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Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints.
Genome Biol Evol. 2019 12 01; 11(12):3393-3408.GB

Abstract

Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. Although mounting evidence highlights the importance of whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs-an extreme mechanism of gene duplication-using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7-18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the nonuniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups.

Authors+Show Affiliations

Florida Museum of Natural History, University of Florida.Florida Museum of Natural History, University of Florida. Department of Biology, University of Florida.Florida Museum of Natural History, University of Florida.Florida Museum of Natural History, University of Florida. 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

31687761

Citation

Godden, Grant T., et al. "Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints." Genome Biology and Evolution, vol. 11, no. 12, 2019, pp. 3393-3408.
Godden GT, Kinser TJ, Soltis PS, et al. Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints. Genome Biol Evol. 2019;11(12):3393-3408.
Godden, G. T., Kinser, T. J., Soltis, P. S., & Soltis, D. E. (2019). Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints. Genome Biology and Evolution, 11(12), 3393-3408. https://doi.org/10.1093/gbe/evz239
Godden GT, et al. Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints. Genome Biol Evol. 2019 12 1;11(12):3393-3408. PubMed PMID: 31687761.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints. AU - Godden,Grant T, AU - Kinser,Taliesin J, AU - Soltis,Pamela S, AU - Soltis,Douglas E, PY - 2019/10/28/accepted PY - 2019/11/7/pubmed PY - 2020/4/22/medline PY - 2019/11/6/entrez KW - Lamiaceae KW - ancient polyploidy KW - gene duplication KW - mints KW - phylotranscriptomics KW - whole-genome duplication SP - 3393 EP - 3408 JF - Genome biology and evolution JO - Genome Biol Evol VL - 11 IS - 12 N2 - Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. Although mounting evidence highlights the importance of whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs-an extreme mechanism of gene duplication-using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7-18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the nonuniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups. SN - 1759-6653 UR - https://www.unboundmedicine.com/medline/citation/31687761/Phylotranscriptomic_Analyses_Reveal_Asymmetrical_Gene_Duplication_Dynamics_and_Signatures_of_Ancient_Polyploidy_in_Mints_ L2 - https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evz239 DB - PRIME DP - Unbound Medicine ER -