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Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
DNA methylation is an important factor regulating gene expression in organisms. However, whether DNA methylation plays a key role in adaptive evolution is unknown. Here, we show evidence of naturally selected DNA methylation in Arabidopsis thaliana. In comparison with single nucleotide polymorphisms...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168577/ https://www.ncbi.nlm.nih.gov/pubmed/34006571 http://dx.doi.org/10.1101/gr.271726.120 |
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author | Shirai, Kazumasa Sato, Mitsuhiko P. Nishi, Ranko Seki, Masahide Suzuki, Yutaka Hanada, Kousuke |
author_facet | Shirai, Kazumasa Sato, Mitsuhiko P. Nishi, Ranko Seki, Masahide Suzuki, Yutaka Hanada, Kousuke |
author_sort | Shirai, Kazumasa |
collection | PubMed |
description | DNA methylation is an important factor regulating gene expression in organisms. However, whether DNA methylation plays a key role in adaptive evolution is unknown. Here, we show evidence of naturally selected DNA methylation in Arabidopsis thaliana. In comparison with single nucleotide polymorphisms, three types of methylation—methylated CGs (mCGs), mCHGs, and mCHHs—contributed highly to variable gene expression levels among an A. thaliana population. Such variably expressed genes largely affect a large variation of specialized metabolic quantities. Among the three types of methylations, only mCGs located in promoter regions of genes associated with specialized metabolites show a selective sweep signature in the A. thaliana population. Thus, naturally selected mCGs appear to be key mutations that cause the expressional diversity associated with specialized metabolites during plant evolution. |
format | Online Article Text |
id | pubmed-8168577 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-81685772021-12-01 Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants Shirai, Kazumasa Sato, Mitsuhiko P. Nishi, Ranko Seki, Masahide Suzuki, Yutaka Hanada, Kousuke Genome Res Research DNA methylation is an important factor regulating gene expression in organisms. However, whether DNA methylation plays a key role in adaptive evolution is unknown. Here, we show evidence of naturally selected DNA methylation in Arabidopsis thaliana. In comparison with single nucleotide polymorphisms, three types of methylation—methylated CGs (mCGs), mCHGs, and mCHHs—contributed highly to variable gene expression levels among an A. thaliana population. Such variably expressed genes largely affect a large variation of specialized metabolic quantities. Among the three types of methylations, only mCGs located in promoter regions of genes associated with specialized metabolites show a selective sweep signature in the A. thaliana population. Thus, naturally selected mCGs appear to be key mutations that cause the expressional diversity associated with specialized metabolites during plant evolution. Cold Spring Harbor Laboratory Press 2021-06 /pmc/articles/PMC8168577/ /pubmed/34006571 http://dx.doi.org/10.1101/gr.271726.120 Text en © 2021 Shirai et al.; Published by Cold Spring Harbor Laboratory Press https://creativecommons.org/licenses/by-nc/4.0/This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) . |
spellingShingle | Research Shirai, Kazumasa Sato, Mitsuhiko P. Nishi, Ranko Seki, Masahide Suzuki, Yutaka Hanada, Kousuke Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants |
title | Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants |
title_full | Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants |
title_fullStr | Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants |
title_full_unstemmed | Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants |
title_short | Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants |
title_sort | positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168577/ https://www.ncbi.nlm.nih.gov/pubmed/34006571 http://dx.doi.org/10.1101/gr.271726.120 |
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