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Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data

Whole-genome duplications (WGDs) have helped shape the genomes of land plants, and recent evidence suggests that the genomes of all angiosperms have experienced at least two ancient WGDs. In plants, WGDs often are followed by rapid fractionation, in which many homeologous gene copies are lost. Thus,...

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Autores principales: Tiley, George P., Ané, Cécile, Burleigh, J. Gordon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860690/
https://www.ncbi.nlm.nih.gov/pubmed/26988251
http://dx.doi.org/10.1093/gbe/evw058
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author Tiley, George P.
Ané, Cécile
Burleigh, J. Gordon
author_facet Tiley, George P.
Ané, Cécile
Burleigh, J. Gordon
author_sort Tiley, George P.
collection PubMed
description Whole-genome duplications (WGDs) have helped shape the genomes of land plants, and recent evidence suggests that the genomes of all angiosperms have experienced at least two ancient WGDs. In plants, WGDs often are followed by rapid fractionation, in which many homeologous gene copies are lost. Thus, it can be extremely difficult to identify, let alone characterize, ancient WGDs. In this study, we use a new maximum likelihood estimator to test for evidence of ancient WGDs in land plants and estimate the fraction of new genes copies that are retained following a WGD using gene count data, the number of gene copies in gene families. We identified evidence of many putative ancient WGDs in land plants and found that the genome fractionation rates vary tremendously among ancient WGDs. Analyses of WGDs within Brassicales also indicate that background gene duplication and loss rates vary across land plants, and different gene families have different probabilities of being retained following a WGD. Although our analyses are largely robust to errors in duplication and loss rates and the choice of priors, simulations indicate that this method can have trouble detecting multiple WGDs that occur on the same branch, especially when the gene retention rates for ancient WGDs are very low. They also suggest that we should carefully evaluate evidence for some ancient plant WGD hypotheses.
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spelling pubmed-48606902016-05-10 Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data Tiley, George P. Ané, Cécile Burleigh, J. Gordon Genome Biol Evol Research Article Whole-genome duplications (WGDs) have helped shape the genomes of land plants, and recent evidence suggests that the genomes of all angiosperms have experienced at least two ancient WGDs. In plants, WGDs often are followed by rapid fractionation, in which many homeologous gene copies are lost. Thus, it can be extremely difficult to identify, let alone characterize, ancient WGDs. In this study, we use a new maximum likelihood estimator to test for evidence of ancient WGDs in land plants and estimate the fraction of new genes copies that are retained following a WGD using gene count data, the number of gene copies in gene families. We identified evidence of many putative ancient WGDs in land plants and found that the genome fractionation rates vary tremendously among ancient WGDs. Analyses of WGDs within Brassicales also indicate that background gene duplication and loss rates vary across land plants, and different gene families have different probabilities of being retained following a WGD. Although our analyses are largely robust to errors in duplication and loss rates and the choice of priors, simulations indicate that this method can have trouble detecting multiple WGDs that occur on the same branch, especially when the gene retention rates for ancient WGDs are very low. They also suggest that we should carefully evaluate evidence for some ancient plant WGD hypotheses. Oxford University Press 2016-03-17 /pmc/articles/PMC4860690/ /pubmed/26988251 http://dx.doi.org/10.1093/gbe/evw058 Text en © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Article
Tiley, George P.
Ané, Cécile
Burleigh, J. Gordon
Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data
title Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data
title_full Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data
title_fullStr Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data
title_full_unstemmed Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data
title_short Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data
title_sort evaluating and characterizing ancient whole-genome duplications in plants with gene count data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860690/
https://www.ncbi.nlm.nih.gov/pubmed/26988251
http://dx.doi.org/10.1093/gbe/evw058
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