High-resolution methylome analysis in the clonalPopulus nigracv. ‘Italica’ reveals environmentally sensitive hotspots and drought-responsive TE superfamilies

Abstract

ABSTRACT/SUMMARYDNA methylation is environment-sensitive and can mediate plant stress responses. In long-lived trees, changing environments might cumulatively shape the methylome landscape over their lifetime. However, because high-resolution methylome studies usually focus on single environments, it remains unclear to what extent the methylation responses are generic or stress-specific, and how this relates to their long-term stability.Here, we studied the methylome plasticity of a single poplar genotype,Populus nigracv. ‘Italica’. Adult poplar trees with diverse environmental histories were clonally propagated, and the ramets exposed to experimental cold, heat, drought, herbivory, rust infection and salicylic acid treatments. Then, we identified and compared stress-induced vs. naturally occurring DNA methylation changes using whole genome bisulfite sequencing data.Methylation changes mainly targeted transposable elements and when occurring in CG/CHG contexts, the same regions were often affected by multiple stresses, indicating a generic response. Drought triggered a unique CHH hypermethylation response in transposable elements, affecting entire superfamilies and often occurring near drought-responsive genes. Stress-induced methylation variation in CG/CHG contexts showed striking overlap with methylation differences observed between trees from distinct geographical locations.Altogether, our results indicate that generic methylome stress responses can persist as epialleles in nature while some environments trigger more transient but large and specific responses, with possible functional consequences.

DNA methylation responses to stress across different plant species

“…This would indicate that a large number of induced DMCs, irrespective of cytosine context, are sensitive to multiple environmental triggers and are thus perhaps part of more generic stress response processes rather than a stress-specific response. This is in agreement with recent observations in P. nigra, where different stresses often caused similar DNA methylation changes in the genome (Peña-Ponton et al, 2022). For the stress-specific DMCs, a relevant question is if these occur in genes (or their regulatory regions) that are functionally involved in the stress response.…”

“…Thus, the relationship between cytosine context responsiveness and stress may be more complex than what has previously been reported. Previously reported stress responses occurring primarily in CHH are likely biased by the fact that there are many more CHH-cytosines than CG or CHG-cytosines present in genomes ( (López et al, 2022;Peña-Ponton et al, 2022) and as seen in our results), increasing the probability of detecting significant CHH methylation changes.…”

“…It is widely believed that cytosine methylation in different sequence contexts (CG, CHG and CHH) responds differently to environmental stimuli, as methylation of these contexts is regulated by very different enzymatic pathways (Richards, 2006;Zhang et al, 2018;Gallego-Bartolomé, 2020). Studies in a variety of plant species, including Populus nigra, Thlaspi arvense and Arabidopsis thaliana, suggest that CHH-type of methylations are more responsive to environmental conditions, whereas CG (and to a lesser extent CHG) are more stable and more often reflecting the genotypic origin of a plant rather than its environmental conditions (Dubin et al, 2015;Galanti et al, 2022;Peña-Ponton et al, 2022). Nevertheless, counterexamples exist such as in the common Duckweed Lemna minor or Fragaria vesca, where exposure to stress induced a large number of changes in methylation in the CHG and/or CG context rather than CHH (López et al, 2022;Van Antro et al, 2022).…”

“…Furthermore, while plant methylome responses to both biotic and abiotic stresses may be common, further studies suggest differences in how DNA methylation responds to stress both within and across plant species (Dubin et al, 2015;Galanti et al, 2022;Peña-Ponton et al, 2022). Conversely, methylation changes in CG context, and to a lesser extent CHG, are extremely stable and more often reflect genomic origin of an individual (Peña-Ponton et al, 2022;Ibañez et al, 2023). Opposing results have been reported in other plants species however ( (López et al, 2022;Van Antro et al, 2022).…”

“…Several studies have reported that cytosine contexts and genomic features are differentially impacted by stress and could thus play different roles in mediating stress responses (Zhang et al, 2018;Gallego-Bartolomé, 2020;Kumar & Mohapatra, 2021). Furthermore, while plant methylome responses to both biotic and abiotic stresses may be common, further studies suggest differences in how DNA methylation responds to stress both within and across plant species (Dubin et al, 2015;Galanti et al, 2022;Peña-Ponton et al, 2022). Conversely, methylation changes in CG context, and to a lesser extent CHG, are extremely stable and more often reflect genomic origin of an individual (Peña-Ponton et al, 2022;Ibañez et al, 2023).…”