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COMPARATIVE GENOMICS OF 274 VIBRIO CHOLERAE GENOMES REVEALS MOBILE FUNCTIONS STRUCTURING THREE NICHE DIMENSIONS
Dutilh, Bas E. et al. | Date Issued: 2014
Author
Dutilh, Bas E.
Thompson, Cristiane C.
Vicente, Ana C. P.
Marin, Michel A.
Lee, Clarence
Schmieder, Robert
Andrade, Bruno G. N.
Chimetto, Luciane
Cuevas, Daniel
Garza, Daniel R.
Okeke, Iruka N.
Aboderin, Aaron Oladipo
Spangler, Jessica
Ross, Tristen
Dinsdale, Elizabeth A.
Thompson, Fabiano L.
Harkins, Timothy T.
Edwards, Robert A.
Affilliation
San 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.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular e Microrganismos. Rio de Janeiro, RJ, Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular e Microrganismos. Rio de Janeiro, RJ, Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular e Microrganismos. Rio de Janeiro, RJ, Brasil.
Advanced Applications Group, Life Technologies, Beverly, MA, USA.
San Diego State University. Department of Computer Science. Computational Science Research Center. San Diego, CA, USA.
San Diego State University. Department of Computer Science. 6Computational Science Research Center. San Diego, CA, USA.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular e Microrganismos. Rio de Janeiro, RJ, Brasil.
Universidade Federal do Rio de Janeiro. Instituto de Biologia. Departamento de Biologia Marinha. Rio de Janeiro, RJ, Brasil.
San Diego State University. Department of Computer Science. San Diego, CA, USA / Advanced Applications Group, Life Technologies, Inc. Beverly, MA, USA.
San Diego State University. Department of Computer Science. San Diego, CA, USA.
Haverford College. Department of Biology. Haverford, PA, USA.
Obafemi Awolowo University. College of Health Sciences. Department of Medical Microbiology & Parasitology. Ile-Ife, Nigeria.
Advanced Applications Group, Life Technologies, Inc. Beverly, MA, USA.
Advanced Applications Group, Life Technologies, Inc. Beverly, MA, USA.
San Diego State University. Department of Biology. San Diego, CA, USA.
Universidade Federal do Rio de Janeiro. Instituto de Biologia. Departamento de Biologia Marinha. Rio de Janeiro, RJ, Brasil.
Advanced Applications Group, Life Technologies, Inc. Beverly, MA, USA.
San 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.
Abstract
Background: 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.
Keywords
Functional genomics
Phages
Niche adaptation
Vibrio
Mobile elements
Genome evolution
Genotype-phenotype association
Random forest
 
DeCS
Bacteriófagos
Vibrio
Genômica
Genótipo
 
Publisher
Biomed Central
Citation
DUTILH, 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.
DOI
10.1186/1471-2164-15-654
ISSN
1471-2164