Jr, Joaquim. Universidade de São Paulo. Instituto de Química. Departamento de Bioquímica; Brasil
Fil: Castelão, Ana Beatriz C. Universidade Federal de Mato Grosso do Sul. Faculdade de Medicina Veterinária e Zootecnia; Brasil
Fil: Nishibe, Christiane. Universidade Federal de Mato Grosso do Sul. Faculdade de Computação; Brasil
Fil: Montera, Luciana. Universidade Federal de Mato Grosso do Sul. Faculdade de Computação; Brasil
Fil: Bigi, Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Zumarraga, Martin Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Cataldi, Angel Adrian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Fonseca Junior, Antônio. Rede de Laboratórios Agropecuários do Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo; Brasil
Fil: Roxo, Eliana. Instituto Biológico de São Paulo; Brasil
Fil: Osório, Ana Luiza Alves Rosa. Universidade Federal de Mato Grosso do Sul. Faculdade de Medicina Veterinária e Zootecnia. Programa de Pós-graduação em Ciência Animal; Brasil
Fil: Jorge, Klaudia dos Santos Goncalves. Universidade Federal de Mato Grosso do Sul. Faculdade de Medicina Veterinária e Zootecnia. Programa de Pós-graduação em Ciência Animal; Brasil
Fil: Thacker, Tyler C. United States Department of Agriculture. Agricultural Research Service. National Animal Disease Center; Estados Unidos
Fil: Almeida, Nalvo F. Universidade Federal de Mato Grosso do Sul. Faculdade de Computação; Brasil
Fil: Araujo, Flabio Ribeiro de. Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Gado de Corte; Brasil
Fil: Setubal, Joâo C. Universidade de São Paulo. Instituto de Química. Departamento de Bioquímica; Brasil. Biocomplexity Institute of Virginia Tech; Estados Unidos
Fuente
Genome Biology and Evolution 9 (3) : 521-535 (March 2017)
Materia
Mycobacterium bovis
Tuberculosis
Filogenia
Epidemiología
Phylogeny
Epidemiology
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/8210
Acceder
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oai_identifier_str oai:localhost:20.500.12123/8210
network_acronym_str INTADig
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network_name_str INTA Digital (INTA)
spelling Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analysesPatané, José S.L.Martins Jr, JoaquimCastelão, Ana Beatriz C.Nishibe, ChristianeMontera, LucianaBigi, FabianaZumarraga, Martin JoseCataldi, Angel AdrianFonseca Junior, AntônioRoxo, ElianaOsório, Ana Luiza Alves RosaJorge, Klaudia dos Santos GoncalvesThacker, Tyler C.Almeida, Nalvo FrancoAraujo, Flabio Ribeiro deSetubal, Joâo C.Mycobacterium bovisTuberculosisFilogeniaEpidemiologíaPhylogenyEpidemiologyMycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from the United Kingdom, South Korea, Brazil, and the United States revealed four novel large-scale structural variations of at least 2,000 bp. A comparative phylogenomic study including 2,483 core genes of 38 taxa from eight countries showed conflicting phylogenetic signal among sites. By minimizing this effect, we obtained a tree that better agrees with sampling locality. Results supported a relatively basal position of African strains (all isolated from Homo sapiens), confirming that Africa was an important region for early diversification and that humans were one of the earliest hosts. Selection analyses revealed that functional categories such as “Lipid transport and metabolism,” “Cell cycle control, cell division, chromosome partitioning” and “Cell motility” were significant for the evolution of the group, besides other categories previously described, showing importance of genes associated with virulence and cholesterol metabolism in the evolution of M. bovis. PE/PPE genes, many of which are known to be associated with virulence, were major targets for large-scale polymorphisms, homologous recombination, and positive selection, evincing for the first time a plethora of evolutionary forces possibly contributing to differential adaptability in M. bovis. By assuming different priors, US strains originated and started to diversify around 150–5,210 ya. By further analyzing the largest set of US genomes to date (76 in total), obtained from 14 host species, we detected that hosts were not clustered in clades (except for a few cases), with some faster-evolving strains being detected, suggesting fast and ongoing reinfections across host species, and therefore, the possibility of new bovine tuberculosis outbreaks.Instituto de BiotecnologíaFil: Patané, José S. L. Universidade de São Paulo. Instituto de Química. Departamento de Bioquímica; BrasilFil: Martins Jr, Joaquim. Universidade de São Paulo. Instituto de Química. Departamento de Bioquímica; BrasilFil: Castelão, Ana Beatriz C. Universidade Federal de Mato Grosso do Sul. Faculdade de Medicina Veterinária e Zootecnia; BrasilFil: Nishibe, Christiane. Universidade Federal de Mato Grosso do Sul. Faculdade de Computação; BrasilFil: Montera, Luciana. Universidade Federal de Mato Grosso do Sul. Faculdade de Computação; BrasilFil: Bigi, Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Zumarraga, Martin Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Cataldi, Angel Adrian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Fonseca Junior, Antônio. Rede de Laboratórios Agropecuários do Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo; BrasilFil: Roxo, Eliana. Instituto Biológico de São Paulo; BrasilFil: Osório, Ana Luiza Alves Rosa. Universidade Federal de Mato Grosso do Sul. Faculdade de Medicina Veterinária e Zootecnia. Programa de Pós-graduação em Ciência Animal; BrasilFil: Jorge, Klaudia dos Santos Goncalves. Universidade Federal de Mato Grosso do Sul. Faculdade de Medicina Veterinária e Zootecnia. Programa de Pós-graduação em Ciência Animal; BrasilFil: Thacker, Tyler C. United States Department of Agriculture. Agricultural Research Service. National Animal Disease Center; Estados UnidosFil: Almeida, Nalvo F. Universidade Federal de Mato Grosso do Sul. Faculdade de Computação; BrasilFil: Araujo, Flabio Ribeiro de. Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Gado de Corte; BrasilFil: Setubal, Joâo C. Universidade de São Paulo. Instituto de Química. Departamento de Bioquímica; Brasil. Biocomplexity Institute of Virginia Tech; Estados UnidosOxford University Press2020-11-06T16:39:40Z2020-11-06T16:39:40Z2017-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/8210https://academic.oup.com/gbe/article/9/3/521/29926131759-6653https://doi.org/10.1093/gbe/evx022Genome Biology and Evolution 9 (3) : 521-535 (March 2017)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-10-16T09:29:56Zoai:localhost:20.500.12123/8210instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-16 09:29:56.727INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses
title Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses
spellingShingle Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses
Patané, José S.L.
Mycobacterium bovis
Tuberculosis
Filogenia
Epidemiología
Phylogeny
Epidemiology
title_short Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses
title_full Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses
title_fullStr Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses
title_full_unstemmed Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses
title_sort Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses
dc.creator.none.fl_str_mv Patané, José S.L.
Martins Jr, Joaquim
Castelão, Ana Beatriz C.
Nishibe, Christiane
Montera, Luciana
Bigi, Fabiana
Zumarraga, Martin Jose
Cataldi, Angel Adrian
Fonseca Junior, Antônio
Roxo, Eliana
Osório, Ana Luiza Alves Rosa
Jorge, Klaudia dos Santos Goncalves
Thacker, Tyler C.
Almeida, Nalvo Franco
Araujo, Flabio Ribeiro de
Setubal, Joâo C.
author Patané, José S.L.
author_facet Patané, José S.L.
Martins Jr, Joaquim
Castelão, Ana Beatriz C.
Nishibe, Christiane
Montera, Luciana
Bigi, Fabiana
Zumarraga, Martin Jose
Cataldi, Angel Adrian
Fonseca Junior, Antônio
Roxo, Eliana
Osório, Ana Luiza Alves Rosa
Jorge, Klaudia dos Santos Goncalves
Thacker, Tyler C.
Almeida, Nalvo Franco
Araujo, Flabio Ribeiro de
Setubal, Joâo C.
author_role author
author2 Martins Jr, Joaquim
Castelão, Ana Beatriz C.
Nishibe, Christiane
Montera, Luciana
Bigi, Fabiana
Zumarraga, Martin Jose
Cataldi, Angel Adrian
Fonseca Junior, Antônio
Roxo, Eliana
Osório, Ana Luiza Alves Rosa
Jorge, Klaudia dos Santos Goncalves
Thacker, Tyler C.
Almeida, Nalvo Franco
Araujo, Flabio Ribeiro de
Setubal, Joâo C.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Mycobacterium bovis
Tuberculosis
Filogenia
Epidemiología
Phylogeny
Epidemiology
topic Mycobacterium bovis
Tuberculosis
Filogenia
Epidemiología
Phylogeny
Epidemiology
dc.description.none.fl_txt_mv Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from the United Kingdom, South Korea, Brazil, and the United States revealed four novel large-scale structural variations of at least 2,000 bp. A comparative phylogenomic study including 2,483 core genes of 38 taxa from eight countries showed conflicting phylogenetic signal among sites. By minimizing this effect, we obtained a tree that better agrees with sampling locality. Results supported a relatively basal position of African strains (all isolated from Homo sapiens), confirming that Africa was an important region for early diversification and that humans were one of the earliest hosts. Selection analyses revealed that functional categories such as “Lipid transport and metabolism,” “Cell cycle control, cell division, chromosome partitioning” and “Cell motility” were significant for the evolution of the group, besides other categories previously described, showing importance of genes associated with virulence and cholesterol metabolism in the evolution of M. bovis. PE/PPE genes, many of which are known to be associated with virulence, were major targets for large-scale polymorphisms, homologous recombination, and positive selection, evincing for the first time a plethora of evolutionary forces possibly contributing to differential adaptability in M. bovis. By assuming different priors, US strains originated and started to diversify around 150–5,210 ya. By further analyzing the largest set of US genomes to date (76 in total), obtained from 14 host species, we detected that hosts were not clustered in clades (except for a few cases), with some faster-evolving strains being detected, suggesting fast and ongoing reinfections across host species, and therefore, the possibility of new bovine tuberculosis outbreaks.
