Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes

Detalhes bibliográficos
Autor(a) principal: Marin, Michel A.
Data de Publicação: 2013
Outros Autores: Vicente, Ana Carolina P.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/12548
Resumo: Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microorganismos. Rio de Janeiro, RJ, Brasil.
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spelling Marin, Michel A.Vicente, Ana Carolina P.2016-01-18T16:39:32Z2016-01-18T16:39:32Z2013MARIN, Miche al; VICENTE, Ana Carolina P. Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes. F1000Res. v.2, n.63, Feb. 2013.2046-1402https://www.arca.fiocruz.br/handle/icict/1254810.12688/f1000research.2-63.v1engF1000ResearchArchitecture of the superintegron in Vibrio cholerae: identification of core and unique genesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microorganismos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microorganismos. Rio de Janeiro, RJ, Brasil.Background: Vibrio cholerae, the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae 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 V. cholerae 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 V. cholerae. Methods: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae 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. Results and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae 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.Vibrio choleraeCholeraV. mimicus genomesColeraVibrio choleraeGenomainfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/12548/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALmichelmarin_anavicente_IOC-2013.pdfmichelmarin_anavicente_IOC-2013.pdfapplication/pdf1323943https://www.arca.fiocruz.br/bitstream/icict/12548/2/michelmarin_anavicente_IOC-2013.pdf0903cb48cad6b6df5b1d26f24b9517c1MD52TEXTmichelmarin_anavicente_IOC-2013.pdf.txtmichelmarin_anavicente_IOC-2013.pdf.txtExtracted texttext/plain30901https://www.arca.fiocruz.br/bitstream/icict/12548/3/michelmarin_anavicente_IOC-2013.pdf.txt09a05210fa69d25bdd270281667c7004MD53icict/125482023-09-05 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dc.title.pt_BR.fl_str_mv Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
title Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
spellingShingle Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
Marin, Michel A.
Vibrio cholerae
Cholera
V. mimicus genomes
Colera
Vibrio cholerae
Genoma
title_short Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
title_full Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
title_fullStr Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
title_full_unstemmed Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
title_sort Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
author Marin, Michel A.
author_facet Marin, Michel A.
Vicente, Ana Carolina P.
author_role author
author2 Vicente, Ana Carolina P.
author2_role author
dc.contributor.author.fl_str_mv Marin, Michel A.
Vicente, Ana Carolina P.
dc.subject.en.pt_BR.fl_str_mv Vibrio cholerae
Cholera
V. mimicus genomes
topic Vibrio cholerae
Cholera
V. mimicus genomes
Colera
Vibrio cholerae
Genoma
dc.subject.decs.pt_BR.fl_str_mv Colera
Vibrio cholerae
Genoma
description Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microorganismos. Rio de Janeiro, RJ, Brasil.
publishDate 2013
dc.date.issued.fl_str_mv 2013
dc.date.accessioned.fl_str_mv 2016-01-18T16:39:32Z
dc.date.available.fl_str_mv 2016-01-18T16:39:32Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv MARIN, Miche al; VICENTE, Ana Carolina P. Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes. F1000Res. v.2, n.63, Feb. 2013.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/12548
dc.identifier.issn.none.fl_str_mv 2046-1402
dc.identifier.doi.none.fl_str_mv 10.12688/f1000research.2-63.v1
identifier_str_mv MARIN, Miche al; VICENTE, Ana Carolina P. Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes. F1000Res. v.2, n.63, Feb. 2013.
2046-1402
10.12688/f1000research.2-63.v1
url https://www.arca.fiocruz.br/handle/icict/12548
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv F1000Research
publisher.none.fl_str_mv F1000Research
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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