A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , |
Tipo de documento: | Capítulo de livro |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1007/978-1-4939-7463-4_7 http://hdl.handle.net/11449/175708 |
Resumo: | Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing. Here, we present a practical guide to explore, compare, and visualize prokaryote MGEs using a combination of available software and databases tailored to small scale genome analyses. This protocol can be coupled with expert MGE annotation and exploited for evolutionary and comparative genomic analyses. |
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A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomesClustered regularly interspaced short palindromic repeatsEvolutionGenomic islandsGenomicsInsertion sequencesIntegrative conjugative elementsIntegronsProphagesTransposonsMobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing. Here, we present a practical guide to explore, compare, and visualize prokaryote MGEs using a combination of available software and databases tailored to small scale genome analyses. This protocol can be coupled with expert MGE annotation and exploited for evolutionary and comparative genomic analyses.Departamento de Tecnologia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista “Júlio de Mesquita Filho”–UNESPDepartamento de Ciências Biológicas–Núcleo de Pesquisas em Ciências Biológicas-NUPEB Universidade Federal de Ouro PretoLaboratoire de Microbiologie et Génétique Moléculaires, CNRS 118, Route de NarbonneDepartamento de Tecnologia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista “Júlio de Mesquita Filho”–UNESPUniversidade Estadual Paulista (Unesp)Universidade Federal de Ouro PretoLaboratoire de Microbiologie et Génétique MoléculairesOliveira Alvarenga, Danillo [UNESP]Moreira, Leandro M.Chandler, MickVarani, Alessandro M. [UNESP]2018-12-11T17:17:10Z2018-12-11T17:17:10Z2018-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/bookPart213-242application/pdfhttp://dx.doi.org/10.1007/978-1-4939-7463-4_7Methods in Molecular Biology, v. 1704, p. 213-242.1064-3745http://hdl.handle.net/11449/17570810.1007/978-1-4939-7463-4_72-s2.0-850398707502-s2.0-85039870750.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMethods in Molecular Biology0,616info:eu-repo/semantics/openAccess2024-01-01T06:21:49Zoai:repositorio.unesp.br:11449/175708Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-01-01T06:21:49Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes |
title |
A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes |
spellingShingle |
A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes Oliveira Alvarenga, Danillo [UNESP] Clustered regularly interspaced short palindromic repeats Evolution Genomic islands Genomics Insertion sequences Integrative conjugative elements Integrons Prophages Transposons |
title_short |
A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes |
title_full |
A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes |
title_fullStr |
A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes |
title_full_unstemmed |
A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes |
title_sort |
A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes |
author |
Oliveira Alvarenga, Danillo [UNESP] |
author_facet |
Oliveira Alvarenga, Danillo [UNESP] Moreira, Leandro M. Chandler, Mick Varani, Alessandro M. [UNESP] |
author_role |
author |
author2 |
Moreira, Leandro M. Chandler, Mick Varani, Alessandro M. [UNESP] |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Universidade Federal de Ouro Preto Laboratoire de Microbiologie et Génétique Moléculaires |
dc.contributor.author.fl_str_mv |
Oliveira Alvarenga, Danillo [UNESP] Moreira, Leandro M. Chandler, Mick Varani, Alessandro M. [UNESP] |
dc.subject.por.fl_str_mv |
Clustered regularly interspaced short palindromic repeats Evolution Genomic islands Genomics Insertion sequences Integrative conjugative elements Integrons Prophages Transposons |
topic |
Clustered regularly interspaced short palindromic repeats Evolution Genomic islands Genomics Insertion sequences Integrative conjugative elements Integrons Prophages Transposons |
description |
Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing. Here, we present a practical guide to explore, compare, and visualize prokaryote MGEs using a combination of available software and databases tailored to small scale genome analyses. This protocol can be coupled with expert MGE annotation and exploited for evolutionary and comparative genomic analyses. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-12-11T17:17:10Z 2018-12-11T17:17:10Z 2018-01-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/bookPart |
format |
bookPart |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1007/978-1-4939-7463-4_7 Methods in Molecular Biology, v. 1704, p. 213-242. 1064-3745 http://hdl.handle.net/11449/175708 10.1007/978-1-4939-7463-4_7 2-s2.0-85039870750 2-s2.0-85039870750.pdf |
url |
http://dx.doi.org/10.1007/978-1-4939-7463-4_7 http://hdl.handle.net/11449/175708 |
identifier_str_mv |
Methods in Molecular Biology, v. 1704, p. 213-242. 1064-3745 10.1007/978-1-4939-7463-4_7 2-s2.0-85039870750 2-s2.0-85039870750.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Methods in Molecular Biology 0,616 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
213-242 application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1799965481038249984 |