Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Lorente-Galdos, Belen, Bleyhl, Jonathan, Santpere, Gabriel, Vives, Laura, Ramírez, Oscar, Hernandez, Jessica, Anglada, Roger, Cooper, Gregory M, Navarro, Arcadi, Eichler, Evan E, Marques-Bonet, Tomas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906575/
https://www.ncbi.nlm.nih.gov/pubmed/23360670
http://dx.doi.org/10.1186/gb-2013-14-1-r9
_version_ 1782301495616602112
author Lorente-Galdos, Belen
Bleyhl, Jonathan
Santpere, Gabriel
Vives, Laura
Ramírez, Oscar
Hernandez, Jessica
Anglada, Roger
Cooper, Gregory M
Navarro, Arcadi
Eichler, Evan E
Marques-Bonet, Tomas
author_facet Lorente-Galdos, Belen
Bleyhl, Jonathan
Santpere, Gabriel
Vives, Laura
Ramírez, Oscar
Hernandez, Jessica
Anglada, Roger
Cooper, Gregory M
Navarro, Arcadi
Eichler, Evan E
Marques-Bonet, Tomas
author_sort Lorente-Galdos, Belen
collection PubMed
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.
format Online
Article
Text
id pubmed-3906575
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-39065752014-02-11 Accelerated exon evolution within primate segmental duplications Lorente-Galdos, Belen Bleyhl, Jonathan Santpere, Gabriel Vives, Laura Ramírez, Oscar Hernandez, Jessica Anglada, Roger Cooper, Gregory M Navarro, Arcadi Eichler, Evan E Marques-Bonet, Tomas Genome Biol Research 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. BioMed Central 2013 2013-01-29 /pmc/articles/PMC3906575/ /pubmed/23360670 http://dx.doi.org/10.1186/gb-2013-14-1-r9 Text en Copyright © 2013 Lorente-Galdos et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Research
Lorente-Galdos, Belen
Bleyhl, Jonathan
Santpere, Gabriel
Vives, Laura
Ramírez, Oscar
Hernandez, Jessica
Anglada, Roger
Cooper, Gregory M
Navarro, Arcadi
Eichler, Evan E
Marques-Bonet, Tomas
Accelerated exon evolution within primate segmental duplications
title 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_short Accelerated exon evolution within primate segmental duplications
title_sort accelerated exon evolution within primate segmental duplications
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906575/
https://www.ncbi.nlm.nih.gov/pubmed/23360670
http://dx.doi.org/10.1186/gb-2013-14-1-r9
work_keys_str_mv AT lorentegaldosbelen acceleratedexonevolutionwithinprimatesegmentalduplications
AT bleyhljonathan acceleratedexonevolutionwithinprimatesegmentalduplications
AT santperegabriel acceleratedexonevolutionwithinprimatesegmentalduplications
AT viveslaura acceleratedexonevolutionwithinprimatesegmentalduplications
AT ramirezoscar acceleratedexonevolutionwithinprimatesegmentalduplications
AT hernandezjessica acceleratedexonevolutionwithinprimatesegmentalduplications
AT angladaroger acceleratedexonevolutionwithinprimatesegmentalduplications
AT coopergregorym acceleratedexonevolutionwithinprimatesegmentalduplications
AT navarroarcadi acceleratedexonevolutionwithinprimatesegmentalduplications
AT eichlerevane acceleratedexonevolutionwithinprimatesegmentalduplications
AT marquesbonettomas acceleratedexonevolutionwithinprimatesegmentalduplications