Cold Stress-Induced DNA Methylation Profiling and Its Association with Terpenoid Biosynthesis in Germinating Mikania micrantha Seeds

Abstract

Mikania micrantha, a highly invasive weed, faces constraints on its northward range expansion in South China due to low winter temperatures. Although DNA methylation is increasingly recognized as a mediator of plant stress adaptation, it remains unknown whether epigenetic regulation couples cold-stress tolerance with the production of allelopathic secondary metabolites in invasive plants. Here, we comprehensively characterized genome-wide DNA methylation dynamics and their transcriptional consequences in germinating embryos under three temperature regimes (14 °C, 25 °C, and 30 °C) by integrating whole-genome bisulfite sequencing and RNA-Seq. Exposure to 14 °C significantly delayed germination without arresting the process. Global methylation levels were highest at CG sites (80.21–84.63%), followed by CHG (63.67–66.77%) and CHH (6.63–7.51%) contexts. Integrative analysis identified 1103 differentially methylated region-associated genes, of which 434 were also differentially expressed. Notably, KEGG enrichment of the 434 overlapping genes revealed significant overrepresentation of the sesquiterpenoid and triterpenoid biosynthesis pathways, with key mevalonate (MVA) pathway genes showing altered expression in association with DMRs at 14 °C. Because this is an integrative methylome–transcriptome association study without metabolite quantification or functional validation, these results are consistent with the hypothesis that cold-induced epigenetic reprogramming is associated with transcriptional changes in terpenoid biosynthesis, which may contribute to antioxidant and membrane-protective functions under chilling stress; the possible accumulation of allelopathic sesquiterpene lactones and any role in maintaining competitive advantage during cold seasons remain working hypotheses that require experimental validation. The results of this study offer new epigenetic perspectives and supporting data for the management and prevention of M. micrantha invasion.