Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes

Bibliographic Details
Main Author: Schneider, Carlos Henrique
Publication Date: 2013
Other Authors: Gross, Maria Claudia, Terêncio, Maria Leandra, Carmo, Edson Júnior do, Martins, Cesar Henrique Rossinoli, Feldberg, Eliana
Format: Article
Language: eng
Source: Repositório Institucional do INPA
Download full: https://repositorio.inpa.gov.br/handle/1/16051
Summary: Background: Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Results: Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Conclusion: Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins. © 2013 Schneider et al.; licensee BioMed Central Ltd.
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spelling Schneider, Carlos HenriqueGross, Maria ClaudiaTerêncio, Maria LeandraCarmo, Edson Júnior doMartins, Cesar Henrique RossinoliFeldberg, Eliana2020-05-22T20:04:33Z2020-05-22T20:04:33Z2013https://repositorio.inpa.gov.br/handle/1/1605110.1186/1471-2148-13-152Background: Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Results: Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Conclusion: Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins. © 2013 Schneider et al.; licensee BioMed Central Ltd.Volume 13, Número 1Attribution-NonCommercial-NoDerivs 3.0 Brazilhttp://creativecommons.org/licenses/by-nc-nd/3.0/br/info:eu-repo/semantics/openAccessBayesian AnalysisChromosomeCichlidGenomeDna, MitochondrialNeotropic EcozoneCichlidaeAmino Acid SequenceAnimalsChromosomeChromosome MapCichlidClassificationGeneticsGenomeGenomicsEvolution, MolecularMolecular GeneticsNucleotide SequencePhylogenyRetroposonAmino Acid SequenceAnimalBase SequenceChromosome MappingChromosomesCichlidsEvolution, MolecularGenomeGenomicsMolecular Sequence DataPhylogenyRetroelementsEvolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleBMC Evolutionary Biologyengreponame:Repositório Institucional do INPAinstname:Instituto Nacional de Pesquisas da Amazônia (INPA)instacron:INPAORIGINALartigo-inpa.pdfartigo-inpa.pdfapplication/pdf2449595https://repositorio.inpa.gov.br/bitstream/1/16051/1/artigo-inpa.pdfb6caed373018f54fe907fe8dab26c47eMD511/160512020-05-22 17:02:33.038oai:repositorio:1/16051Repositório de PublicaçõesPUBhttps://repositorio.inpa.gov.br/oai/requestopendoar:2020-05-22T21:02:33Repositório Institucional do INPA - Instituto Nacional de Pesquisas da Amazônia (INPA)false
dc.title.en.fl_str_mv Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes
title Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes
spellingShingle Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes
Schneider, Carlos Henrique
Bayesian Analysis
Chromosome
Cichlid
Genome
Dna, Mitochondrial
Neotropic Ecozone
Cichlidae
Amino Acid Sequence
Animals
Chromosome
Chromosome Map
Cichlid
Classification
Genetics
Genome
Genomics
Evolution, Molecular
Molecular Genetics
Nucleotide Sequence
Phylogeny
Retroposon
Amino Acid Sequence
Animal
Base Sequence
Chromosome Mapping
Chromosomes
Cichlids
Evolution, Molecular
Genome
Genomics
Molecular Sequence Data
Phylogeny
Retroelements
title_short Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes
title_full Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes
title_fullStr Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes
title_full_unstemmed Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes
title_sort Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes
author Schneider, Carlos Henrique
author_facet Schneider, Carlos Henrique
Gross, Maria Claudia
Terêncio, Maria Leandra
Carmo, Edson Júnior do
Martins, Cesar Henrique Rossinoli
Feldberg, Eliana
author_role author
author2 Gross, Maria Claudia
Terêncio, Maria Leandra
Carmo, Edson Júnior do
Martins, Cesar Henrique Rossinoli
Feldberg, Eliana
author2_role author
author
author
author
author
dc.contributor.author.fl_str_mv Schneider, Carlos Henrique
Gross, Maria Claudia
Terêncio, Maria Leandra
Carmo, Edson Júnior do
Martins, Cesar Henrique Rossinoli
Feldberg, Eliana
dc.subject.eng.fl_str_mv Bayesian Analysis
Chromosome
Cichlid
Genome
Dna, Mitochondrial
Neotropic Ecozone
Cichlidae
Amino Acid Sequence
Animals
Chromosome
Chromosome Map
Cichlid
Classification
Genetics
Genome
Genomics
Evolution, Molecular
Molecular Genetics
Nucleotide Sequence
Phylogeny
Retroposon
Amino Acid Sequence
Animal
Base Sequence
Chromosome Mapping
Chromosomes
Cichlids
Evolution, Molecular
Genome
Genomics
Molecular Sequence Data
Phylogeny
Retroelements
topic Bayesian Analysis
Chromosome
Cichlid
Genome
Dna, Mitochondrial
Neotropic Ecozone
Cichlidae
Amino Acid Sequence
Animals
Chromosome
Chromosome Map
Cichlid
Classification
Genetics
Genome
Genomics
Evolution, Molecular
Molecular Genetics
Nucleotide Sequence
Phylogeny
Retroposon
Amino Acid Sequence
Animal
Base Sequence
Chromosome Mapping
Chromosomes
Cichlids
Evolution, Molecular
Genome
Genomics
Molecular Sequence Data
Phylogeny
Retroelements
description Background: Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Results: Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Conclusion: Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins. © 2013 Schneider et al.; licensee BioMed Central Ltd.
publishDate 2013
dc.date.issued.fl_str_mv 2013
dc.date.accessioned.fl_str_mv 2020-05-22T20:04:33Z
dc.date.available.fl_str_mv 2020-05-22T20:04:33Z
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 https://repositorio.inpa.gov.br/handle/1/16051
dc.identifier.doi.none.fl_str_mv 10.1186/1471-2148-13-152
url https://repositorio.inpa.gov.br/handle/1/16051
identifier_str_mv 10.1186/1471-2148-13-152
dc.language.iso.fl_str_mv eng
language eng
dc.relation.ispartof.pt_BR.fl_str_mv Volume 13, Número 1
dc.rights.driver.fl_str_mv Attribution-NonCommercial-NoDerivs 3.0 Brazil
http://creativecommons.org/licenses/by-nc-nd/3.0/br/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Attribution-NonCommercial-NoDerivs 3.0 Brazil
http://creativecommons.org/licenses/by-nc-nd/3.0/br/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BMC Evolutionary Biology
publisher.none.fl_str_mv BMC Evolutionary Biology
dc.source.none.fl_str_mv reponame:Repositório Institucional do INPA
instname:Instituto Nacional de Pesquisas da Amazônia (INPA)
instacron:INPA
instname_str Instituto Nacional de Pesquisas da Amazônia (INPA)
instacron_str INPA
institution INPA
reponame_str Repositório Institucional do INPA
collection Repositório Institucional do INPA
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