Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Bas E Dutilh, Cristiane C Thompson, Ana CP Vicente, Michel A Marin, Clarence Lee, Genivaldo GZ Silva, Robert Schmieder, Bruno GN Andrade, Luciane Chimetto, Daniel Cuevas, Daniel R Garza, Iruka N Okeke (+7 others)
2014 BMC Genomics  
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
more » ... dy 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.
doi:10.1186/1471-2164-15-654 pmid:25096633 pmcid:PMC4141962 fatcat:h2dyysezhbgq3ji5z7wxrpdw2a