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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...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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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 |
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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 |
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