Accelerated exon evolution within primate segmental duplications

BACKGROUND: The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies an...

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Detalles Bibliográficos
Autores: Lorente-Galdós, Belén, 1981-, Bleyhl, Jonathan, Santpere Baró, Gabriel, 1981-, Vives, Laura, Ramírez, Oscar, Hernández Rodríguez, Jéssica, 1983-, Anglada Busquets, Roger, Cooper, Gregory M., Navarro i Cuartiellas, Arcadi, 1969-, Eichler, Evan E., Marquès i Bonet, Tomàs, 1975-
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:10230/25305
Acceso en línea:http://hdl.handle.net/10230/25305
http://dx.doi.org/10.1186/gb-2013-14-1-r9
Access Level:acceso abierto
Palabra clave:Evolució molecular
Genoma humà
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spelling Accelerated exon evolution within primate segmental duplicationsLorente-Galdós, Belén, 1981-Bleyhl, JonathanSantpere Baró, Gabriel, 1981-Vives, LauraRamírez, OscarHernández Rodríguez, Jéssica, 1983-Anglada Busquets, RogerCooper, Gregory M.Navarro i Cuartiellas, Arcadi, 1969-Eichler, Evan E.Marquès i Bonet, Tomàs, 1975-Evolució molecularGenoma humàBACKGROUND: The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodological reliance on accurate gene trees, which are difficult to obtain for duplicated genes. RESULTS: In this work, we detected exons with an accumulation of high-quality nucleotide differences between the human assembly and shotgun sequencing reads from single human and macaque individuals. Comparing the observed rates of nucleotide differences between coding exons and their flanking intronic sequences with a likelihood-ratio test, we identified 74 exons with evidence for rapid coding sequence evolution during the evolution of humans and Old World monkeys. Fifty-five percent of rapidly evolving exons were either partially or totally duplicated, which is a significant enrichment of the 6% rate observed across all human coding exons. CONCLUSIONS: Our results provide a more comprehensive view of the action of selection upon segmental duplications, which are the most complex regions of our genomes. In light of these findings, we suggest that segmental duplications could be subjected to rapid evolution more frequently than previously thought.The Spanish Government for grants BFU2009-13409-C02-02 to AN and BFU2011-28549 to TM-B. The European Community for an ERC Starting Grant (StG_20091118)) to TM-B.BioMed Central201520152013info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/25305http://dx.doi.org/10.1186/gb-2013-14-1-r9reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésGenome biology. 2013;14(1):R9info:eu-repo/grantAgreement/EC/FP7/20091118info:eu-repo/grantAgreement/ES/3PN/BFU2009-13409info:eu-repo/grantAgreement/ES/3PN/BFU2011-28549© 2013 Lorente-Galdos et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by/2.0info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/253052026-06-12T07:21:37Z
dc.title.none.fl_str_mv Accelerated exon evolution within primate segmental duplications
title Accelerated exon evolution within primate segmental duplications
spellingShingle Accelerated exon evolution within primate segmental duplications
Lorente-Galdós, Belén, 1981-
Evolució molecular
Genoma humà
title_short Accelerated exon evolution within primate segmental duplications
title_full Accelerated exon evolution within primate segmental duplications
title_fullStr Accelerated exon evolution within primate segmental duplications
title_full_unstemmed Accelerated exon evolution within primate segmental duplications
title_sort Accelerated exon evolution within primate segmental duplications
dc.creator.none.fl_str_mv Lorente-Galdós, Belén, 1981-
Bleyhl, Jonathan
Santpere Baró, Gabriel, 1981-
Vives, Laura
Ramírez, Oscar
Hernández Rodríguez, Jéssica, 1983-
Anglada Busquets, Roger
Cooper, Gregory M.
Navarro i Cuartiellas, Arcadi, 1969-
Eichler, Evan E.
Marquès i Bonet, Tomàs, 1975-
author Lorente-Galdós, Belén, 1981-
author_facet Lorente-Galdós, Belén, 1981-
Bleyhl, Jonathan
Santpere Baró, Gabriel, 1981-
Vives, Laura
Ramírez, Oscar
Hernández Rodríguez, Jéssica, 1983-
Anglada Busquets, Roger
Cooper, Gregory M.
Navarro i Cuartiellas, Arcadi, 1969-
Eichler, Evan E.
Marquès i Bonet, Tomàs, 1975-
author_role author
author2 Bleyhl, Jonathan
Santpere Baró, Gabriel, 1981-
Vives, Laura
Ramírez, Oscar
Hernández Rodríguez, Jéssica, 1983-
Anglada Busquets, Roger
Cooper, Gregory M.
Navarro i Cuartiellas, Arcadi, 1969-
Eichler, Evan E.
Marquès i Bonet, Tomàs, 1975-
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Evolució molecular
Genoma humà
topic Evolució molecular
Genoma humà
description BACKGROUND: The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodological reliance on accurate gene trees, which are difficult to obtain for duplicated genes. RESULTS: In this work, we detected exons with an accumulation of high-quality nucleotide differences between the human assembly and shotgun sequencing reads from single human and macaque individuals. Comparing the observed rates of nucleotide differences between coding exons and their flanking intronic sequences with a likelihood-ratio test, we identified 74 exons with evidence for rapid coding sequence evolution during the evolution of humans and Old World monkeys. Fifty-five percent of rapidly evolving exons were either partially or totally duplicated, which is a significant enrichment of the 6% rate observed across all human coding exons. CONCLUSIONS: Our results provide a more comprehensive view of the action of selection upon segmental duplications, which are the most complex regions of our genomes. In light of these findings, we suggest that segmental duplications could be subjected to rapid evolution more frequently than previously thought.
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/10230/25305
http://dx.doi.org/10.1186/gb-2013-14-1-r9
url http://hdl.handle.net/10230/25305
http://dx.doi.org/10.1186/gb-2013-14-1-r9
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Genome biology. 2013;14(1):R9
info:eu-repo/grantAgreement/EC/FP7/20091118
info:eu-repo/grantAgreement/ES/3PN/BFU2009-13409
info:eu-repo/grantAgreement/ES/3PN/BFU2011-28549
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/2.0
info:eu-repo/semantics/openAccess
rights_invalid_str_mv 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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