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AutorDutilh, Bas E.
AutorThompson, Cristiane C.
AutorVicente, Ana C. P.
AutorMarin, Michel A.
AutorLee, Clarence
AutorSchmieder, Robert
AutorAndrade, Bruno G. N.
AutorChimetto, Luciane
AutorCuevas, Daniel
AutorGarza, Daniel R.
AutorOkeke, Iruka N.
AutorAboderin, Aaron Oladipo
AutorSpangler, Jessica
AutorRoss, Tristen
AutorDinsdale, Elizabeth A.
AutorThompson, Fabiano L.
AutorHarkins, Timothy T.
AutorEdwards, Robert A.
Fecha de acceso2015-05-19T13:26:02Z
Fecha de disponibilización2015-05-19T13:26:02Z
Fecha de publicación2014
ReferenciaDUTILH, Bas E. et al. Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions. BMC Genomics, San Diego, v. 15, n. 654, p. 1-11, 2014.pt_BR
ISSN1471-2164pt_BR
URIhttps://www.arca.fiocruz.br/handle/icict/10390
Idiomaengpt_BR
EditorBiomed Centralpt_BR
Derechos de autoropen access
TítuloComparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensionspt_BR
Tipo del documentoArticle
DOI10.1186/1471-2164-15-654pt_BR
Resumen en InglésBackground: Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat. Results: Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages. Conclusions: Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.pt_BR
AfiliaciónSan Diego State University. Department of Biology. Department of Computer Science. San Diego, CA, USA / Radboud University Medical Centre. Radboud Institute for Molecular Life Sciences. Centre for Molecular and Biomolecular Informatics. Nijmegen, The Netherlands / Universidade Federal do Rio de Janeiro. Instituto de Biologia. Departamento de Biologia Marinha. Rio de janeiro, RJ, Brasil.pt_BR
AfiliaciónFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular e Microrganismos. Rio de Janeiro, RJ, Brasil.pt_BR
AfiliaciónFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular e Microrganismos. Rio de Janeiro, RJ, Brasil.pt_BR
AfiliaciónFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular e Microrganismos. Rio de Janeiro, RJ, Brasil.pt_BR
AfiliaciónAdvanced Applications Group, Life Technologies, Beverly, MA, USA.pt_BR
AfiliaciónSan Diego State University. Department of Computer Science. Computational Science Research Center. San Diego, CA, USA.pt_BR
AfiliaciónSan Diego State University. Department of Computer Science. 6Computational Science Research Center. San Diego, CA, USA.pt_BR
AfiliaciónFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular e Microrganismos. Rio de Janeiro, RJ, Brasil.pt_BR
AfiliaciónUniversidade Federal do Rio de Janeiro. Instituto de Biologia. Departamento de Biologia Marinha. Rio de Janeiro, RJ, Brasil.pt_BR
AfiliaciónSan Diego State University. Department of Computer Science. San Diego, CA, USA / Advanced Applications Group, Life Technologies, Inc. Beverly, MA, USA.pt_BR
AfiliaciónSan Diego State University. Department of Computer Science. San Diego, CA, USA.pt_BR
AfiliaciónHaverford College. Department of Biology. Haverford, PA, USA.pt_BR
AfiliaciónObafemi Awolowo University. College of Health Sciences. Department of Medical Microbiology & Parasitology. Ile-Ife, Nigeria.pt_BR
AfiliaciónAdvanced Applications Group, Life Technologies, Inc. Beverly, MA, USA.pt_BR
AfiliaciónAdvanced Applications Group, Life Technologies, Inc. Beverly, MA, USA.pt_BR
AfiliaciónSan Diego State University. Department of Biology. San Diego, CA, USA.pt_BR
AfiliaciónUniversidade Federal do Rio de Janeiro. Instituto de Biologia. Departamento de Biologia Marinha. Rio de Janeiro, RJ, Brasil.pt_BR
AfiliaciónAdvanced Applications Group, Life Technologies, Inc. Beverly, MA, USA.pt_BR
AfiliaciónSan Diego State University. Department of Biology. Department of Computer Science. San Diego, CA, USA /Universidade Federal do Rio de Janeiro. Instituto de Biologia. Departamento de Biologia Marinha. Rio de Janeiro, RJ, Brasil / San Diego State University. Computational Science Research Center. San Diego, CA, USA / Argonne National Laboratory. Mathematics and Computer Science Division. Argonne, Il, USA.pt_BR
Palavras clave en InglêsFunctional genomicspt_BR
Palavras clave en InglêsPhagespt_BR
Palavras clave en InglêsNiche adaptationpt_BR
Palavras clave en InglêsVibriopt_BR
Palavras clave en InglêsMobile elementspt_BR
Palavras clave en InglêsGenome evolutionpt_BR
Palavras clave en InglêsGenotype-phenotype associationpt_BR
Palavras clave en InglêsRandom forestpt_BR
DeCSBacteriófagospt_BR
DeCSVibriopt_BR
DeCSGenômicapt_BR
DeCSGenótipopt_BR
xmlui.metadata.dc.subject.ods15 Vida terrestre


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