Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciata
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3390/genes9060269 http://hdl.handle.net/11449/179914 |
Resumo: | B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B-and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome. |
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Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciataCytogeneticsEvolutionExtra chromosomesGenomicsRepetitive elementsRNA-SeqSupernumerary elementsB chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B-and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Department of Morphology Institute of Biosciences São Paulo State University (UNESP)Department of Morphology Institute of Biosciences São Paulo State University (UNESP)CNPq: 134446/2014-3FAPESP: 2013/04533-3FAPESP: 2014/16763-6FAPESP: 2015/16661-1CNPq: 305321/2015-3Universidade Estadual Paulista (Unesp)Coan, Rafael L. B. [UNESP]Martins, Cesar [UNESP]2018-12-11T17:37:16Z2018-12-11T17:37:16Z2018-06-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.3390/genes9060269Genes, v. 9, n. 6, 2018.2073-4425http://hdl.handle.net/11449/17991410.3390/genes90602692-s2.0-850479216842-s2.0-85047921684.pdf88588006994253520000-0003-3534-974XScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGenes1,820info:eu-repo/semantics/openAccess2023-11-06T06:14:59Zoai:repositorio.unesp.br:11449/179914Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:03:26.511533Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciata |
title |
Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciata |
spellingShingle |
Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciata Coan, Rafael L. B. [UNESP] Cytogenetics Evolution Extra chromosomes Genomics Repetitive elements RNA-Seq Supernumerary elements |
title_short |
Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciata |
title_full |
Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciata |
title_fullStr |
Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciata |
title_full_unstemmed |
Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciata |
title_sort |
Landscape of transposable elements focusing on the B chromosome of the cichlid fish astatotilapia latifasciata |
author |
Coan, Rafael L. B. [UNESP] |
author_facet |
Coan, Rafael L. B. [UNESP] Martins, Cesar [UNESP] |
author_role |
author |
author2 |
Martins, Cesar [UNESP] |
author2_role |
author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Coan, Rafael L. B. [UNESP] Martins, Cesar [UNESP] |
dc.subject.por.fl_str_mv |
Cytogenetics Evolution Extra chromosomes Genomics Repetitive elements RNA-Seq Supernumerary elements |
topic |
Cytogenetics Evolution Extra chromosomes Genomics Repetitive elements RNA-Seq Supernumerary elements |
description |
B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B-and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-12-11T17:37:16Z 2018-12-11T17:37:16Z 2018-06-01 |
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.uri.fl_str_mv |
http://dx.doi.org/10.3390/genes9060269 Genes, v. 9, n. 6, 2018. 2073-4425 http://hdl.handle.net/11449/179914 10.3390/genes9060269 2-s2.0-85047921684 2-s2.0-85047921684.pdf 8858800699425352 0000-0003-3534-974X |
url |
http://dx.doi.org/10.3390/genes9060269 http://hdl.handle.net/11449/179914 |
identifier_str_mv |
Genes, v. 9, n. 6, 2018. 2073-4425 10.3390/genes9060269 2-s2.0-85047921684 2-s2.0-85047921684.pdf 8858800699425352 0000-0003-3534-974X |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Genes 1,820 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
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 |
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1808128747613716480 |