{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T22:31:35Z","timestamp":1790807495847,"version":"4.1.0"},"reference-count":17,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2013,2,27]],"date-time":"2013-02-27T00:00:00Z","timestamp":1361923200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"\n \n Background:\n \n <\/ns4:bold>\n Vibrio<\/ns4:italic>\n \n cholerae<\/ns4:italic>\n , the etiologic agent of cholera, is indigenous to aquatic environments. The\n V. cholerae<\/ns4:italic>\n genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of\n V.<\/ns4:italic>\n \n cholerae<\/ns4:italic>\n diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of\n V. cholerae<\/ns4:italic>\n .\n <\/ns4:p>\n \n Methods:<\/ns4:bold>\n From the complete genomes of seven\n V.<\/ns4:italic>\n \n cholerae<\/ns4:italic>\n and one\n Vibrio mimicus<\/ns4:italic>\n representative strains,\n \n we recovered the SI sequences based on the locations of the structural gene\n IntI4<\/ns4:italic>\n and the\n V.<\/ns4:italic>\n \n cholerae<\/ns4:italic>\n \n repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR.\n <\/ns4:p>\n \n Results and conclusions:<\/ns4:bold>\n Here, we reveal the genetic architecture of the\n V. cholerae<\/ns4:italic>\n SI. It contains eight core genes when\n V. mimicus<\/ns4:italic>\n is included and 21 core genes when only\n V. cholerae<\/ns4:italic>\n strains are considered; many of them are present in several copies. The\n V. cholerae<\/ns4:italic>\n SI has an open pangenome, which means that\n V. cholerae<\/ns4:italic>\n may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.\n <\/ns4:p>","DOI":"10.12688\/f1000research.2-63.v1","type":"journal-article","created":{"date-parts":[[2013,5,9]],"date-time":"2013-05-09T12:08:38Z","timestamp":1368101318000},"page":"63","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes"],"prefix":"10.12688","volume":"2","author":[{"given":"Michel A","family":"Marin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Carolina P","family":"Vicente","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2013,2,27]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"e81","DOI":"10.1371\/journal.ppat.0030081","article-title":"Serogroup conversion of Vibrio cholerae in aquatic reservoirs.","volume":"3","author":"M Blokesch","year":"2007","journal-title":"PLoS Pathog."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"477-83","DOI":"10.1038\/35020000","article-title":"DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.","volume":"406","author":"J Heidelberg","year":"2000","journal-title":"Nature."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"608-20","DOI":"10.1038\/nrmicro1462","article-title":"Integrons: agents of bacterial evolution.","volume":"4","author":"D Mazel","year":"2006","journal-title":"Nat Rev Microbiol."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"641-51","DOI":"10.1016\/S0923-2508(99)00127-8","article-title":"Super-integrons.","volume":"150","author":"D Rowe-Magnus","year":"1999","journal-title":"Res Microbiol."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"141-66","DOI":"10.1146\/annurev-genet-102209-163504","article-title":"Integrons.","volume":"44","author":"G Cambray","year":"2010","journal-title":"Annu Rev Genet."},{"key":"ref-6","doi-asserted-by":"publisher","first-page":"397-411","DOI":"10.1111\/j.1365-2958.2006.05385.x","article-title":"Two higBA loci in the Vibrio cholerae superintegron encode mRNA cleaving enzymes and can stabilize plasmids.","volume":"62","author":"M Christensen-Dalsgaard","year":"2006","journal-title":"Mol Microbiol."},{"key":"ref-7","doi-asserted-by":"publisher","first-page":"589-94","DOI":"10.1016\/j.gde.2005.09.006","article-title":"The microbial pan-genome.","volume":"15","author":"D Medini","year":"2005","journal-title":"Curr Opin Genet Dev."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"e00335-10","DOI":"10.1128\/mBio.00335-10","article-title":"Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations.","volume":"2","author":"Y Boucher","year":"2011","journal-title":"MBio."},{"key":"ref-9","doi-asserted-by":"publisher","first-page":"1166-7","DOI":"10.1093\/bioinformatics\/bts091","article-title":"Unipro UGENE: a unified bioinformatics toolkit.","volume":"28","author":"K Okonechnikov","year":"2012","journal-title":"Bioinformatics."},{"key":"ref-10","doi-asserted-by":"publisher","first-page":"416-8","DOI":"10.1093\/bioinformatics\/btr655","article-title":"PGAP: pan-genomes analysis pipeline.","volume":"28","author":"Y Zhao","year":"2012","journal-title":"Bioinformatics."},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"254-67","DOI":"10.1093\/molbev\/msj030","article-title":"Application of phylogenetic networks in evolutionary studies.","volume":"23","author":"D Huson","year":"2006","journal-title":"Mol Biol Evol."},{"key":"ref-12","doi-asserted-by":"publisher","first-page":"2044-9","DOI":"10.1093\/bioinformatics\/bth198","article-title":"Phylogenetic trees based on gene content.","volume":"20","author":"D Huson","year":"2004","journal-title":"Bioinformatics."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"2334-5","DOI":"10.1093\/bioinformatics\/btq413","article-title":"genoPlotR: comparative gene and genome visualization in R.","volume":"26","author":"L Guy","year":"2010","journal-title":"Bioinformatics."},{"key":"ref-14","doi-asserted-by":"publisher","first-page":"966-76","DOI":"10.1093\/nar\/gki201","article-title":"Toxin-antitoxin loci are highly abundant in free-living 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.1158.r937, Thandavarayan Ramamurthy, National Institute of Cholera and Enteric Diseases, Kolkata, India, 09 May 2013, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/2-63\/v1#referee-response-937","order":0,"name":"referee-response-937","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.1158.r3764, Yan Boucher, Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada, 14 Mar 2014, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/2-63\/v1#referee-response-3764","order":1,"name":"referee-response-3764","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.1158.r4479, Nur Hasan, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA, 14 Apr 2014, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/2-63\/v1#referee-response-4479","order":2,"name":"referee-response-4479","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior (CAPES) doctoral fellowship to MAM.\nThe funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Data associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).","order":0,"name":"copyright-info","label":"Copyright"}]}}