Instituto de Biotecnología
Fil: Patané, José S. L. Universidade de São Paulo. Instituto de Química. Departamento de Bioquímica; Brasil
Fil: Martins Jr, Joaquim. Universidade de São Paulo. Instituto de Química. Departamento de Bioquímica; Brasil
Fil: Castelão, Ana Beatriz C. Universidade Federal de Mato Grosso do Sul. Faculdade de Medicina Veterinária e Zootecnia; Brasil
Fil: Nishibe, Christiane. Universidade Federal de Mato Grosso do Sul. Faculdade de Computação; Brasil
Fil: Montera, Luciana. Universidade Federal de Mato Grosso do Sul. Faculdade de Computação; Brasil
Fil: Bigi, Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Zumarraga, Martin Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Cataldi, Angel Adrian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Fonseca Junior, Antônio. Rede de Laboratórios Agropecuários do Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo; Brasil
Fil: Roxo, Eliana. Instituto Biológico de São Paulo; Brasil
Fil: Osório, Ana Luiza Alves Rosa. Universidade Federal de Mato Grosso do Sul. Faculdade de Medicina Veterinária e Zootecnia. Programa de Pós-graduação em Ciência Animal; Brasil
Fil: Jorge, Klaudia dos Santos Goncalves. Universidade Federal de Mato Grosso do Sul. Faculdade de Medicina Veterinária e Zootecnia. Programa de Pós-graduação em Ciência Animal; Brasil
Fil: Thacker, Tyler C. United States Department of Agriculture. Agricultural Research Service. National Animal Disease Center; Estados Unidos
Fil: Almeida, Nalvo F. Universidade Federal de Mato Grosso do Sul. Faculdade de Computação; Brasil
Fil: Araujo, Flabio Ribeiro de. Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Gado de Corte; Brasil
Fil: Setubal, Joâo C. Universidade de São Paulo. Instituto de Química. Departamento de Bioquímica; Brasil. Biocomplexity Institute of Virginia Tech; Estados Unidos
description Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from the United Kingdom, South Korea, Brazil, and the United States revealed four novel large-scale structural variations of at least 2,000 bp. A comparative phylogenomic study including 2,483 core genes of 38 taxa from eight countries showed conflicting phylogenetic signal among sites. By minimizing this effect, we obtained a tree that better agrees with sampling locality. Results supported a relatively basal position of African strains (all isolated from Homo sapiens), confirming that Africa was an important region for early diversification and that humans were one of the earliest hosts. Selection analyses revealed that functional categories such as “Lipid transport and metabolism,” “Cell cycle control, cell division, chromosome partitioning” and “Cell motility” were significant for the evolution of the group, besides other categories previously described, showing importance of genes associated with virulence and cholesterol metabolism in the evolution of M. bovis. PE/PPE genes, many of which are known to be associated with virulence, were major targets for large-scale polymorphisms, homologous recombination, and positive selection, evincing for the first time a plethora of evolutionary forces possibly contributing to differential adaptability in M. bovis. By assuming different priors, US strains originated and started to diversify around 150–5,210 ya. By further analyzing the largest set of US genomes to date (76 in total), obtained from 14 host species, we detected that hosts were not clustered in clades (except for a few cases), with some faster-evolving strains being detected, suggesting fast and ongoing reinfections across host species, and therefore, the possibility of new bovine tuberculosis outbreaks.
publishDate 2017
dc.date.none.fl_str_mv 2017-03
2020-11-06T16:39:40Z
2020-11-06T16:39:40Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/8210
https://academic.oup.com/gbe/article/9/3/521/2992613
1759-6653
https://doi.org/10.1093/gbe/evx022
url http://hdl.handle.net/20.500.12123/8210
https://academic.oup.com/gbe/article/9/3/521/2992613
https://doi.org/10.1093/gbe/evx022
identifier_str_mv 1759-6653
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv Genome Biology and Evolution 9 (3) : 521-535 (March 2017)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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