title: Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions.
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.
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.forename: Cristiane C
authors.initials: CC
authors.lastname: Thompson
authors.forename: Ana C P
authors.initials: AC
authors.lastname: Vicente
authors.forename: Michel A
authors.initials: MA
authors.lastname: Marin
authors.forename: Clarence
authors.initials: C
authors.lastname: Lee
authors.forename: Genivaldo G Z
authors.initials: GG
authors.lastname: Silva
authors.forename: Robert
authors.initials: R
authors.lastname: Schmieder
authors.forename: Bruno G N
authors.initials: BG
authors.lastname: Andrade
authors.forename: Luciane
authors.initials: L
authors.lastname: Chimetto
authors.forename: Daniel
authors.initials: D
authors.lastname: Cuevas
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Garza
authors.forename: Iruka N
authors.initials: IN
authors.lastname: Okeke
authors.forename: Aaron Oladipo
authors.initials: AO
authors.lastname: Aboderin
authors.forename: Jessica
authors.initials: J
authors.lastname: Spangler
authors.forename: Tristen
authors.initials: T
authors.lastname: Ross
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Dinsdale
authors.forename: Fabiano L
authors.initials: FL
authors.lastname: Thompson
authors.forename: Timothy T
authors.initials: TT
authors.lastname: Harkins
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA. redwards@sciences.sdsu.edu.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
mesh_terms: D002771:Cholera / Q000453:epidemiology / Q000382:microbiology; D004251:DNA Transposable Elements; D004783:Environmental Microbiology; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D014734:Vibrio cholerae / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D004251:DNA Transposable Elements
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