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The gain and loss of genes during 600 million years of vertebrate evolution

BACKGROUND: Gene duplication is assumed to have played a crucial role in the evolution of vertebrate organisms. Apart from a continuous mode of duplication, two or three whole genome duplication events have been proposed during the evolution of vertebrates, one or two at the dawn of vertebrate evolu...

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Autores principales: Blomme, Tine, Vandepoele, Klaas, De Bodt, Stefanie, Simillion, Cedric, Maere, Steven, Van de Peer, Yves
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779523/
https://www.ncbi.nlm.nih.gov/pubmed/16723033
http://dx.doi.org/10.1186/gb-2006-7-5-r43
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author Blomme, Tine
Vandepoele, Klaas
De Bodt, Stefanie
Simillion, Cedric
Maere, Steven
Van de Peer, Yves
author_facet Blomme, Tine
Vandepoele, Klaas
De Bodt, Stefanie
Simillion, Cedric
Maere, Steven
Van de Peer, Yves
author_sort Blomme, Tine
collection PubMed
description BACKGROUND: Gene duplication is assumed to have played a crucial role in the evolution of vertebrate organisms. Apart from a continuous mode of duplication, two or three whole genome duplication events have been proposed during the evolution of vertebrates, one or two at the dawn of vertebrate evolution, and an additional one in the fish lineage, not shared with land vertebrates. Here, we have studied gene gain and loss in seven different vertebrate genomes, spanning an evolutionary period of about 600 million years. RESULTS: We show that: first, the majority of duplicated genes in extant vertebrate genomes are ancient and were created at times that coincide with proposed whole genome duplication events; second, there exist significant differences in gene retention for different functional categories of genes between fishes and land vertebrates; third, there seems to be a considerable bias in gene retention of regulatory genes towards the mode of gene duplication (whole genome duplication events compared to smaller-scale events), which is in accordance with the so-called gene balance hypothesis; and fourth, that ancient duplicates that have survived for many hundreds of millions of years can still be lost. CONCLUSION: Based on phylogenetic analyses, we show that both the mode of duplication and the functional class the duplicated genes belong to have been of major importance for the evolution of the vertebrates. In particular, we provide evidence that massive gene duplication (probably as a consequence of entire genome duplications) at the dawn of vertebrate evolution might have been particularly important for the evolution of complex vertebrates.
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spelling pubmed-17795232007-01-19 The gain and loss of genes during 600 million years of vertebrate evolution Blomme, Tine Vandepoele, Klaas De Bodt, Stefanie Simillion, Cedric Maere, Steven Van de Peer, Yves Genome Biol Research BACKGROUND: Gene duplication is assumed to have played a crucial role in the evolution of vertebrate organisms. Apart from a continuous mode of duplication, two or three whole genome duplication events have been proposed during the evolution of vertebrates, one or two at the dawn of vertebrate evolution, and an additional one in the fish lineage, not shared with land vertebrates. Here, we have studied gene gain and loss in seven different vertebrate genomes, spanning an evolutionary period of about 600 million years. RESULTS: We show that: first, the majority of duplicated genes in extant vertebrate genomes are ancient and were created at times that coincide with proposed whole genome duplication events; second, there exist significant differences in gene retention for different functional categories of genes between fishes and land vertebrates; third, there seems to be a considerable bias in gene retention of regulatory genes towards the mode of gene duplication (whole genome duplication events compared to smaller-scale events), which is in accordance with the so-called gene balance hypothesis; and fourth, that ancient duplicates that have survived for many hundreds of millions of years can still be lost. CONCLUSION: Based on phylogenetic analyses, we show that both the mode of duplication and the functional class the duplicated genes belong to have been of major importance for the evolution of the vertebrates. In particular, we provide evidence that massive gene duplication (probably as a consequence of entire genome duplications) at the dawn of vertebrate evolution might have been particularly important for the evolution of complex vertebrates. BioMed Central 2006 2006-05-24 /pmc/articles/PMC1779523/ /pubmed/16723033 http://dx.doi.org/10.1186/gb-2006-7-5-r43 Text en Copyright © 2006 Blomme 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
Blomme, Tine
Vandepoele, Klaas
De Bodt, Stefanie
Simillion, Cedric
Maere, Steven
Van de Peer, Yves
The gain and loss of genes during 600 million years of vertebrate evolution
title The gain and loss of genes during 600 million years of vertebrate evolution
title_full The gain and loss of genes during 600 million years of vertebrate evolution
title_fullStr The gain and loss of genes during 600 million years of vertebrate evolution
title_full_unstemmed The gain and loss of genes during 600 million years of vertebrate evolution
title_short The gain and loss of genes during 600 million years of vertebrate evolution
title_sort gain and loss of genes during 600 million years of vertebrate evolution
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779523/
https://www.ncbi.nlm.nih.gov/pubmed/16723033
http://dx.doi.org/10.1186/gb-2006-7-5-r43
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