DNA methylation analysis of Jack pine (Pinus banksiana) under nickel stress reveals a highly targeted epigenetic response

Plants use DNA methylation to quickly adjust gene activity in response to environmental stressors helping them adapt and survive. Conifers have large genomes and unique metal responses, making conifer DNA methylation research highly compelling. This study evaluated how excess nickel exposure affects methylation patterns and identified differentially methylated regions (DMRs) in Pinus banksiana . Reduced representation bisulfite sequencing (RRBS) was used to assess global methylation changes in nickel-treated seedlings. Nickel sulfate minimally affected overall global methylation; however, it induced significant levels of methylation within specific, localized regions of the genome. The increase in global CG methylation was largely due to hypermethylated DMRs that had methylation levels exceeding 80 %. The observed global hypermethylation was localized predominantly to constitutively hypermethylated regions. A total of 1173 DMRs were found to be hypermethylated, while 239 were hypomethylated. Notably, 97 % of these DMRs were intergenic and displayed high levels of CG methylation, leading to the suggestion that they may be located within transposable elements (TEs). All gene-annotated Differentially Methylated Regions (DMRs) spanned two distinct areas of the gene body, potentially suggesting a strong bias toward gene upregulation. DMR-covered genes, associated with stress mitigation, encode proteins including DEAD-box ATP-dependent RNA helicase, calcium/calmodulin-dependent protein kinase, and UDP-glycosyltransferase. Methylation analyses reveal epigenetic changes that can help discover how P. banksiana resist nickel and adapt long-term to contamination. For this study, RRBS was a suitable compromise because it allowed for precise analysis of specific, relevant regions.