Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina

Background: Transposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications (e.g., in evolution) and applications (e.g., as transgenic tools). They also represent a major challenge for the assembly and annotation of genomic sequences. However, they are stil...

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Detalles Bibliográficos
Autores: Negre de Bofarull, Bárbara, Simpson, Pat
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2013
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/23322
Acceso en línea:http://hdl.handle.net/10230/23322
http://dx.doi.org/10.1186/1759-8753-4-13
Access Level:acceso abierto
Palabra clave:Genètica evolutiva
Calliphora vicina
Diptera
Helitrons
Horizontal transfer
Repeats
Retrotransposons
Transposable elements
Transposons
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oai_identifier_str oai:repositori.upf.edu:10230/23322
network_acronym_str ES
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repository_id_str
spelling Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicinaNegre de Bofarull, BárbaraSimpson, PatGenètica evolutivaCalliphora vicinaDipteraHelitronsHorizontal transferRepeatsRetrotransposonsTransposable elementsTransposonsBackground: Transposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications (e.g., in evolution) and applications (e.g., as transgenic tools). They also represent a major challenge for the assembly and annotation of genomic sequences. However, they are still largely unknown in non-model species. Results: Here, we have annotated the repeats and transposable elements present in a 600 kb genomic region of the blowfly Calliphora vicina (Diptera: Calliphoridae) which contains most of the achaete-scute gene complex of this species. This is the largest genomic region to be sequenced and analyzed in higher flies outside the Drosophila genus. We find that the repeat content spans at least 24% of the sequence. It includes 318 insertions classified as 3 LTR retrotransposons, 21 LINEs, 14 cut-and-paste DNA transposons, 4 helitrons and 33 unclassified repeats. Conclusions: This is the most detailed description of TEs and repeats in the Calliphoridae to date. This contribution not only adds to our knowledge about TE evolution but will also help in the annotation of repeats on Dipteran whole genome sequences.This work was supported by the Wellcome Trust grant 29156BioMed Central201520152013info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/23322http://dx.doi.org/10.1186/1759-8753-4-13reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésMobille DNA. 2013; 4: 13© 2013 Negre and Simpson; licensee BioMed Central Ltd.http://creativecommons.org/licenses/by/2.0info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/233222026-06-12T07:21:37Z
dc.title.none.fl_str_mv Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
title Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
spellingShingle Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
Negre de Bofarull, Bárbara
Genètica evolutiva
Calliphora vicina
Diptera
Helitrons
Horizontal transfer
Repeats
Retrotransposons
Transposable elements
Transposons
title_short Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
title_full Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
title_fullStr Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
title_full_unstemmed Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
title_sort Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
dc.creator.none.fl_str_mv Negre de Bofarull, Bárbara
Simpson, Pat
author Negre de Bofarull, Bárbara
author_facet Negre de Bofarull, Bárbara
Simpson, Pat
author_role author
author2 Simpson, Pat
author2_role author
dc.subject.none.fl_str_mv Genètica evolutiva
Calliphora vicina
Diptera
Helitrons
Horizontal transfer
Repeats
Retrotransposons
Transposable elements
Transposons
topic Genètica evolutiva
Calliphora vicina
Diptera
Helitrons
Horizontal transfer
Repeats
Retrotransposons
Transposable elements
Transposons
description Background: Transposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications (e.g., in evolution) and applications (e.g., as transgenic tools). They also represent a major challenge for the assembly and annotation of genomic sequences. However, they are still largely unknown in non-model species. Results: Here, we have annotated the repeats and transposable elements present in a 600 kb genomic region of the blowfly Calliphora vicina (Diptera: Calliphoridae) which contains most of the achaete-scute gene complex of this species. This is the largest genomic region to be sequenced and analyzed in higher flies outside the Drosophila genus. We find that the repeat content spans at least 24% of the sequence. It includes 318 insertions classified as 3 LTR retrotransposons, 21 LINEs, 14 cut-and-paste DNA transposons, 4 helitrons and 33 unclassified repeats. Conclusions: This is the most detailed description of TEs and repeats in the Calliphoridae to date. This contribution not only adds to our knowledge about TE evolution but will also help in the annotation of repeats on Dipteran whole genome sequences.
publishDate 2013
dc.date.none.fl_str_mv 2013
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/23322
http://dx.doi.org/10.1186/1759-8753-4-13
url http://hdl.handle.net/10230/23322
http://dx.doi.org/10.1186/1759-8753-4-13
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Mobille DNA. 2013; 4: 13
dc.rights.none.fl_str_mv © 2013 Negre and Simpson; licensee BioMed Central Ltd.
http://creativecommons.org/licenses/by/2.0
info:eu-repo/semantics/openAccess
rights_invalid_str_mv © 2013 Negre and Simpson; licensee BioMed Central Ltd.
http://creativecommons.org/licenses/by/2.0
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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