Genome Biology and Evolution

Autor: Luciana Montera, Ana Beatriz Canevari Castelão, Nalvo F. Almeida, José S. L. Patané, Antônio Augusto Fonseca Júnior, Fabiana Bigi, Eliana Roxo, Ángel Adrián Cataldi, João C. Setubal, Christiane Nishibe, Joaquim Martins, Martín José Zumárraga, Tyler C. Thacker, Ana Luiza Alves Rosa Osório, Flábio R. Araújo, Kláudia S. G. Jorge
Přispěvatelé: José S. L. Patane, Departamento de Bioquímica/Instituto de Química, Universidade de São Paulo, Joaquim Martins Jr, Departamento de Bioquímica/Instituto de Química, Universidade de São Paulo, Ana Beatriz Castelão, Universidade Federal de Mato Grosso do Sul - UFMS, Christiane Nishibe, Faculdade de Computação/Universidade Federal de Mato Grosso do Sul - UFMS, Luciana Montera, Faculdade de Computacão Universidade Federal de Mato Grosso do Sul - UFMS, Fabiana Bigi, Instituto Nacional de Tecnologia Agropecuária de Córdoba, Martin J. Zumárraga, Instituto Nacional de Tecnologia Agropecuária de Córdoba, Angel A. Cataldi, Instituto Nacional de Tecnologia Agropecuária de Córdoba, Antônio Fonseca Junior, Rede de Laboratórios Agropecuários do Ministério da Agricultura, Pecuária e Abastecimento, Eliana Roxo, Instituto Biológico de São Paulo, IB-USP, Ana Luiza A. R. Osório, Programa em Ciência Animal Universidade Federal de Mato Grosso do Sul, Klaudia S. Jorge, Programa em Ciência Animal Universidade Federal de Mato Grosso do Sul, Tyler C. Thacker, Agricultural Research Service, United States Department of Agriculture, Nalvo F. Almeida, Faculdade de Computação Universidade Federal de Mato Grosso do Sul, FLABIO RIBEIRO ARAUJO, CNPGC, João C. Setubal, Biocomplexity Institute of Virginia Tech.
Jazyk: angličtina
Rok vydání: 2017
Předmět:
Zdroj: Genome Biology and Evolution 9 (3) : 521-535 (March 2017)
INTA Digital (INTA)
Instituto Nacional de Tecnología Agropecuaria
instacron:INTA
Genome Biology and Evolution
Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA-Alice)
Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron:EMBRAPA
Popis: Mycobacterium bovis is an important animal pathogen worldwide, parasitizing wild and domesticated vertebrate live stocks as well as humans. We investigated evolutionary patterns and processes in 38 sequenced genomes of M. bovis from the Americas, Europe, Asia, and Africa. We found that US strains are evolving distinctly (though with low magnitude) from most South American lineages regarding core-coding size, GC-content, and codon usage bias, and we further employ agreement to this pattern as proxy for phylogenetic reliability. Three data types were used for tree inference: 1. Single copy core-coding genes (core-coding); 2. Indel blocks coded as numeric characters (indels); 3. Gene presence/absence similarly coded (pangenome). Core-coding´s performance was below expected regarded we used 2,000+ genes, but indels and pangenome individually estimated reasonable trees, with HGT rates as high as 200x the DNA substitution rate. In addressing why core-coding performed poorly, we excluded phylogenetic method bias, homologous recombination, positive, and purifying selection as possible causes, whilst transient retention of random mildly deleterious mutations due to recent diversification, and also ongoing pseudogeneization, may be plausible. Although total evidence´s retention index was as good as presence/absence data individually in identifying US samples, it additionaly found a South American clade with more lineages excluding only two Brazilian samples. We further inferred divergence times using indels + pangenome due to lack of informativeness of core-coding, recovering relatively similar date estimates to previous studies on the origin of M. bovis (< 10,000 y) regardless of the dating prior (strict vs. uncorrelated clock, uniform vs. exponential clock, different age/rate standard deviation priors), evincing the suitability and unsuspected robustness of using strictly genomic-wide presence/absence data to dating, while also decisively rejecting a strict clock for our dataset. All trees supported a relatively basal position of African strains, which were isolated from Homo sapiens, suggesting it was an important region for early diversification and confirming we were one of the earliest hosts of the species. Evolution of US strains was affected by lateral acquisition of 57 exclusive genes from, including genes important for virulence. A clade of three US localities, distant from one another, is under even faster evolutionary rates supported by core-coding, indels, and pangenome. Fil: Patané, José S.L.. Universidade de Sao Paulo; Brasil Fil: Martins, Joaquim. Universidade de Sao Paulo; Brasil Fil: Castelão, Ana Beatriz. Universidade Federal do Mato Grosso do Sul; Brasil Fil: Nishibe, Christiane. Universidade Federal do Mato Grosso do Sul; Brasil Fil: Montera, Luciana. Universidade Federal do Mato Grosso do Sul; Brasil Fil: Bigi, Fabiana. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Zumárraga, Martín José. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Cataldi, Ángel Adrián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias; Argentina Fil: Junior, Antônio Fonseca. Ministerio da Agricultura Pecuaria e Abastecimento de Brasil. Empresa Brasileira de Pesquisa Agropecuaria; Brasil Fil: Roxo, Eliana. Instituto Biológico de São Pablo; Brasil Fil: Osório, Ana Luiza A. R.. Universidade Federal do Mato Grosso do Sul; Brasil Fil: Jorge, Klaudia S.. Universidade Federal do Mato Grosso do Sul; Brasil Fil: Thacker, Tyler C.. United States Department of Agriculture; Estados Unidos Fil: Almeida, Nalvo F.. Universidade Federal do Mato Grosso do Sul; Brasil Fil: Araújo, Flabio R.. Ministerio da Agricultura Pecuaria e Abastecimento de Brasil. Empresa Brasileira de Pesquisa Agropecuaria; Brasil Fil: Setubal, João C.. Universidade de Sao Paulo; Brasil. Biocomplexity Institute of Virginia Tech; Estados Unidos
Databáze: OpenAIRE
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