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Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting bot...

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Detalles Bibliográficos
Autores principales: Vanneste, Kevin, Baele, Guy, Maere, Steven, Van de Peer, Yves
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4120086/
https://www.ncbi.nlm.nih.gov/pubmed/24835588
http://dx.doi.org/10.1101/gr.168997.113
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author Vanneste, Kevin
Baele, Guy
Maere, Steven
Van de Peer, Yves
author_facet Vanneste, Kevin
Baele, Guy
Maere, Steven
Van de Peer, Yves
author_sort Vanneste, Kevin
collection PubMed
description Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous–Paleogene (K–Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K–Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids.
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spelling pubmed-41200862014-08-05 Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary Vanneste, Kevin Baele, Guy Maere, Steven Van de Peer, Yves Genome Res Research Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous–Paleogene (K–Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K–Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids. Cold Spring Harbor Laboratory Press 2014-08 /pmc/articles/PMC4120086/ /pubmed/24835588 http://dx.doi.org/10.1101/gr.168997.113 Text en © 2014 Vanneste et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0.
spellingShingle Research
Vanneste, Kevin
Baele, Guy
Maere, Steven
Van de Peer, Yves
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
title Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
title_full Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
title_fullStr Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
title_full_unstemmed Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
title_short Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
title_sort analysis of 41 plant genomes supports a wave of successful genome duplications in association with the cretaceous–paleogene boundary
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4120086/
https://www.ncbi.nlm.nih.gov/pubmed/24835588
http://dx.doi.org/10.1101/gr.168997.113
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