Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFRGS |
Texto Completo: | http://hdl.handle.net/10183/115040 |
Resumo: | Background: Galileo is one of three members of the P superfamily of DNA transposons. It was originally discovered in Drosophila buzzatii, in which three segregating chromosomal inversions were shown to have been generated by ectopic recombination between Galileo copies. Subsequently, Galileo was identified in six of 12 sequenced Drosophila genomes, indicating its widespread distribution within this genus. Galileo is strikingly abundant in Drosophila willistoni, a neotropical species that is highly polymorphic for chromosomal inversions, suggesting a role for this transposon in the evolution of its genome. Results: We carried out a detailed characterization of all Galileo copies present in the D. willistoni genome. A total of 191 copies, including 133 with two terminal inverted repeats (TIRs), were classified according to structure in six groups. The TIRs exhibited remarkable variation in their length and structure compared to the most complete copy. Three copies showed extended TIRs due to internal tandem repeats, the insertion of other transposable elements (TEs), or the incorporation of non-TIR sequences into the TIRs. Phylogenetic analyses of the transposase (TPase)-encoding and TIR segments yielded two divergent clades, which we termed Galileo subfamilies V and W. Target-site duplications (TSDs) in D. willistoni Galileo copies were 7- or 8-bp in length, with the consensus sequence GTATTAC. Analysis of the region around the TSDs revealed a target site motif (TSM) with a 15-bp palindrome that may give rise to a stem-loop secondary structure. Conclusions: There is a remarkable abundance and diversity of Galileo copies in the D. willistoni genome, although no functional copies were found. The TIRs in particular have a dynamic structure and extend in different ways, but their ends (required for transposition) are more conserved than the rest of the element. The D. willistoni genome harbors two Galileo subfamilies (V and W) that diverged ~9 million years ago and may have descended from an ancestral element in the genome. Galileo shows a significant insertion preference for a 15-bp palindromic TSM. |
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Gonçalves, Juliana WolmannValiati, Victor HugoDelprat, AlejandraGaiesky, Vera Lúcia da Silva ValenteRuiz, Alfredo2015-04-08T01:58:47Z2014http://hdl.handle.net/10183/115040000955033Background: Galileo is one of three members of the P superfamily of DNA transposons. It was originally discovered in Drosophila buzzatii, in which three segregating chromosomal inversions were shown to have been generated by ectopic recombination between Galileo copies. Subsequently, Galileo was identified in six of 12 sequenced Drosophila genomes, indicating its widespread distribution within this genus. Galileo is strikingly abundant in Drosophila willistoni, a neotropical species that is highly polymorphic for chromosomal inversions, suggesting a role for this transposon in the evolution of its genome. Results: We carried out a detailed characterization of all Galileo copies present in the D. willistoni genome. A total of 191 copies, including 133 with two terminal inverted repeats (TIRs), were classified according to structure in six groups. The TIRs exhibited remarkable variation in their length and structure compared to the most complete copy. Three copies showed extended TIRs due to internal tandem repeats, the insertion of other transposable elements (TEs), or the incorporation of non-TIR sequences into the TIRs. Phylogenetic analyses of the transposase (TPase)-encoding and TIR segments yielded two divergent clades, which we termed Galileo subfamilies V and W. Target-site duplications (TSDs) in D. willistoni Galileo copies were 7- or 8-bp in length, with the consensus sequence GTATTAC. Analysis of the region around the TSDs revealed a target site motif (TSM) with a 15-bp palindrome that may give rise to a stem-loop secondary structure. Conclusions: There is a remarkable abundance and diversity of Galileo copies in the D. willistoni genome, although no functional copies were found. The TIRs in particular have a dynamic structure and extend in different ways, but their ends (required for transposition) are more conserved than the rest of the element. The D. willistoni genome harbors two Galileo subfamilies (V and W) that diverged ~9 million years ago and may have descended from an ancestral element in the genome. Galileo shows a significant insertion preference for a 15-bp palindromic TSM.application/pdfengBMC Genomics. London. Vol. 15, (Sept. 2013), e792, 11 p.Drosophila willistoniGenomaTransposable elementD. willistoniTerminal inverted repeatsP superfamilyTarget site duplicationsStructural and sequence diversity of the transposon Galileo in the Drosophila willistoni genomeEstrangeiroinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRGSinstname:Universidade Federal do Rio Grande do Sul (UFRGS)instacron:UFRGSORIGINAL000955033.pdf000955033.pdfTexto completo (inglês)application/pdf1606142http://www.lume.ufrgs.br/bitstream/10183/115040/1/000955033.pdfe6dbb9c0fcc9aa70f77cd095eb81bd8fMD51TEXT000955033.pdf.txt000955033.pdf.txtExtracted Texttext/plain49909http://www.lume.ufrgs.br/bitstream/10183/115040/2/000955033.pdf.txt8a2ed339d72e784f120388252da70044MD52THUMBNAIL000955033.pdf.jpg000955033.pdf.jpgGenerated Thumbnailimage/jpeg1952http://www.lume.ufrgs.br/bitstream/10183/115040/3/000955033.pdf.jpg55a901fdd66e44628ef02dff991a38e9MD5310183/1150402023-07-06 03:54:05.13664oai:www.lume.ufrgs.br:10183/115040Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2023-07-06T06:54:05Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false |
