Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups

Detalhes bibliográficos
Autor(a) principal: De Almeida, Luciane M.
Data de Publicação: 2006
Outros Autores: Carareto, Claudia M. A.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1051/gse:2006020
http://hdl.handle.net/11449/38368
Resumo: Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5' LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. on the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families.
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spelling Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groupscopia retrotransposonnucleotide diversitycopia familiesAlthough the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5' LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. on the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families.Univ Estadual Paulista, Dept Biol, BR-15054000 Sao Jose do Rio Preto, SP, BrazilUniv Estadual Paulista, Dept Biol, BR-15054000 Sao Jose do Rio Preto, SP, BrazilEdp Sciences S AUniversidade Estadual Paulista (Unesp)De Almeida, Luciane M.Carareto, Claudia M. A.2014-05-20T15:28:35Z2014-05-20T15:28:35Z2006-09-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article535-550application/pdfhttp://dx.doi.org/10.1051/gse:2006020Genetics Selection Evolution. Les Ulis Cedex A: Edp Sciences S A, v. 38, n. 5, p. 535-550, 2006.0999-193Xhttp://hdl.handle.net/11449/3836810.1051/gse:2006020WOS:000240329300007WOS000240329300007.pdf34257729983192160000-0002-0298-1354Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGenetics Selection Evolution3.743info:eu-repo/semantics/openAccess2023-11-28T06:17:09Zoai:repositorio.unesp.br:11449/38368Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T18:58:35.131680Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups
title Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups
spellingShingle Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups
De Almeida, Luciane M.
copia retrotransposon
nucleotide diversity
copia families
title_short Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups
title_full Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups
title_fullStr Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups
title_full_unstemmed Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups
title_sort Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups
author De Almeida, Luciane M.
author_facet De Almeida, Luciane M.
Carareto, Claudia M. A.
author_role author
author2 Carareto, Claudia M. A.
author2_role author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
dc.contributor.author.fl_str_mv De Almeida, Luciane M.
Carareto, Claudia M. A.
dc.subject.por.fl_str_mv copia retrotransposon
nucleotide diversity
copia families
topic copia retrotransposon
nucleotide diversity
copia families
description Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5' LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. on the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families.
publishDate 2006
dc.date.none.fl_str_mv 2006-09-01
2014-05-20T15:28:35Z
2014-05-20T15:28:35Z
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/10.1051/gse:2006020
Genetics Selection Evolution. Les Ulis Cedex A: Edp Sciences S A, v. 38, n. 5, p. 535-550, 2006.
0999-193X
http://hdl.handle.net/11449/38368
10.1051/gse:2006020
WOS:000240329300007
WOS000240329300007.pdf
3425772998319216
0000-0002-0298-1354
url http://dx.doi.org/10.1051/gse:2006020
http://hdl.handle.net/11449/38368
identifier_str_mv Genetics Selection Evolution. Les Ulis Cedex A: Edp Sciences S A, v. 38, n. 5, p. 535-550, 2006.
0999-193X
10.1051/gse:2006020
WOS:000240329300007
WOS000240329300007.pdf
3425772998319216
0000-0002-0298-1354
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Genetics Selection Evolution
3.743
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 535-550
application/pdf
dc.publisher.none.fl_str_mv Edp Sciences S A
publisher.none.fl_str_mv Edp Sciences S A
dc.source.none.fl_str_mv Web of Science
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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