Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses
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 structur...
| Autores principales: | , , , , , , , , , , , , , , , |
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| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2020
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| Materias: | |
| Acceso en línea: | 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 |
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| author | 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_browse | Almeida, Nalvo Franco Araujo, Flabio Ribeiro de Bigi, Fabiana Castelão, Ana Beatriz C. Cataldi, Angel Adrian Fonseca Junior, Antônio Jorge, Klaudia dos Santos Goncalves Martins Jr, Joaquim Montera, Luciana Nishibe, Christiane Osório, Ana Luiza Alves Rosa Patané, José S.L. Roxo, Eliana Setubal, Joâo C. Thacker, Tyler C. Zumarraga, Martin Jose |
| 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_sort | Patané, José S.L. |
| collection | INTA Digital |
| 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. |
| format | info:ar-repo/semantics/artículo |
| id | INTA8210 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | INTA82102022-08-12T16:27:41Z Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses 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. Mycobacterium bovis Tuberculosis Filogenia Epidemiología Phylogeny Epidemiology 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 2020-11-06T16:39:40Z 2020-11-06T16:39:40Z 2017-03 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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) application/pdf Oxford University Press Genome Biology and Evolution 9 (3) : 521-535 (March 2017) |
| spellingShingle | Mycobacterium bovis Tuberculosis Filogenia Epidemiología Phylogeny Epidemiology 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. Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses |
| title | 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_short | Patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses |
| title_sort | patterns and processes of mycobacterium bovis evolution revealed by phylogenomic analyses |
| topic | Mycobacterium bovis Tuberculosis Filogenia Epidemiología Phylogeny Epidemiology |
| 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 |
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