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Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data.
Genome Biol Evol. 2016 Apr 11; 8(4):1023-37.GB

Abstract

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.

Authors+Show Affiliations

Department of Biology, University of Florida gtiley@ufl.edu.Department of Statistics, University of Wisconsin-Madison Department of Botany, University of Wisconsin-Madison.Department of Biology, University of Florida.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

26988251

Citation

Tiley, George P., et al. "Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants With Gene Count Data." Genome Biology and Evolution, vol. 8, no. 4, 2016, pp. 1023-37.
Tiley GP, Ané C, Burleigh JG. Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data. Genome Biol Evol. 2016;8(4):1023-37.
Tiley, G. P., Ané, C., & Burleigh, J. G. (2016). Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data. Genome Biology and Evolution, 8(4), 1023-37. https://doi.org/10.1093/gbe/evw058
Tiley GP, Ané C, Burleigh JG. Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants With Gene Count Data. Genome Biol Evol. 2016 Apr 11;8(4):1023-37. PubMed PMID: 26988251.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data. AU - Tiley,George P, AU - Ané,Cécile, AU - Burleigh,J Gordon, Y1 - 2016/04/11/ PY - 2016/3/19/entrez PY - 2016/3/19/pubmed PY - 2017/3/14/medline KW - gene count KW - gene duplication and loss KW - gene family evolution KW - gene retention KW - paleopolyploidy KW - whole-genome duplication SP - 1023 EP - 37 JF - Genome biology and evolution JO - Genome Biol Evol VL - 8 IS - 4 N2 - 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. SN - 1759-6653 UR - https://www.unboundmedicine.com/medline/citation/26988251/Evaluating_and_Characterizing_Ancient_Whole_Genome_Duplications_in_Plants_with_Gene_Count_Data_ L2 - https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evw058 DB - PRIME DP - Unbound Medicine ER -