University of Oulu

Tuomas Hämälä, Weixuan Ning, Helmi Kuittinen, Nader Aryamanesh, Outi Savolainen (2022) Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata eLife 11:e83115.

Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata

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Author: Hämälä, Tuomas1,2; Ning, Weixuan3,4; Kuittinen, Helmi1;
Organizations: 1Department of Ecology and Genetics, University of Oulu, Oulu, Finland
2School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
3Department of Ecology and Genetics, University of Oulu, Finland
4School of Natural Sciences, Massey University, Palmerston North, New Zealand
5Embryology Research Unit, Bioinformatics Group, Children’s Medical Research Institute, University of Sydney, Westmead, Australia
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.2 MB)
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Language: English
Published: eLife Sciences Publications, 2022
Publish Date: 2023-05-25


Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint — the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.

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Series: eLife
ISSN: 2050-084X
ISSN-E: 2050-084X
ISSN-L: 2050-084X
Volume: 11
DOI: 10.7554/eLife.83115
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
Funding: Academy of Finland 132611 Outi Savolainen, Academy of Finland 339702 Tuomas Hämälä.
Academy of Finland Grant Number: 132611
Detailed Information: 132611 (Academy of Finland Funding decision)
Copyright information: © Hämälä et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.