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

Kevin Vanneste (UGent) , Guy Baele (UGent) , Steven Maere (UGent) and Yves Van de Peer (UGent)
(2014) GENOME RESEARCH. 24(8). p.1334-1347
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
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.
Keywords
FOSSIL CALIBRATIONS, BAYESIAN-ESTIMATION, ARABIDOPSIS-THALIANA, STATISTICAL PHYLOGENETICS, MASS EXTINCTION, FLOWERING PLANTS, MOLECULAR EVOLUTION, RELAXED-CLOCK METHODS, ESTIMATING DIVERGENCE TIMES, GREEN RIVER FORMATION

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Citation

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Chicago
Vanneste, Kevin, Guy Baele, Steven Maere, and Yves Van de Peer. 2014. “Analysis of 41 Plant Genomes Supports a Wave of Successful Genome Duplications in Association with the Cretaceous-Paleogene Boundary.” Genome Research 24 (8): 1334–1347.
APA
Vanneste, Kevin, Baele, G., Maere, S., & Van de Peer, Y. (2014). Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. GENOME RESEARCH, 24(8), 1334–1347.
Vancouver
1.
Vanneste K, Baele G, Maere S, Van de Peer Y. Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. GENOME RESEARCH. 2014;24(8):1334–47.
MLA
Vanneste, Kevin, Guy Baele, Steven Maere, et al. “Analysis of 41 Plant Genomes Supports a Wave of Successful Genome Duplications in Association with the Cretaceous-Paleogene Boundary.” GENOME RESEARCH 24.8 (2014): 1334–1347. Print.
@article{5821895,
  abstract     = {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.},
  author       = {Vanneste, Kevin and Baele, Guy and Maere, Steven and Van de Peer, Yves},
  issn         = {1088-9051},
  journal      = {GENOME RESEARCH},
  keyword      = {FOSSIL CALIBRATIONS,BAYESIAN-ESTIMATION,ARABIDOPSIS-THALIANA,STATISTICAL PHYLOGENETICS,MASS EXTINCTION,FLOWERING PLANTS,MOLECULAR EVOLUTION,RELAXED-CLOCK METHODS,ESTIMATING DIVERGENCE TIMES,GREEN RIVER FORMATION},
  language     = {eng},
  number       = {8},
  pages        = {1334--1347},
  title        = {Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary},
  url          = {http://dx.doi.org/10.1101/gr.168997.113},
  volume       = {24},
  year         = {2014},
}

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