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

dc.creatorDutilh, Bas E.
dc.creatorThompson, Cristiane C.
dc.creatorVicente, Ana C. P.
dc.creatorMarin, Michel A.
dc.creatorLee, Clarence
dc.creatorSchmieder, Robert
dc.creatorAndrade, Bruno G. N.
dc.creatorChimetto, Luciane
dc.creatorCuevas, Daniel
dc.creatorGarza, Daniel R.
dc.creatorOkeke, Iruka N.
dc.creatorAboderin, Aaron Oladipo
dc.creatorSpangler, Jessica
dc.creatorRoss, Tristen
dc.creatorDinsdale, Elizabeth A.
dc.creatorThompson, Fabiano L.
dc.creatorHarkins, Timothy T.
dc.creatorEdwards, Robert A.
dc.date2015-05-19T13:26:02Z
dc.date2015-05-19T13:26:02Z
dc.date2014
dc.date.accessioned2023-09-26T20:34:03Z
dc.date.available2023-09-26T20:34:03Z
dc.identifierDUTILH, 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.
dc.identifier1471-2164
dc.identifierhttps://www.arca.fiocruz.br/handle/icict/10390
dc.identifier10.1186/1471-2164-15-654
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/8859681
dc.descriptionBackground: 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.
dc.formatapplication/pdf
dc.languageeng
dc.publisherBiomed Central
dc.rightsopen access
dc.subjectFunctional genomics
dc.subjectPhages
dc.subjectNiche adaptation
dc.subjectVibrio
dc.subjectMobile elements
dc.subjectGenome evolution
dc.subjectGenotype-phenotype association
dc.subjectRandom forest
dc.subjectBacteriófagos
dc.subjectVibrio
dc.subjectGenômica
dc.subjectGenótipo
dc.titleComparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions
dc.typeArticle


Este ítem pertenece a la siguiente institución