dc.title.pt_BR.fl_str_mv |
Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome |
title |
Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome |
spellingShingle |
Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome Gonçalves, Juliana Wolmann Drosophila willistoni Genoma Transposable element D. willistoni Terminal inverted repeats P superfamily Target site duplications |
title_short |
Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome |
title_full |
Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome |
title_fullStr |
Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome |
title_full_unstemmed |
Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome |
title_sort |
Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome |
author |
Gonçalves, Juliana Wolmann |
author_facet |
Gonçalves, Juliana Wolmann Valiati, Victor Hugo Delprat, Alejandra Gaiesky, Vera Lúcia da Silva Valente Ruiz, Alfredo |
author_role |
author |
author2 |
Valiati, Victor Hugo Delprat, Alejandra Gaiesky, Vera Lúcia da Silva Valente Ruiz, Alfredo |
author2_role |
author author author author |
dc.contributor.author.fl_str_mv |
Gonçalves, Juliana Wolmann Valiati, Victor Hugo Delprat, Alejandra Gaiesky, Vera Lúcia da Silva Valente Ruiz, Alfredo |
dc.subject.por.fl_str_mv |
Drosophila willistoni Genoma |
topic |
Drosophila willistoni Genoma Transposable element D. willistoni Terminal inverted repeats P superfamily Target site duplications |
dc.subject.eng.fl_str_mv |
Transposable element D. willistoni Terminal inverted repeats P superfamily Target site duplications |
description |
Background: Galileo is one of three members of the P superfamily of DNA transposons. It was originally discovered in Drosophila buzzatii, in which three segregating chromosomal inversions were shown to have been generated by ectopic recombination between Galileo copies. Subsequently, Galileo was identified in six of 12 sequenced Drosophila genomes, indicating its widespread distribution within this genus. Galileo is strikingly abundant in Drosophila willistoni, a neotropical species that is highly polymorphic for chromosomal inversions, suggesting a role for this transposon in the evolution of its genome. Results: We carried out a detailed characterization of all Galileo copies present in the D. willistoni genome. A total of 191 copies, including 133 with two terminal inverted repeats (TIRs), were classified according to structure in six groups. The TIRs exhibited remarkable variation in their length and structure compared to the most complete copy. Three copies showed extended TIRs due to internal tandem repeats, the insertion of other transposable elements (TEs), or the incorporation of non-TIR sequences into the TIRs. Phylogenetic analyses of the transposase (TPase)-encoding and TIR segments yielded two divergent clades, which we termed Galileo subfamilies V and W. Target-site duplications (TSDs) in D. willistoni Galileo copies were 7- or 8-bp in length, with the consensus sequence GTATTAC. Analysis of the region around the TSDs revealed a target site motif (TSM) with a 15-bp palindrome that may give rise to a stem-loop secondary structure. Conclusions: There is a remarkable abundance and diversity of Galileo copies in the D. willistoni genome, although no functional copies were found. The TIRs in particular have a dynamic structure and extend in different ways, but their ends (required for transposition) are more conserved than the rest of the element. The D. willistoni genome harbors two Galileo subfamilies (V and W) that diverged ~9 million years ago and may have descended from an ancestral element in the genome. Galileo shows a significant insertion preference for a 15-bp palindromic TSM. |
publishDate |
2014 |
dc.date.issued.fl_str_mv |
2014 |
dc.date.accessioned.fl_str_mv |
2015-04-08T01:58:47Z |
dc.type.driver.fl_str_mv |
Estrangeiro info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
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publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10183/115040 |
dc.identifier.nrb.pt_BR.fl_str_mv |
000955033 |
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dc.language.iso.fl_str_mv |
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language |
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dc.relation.ispartof.pt_BR.fl_str_mv |
BMC Genomics. London. Vol. 15, (Sept. 2013), e792, 11 p. |
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openAccess |
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