Decoding the root lignification mechanism of Angelica sinensis through genome-wide DNA methylation analysis

Angelica sinensis is a traditional Chinese herbal medicine with significant economic and medicinal value. Early bolting and flowering can occur during the second year of the vegetative growth period, rendering the roots unviable for medicinal use and resulting in substantial economic losses. Consequently, there is growing interest in studying the molecular mechanisms underlying early bolting and increased root lignification in A. sinensis. Here, we conducted whole-genome bisulfite sequencing and observed an increase in whole-genome DNA methylation levels after bolting. Comparative analysis revealed differential methylation patterns of genic regions and transposable elements in the upstream, gene body, and downstream regions in the context of CG, CHG, and CHH, suggesting a possible association between CHH-type methylation of promoters and phenylpropanoid biosynthesis. Furthermore, combined analysis of transcriptomic and methylomics data revealed a positive correlation between DNA methylation and gene expression. We identified the hyperDMR gene in the CHH context within the promoter region of key gene AsCOMT1, which exhibits a dual catalytic activity and facilitates the synthesis of both ferulic acid and lignin. Enzyme kinetic analysis demonstrated that AsCOMT1 preferentially catalyses the synthesis of lignin monomer precursors. These findings highlight the important regulatory role of DNA methylation in bolting and the synthesis of secondary metabolites in A. sinensis, providing valuable insights into the underlying molecular mechanism. DNA methylation influenced bolting and secondary metabolite synthesis in Angelica sinensis and positively correlated with gene expression changes, with AsCOMT1 preferentially catalysing lignin precursor synthesis.