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Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints
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)...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145710/ https://www.ncbi.nlm.nih.gov/pubmed/31687761 http://dx.doi.org/10.1093/gbe/evz239 |
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author | Godden, Grant T Kinser, Taliesin J Soltis, Pamela S Soltis, Douglas E |
author_facet | Godden, Grant T Kinser, Taliesin J Soltis, Pamela S Soltis, Douglas E |
author_sort | Godden, Grant T |
collection | PubMed |
description | 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 (K(S)), 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. |
format | Online Article Text |
id | pubmed-7145710 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-71457102020-04-13 Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints Godden, Grant T Kinser, Taliesin J Soltis, Pamela S Soltis, Douglas E Genome Biol Evol Research Article 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 (K(S)), 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. Oxford University Press 2019-11-05 /pmc/articles/PMC7145710/ /pubmed/31687761 http://dx.doi.org/10.1093/gbe/evz239 Text en © The Author(s) 2019. 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 Godden, Grant T Kinser, Taliesin J Soltis, Pamela S Soltis, Douglas E Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints |
title | Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints |
title_full | Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints |
title_fullStr | Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints |
title_full_unstemmed | Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints |
title_short | Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints |
title_sort | phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145710/ https://www.ncbi.nlm.nih.gov/pubmed/31687761 http://dx.doi.org/10.1093/gbe/evz239 |
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