Dynamic DNA methylation modification in catechins and terpenoids biosynthesis during tea plant (Camellia sinensis) leaf development

DNA methylation plays important roles in regulating gene expression during development. However, little is known about the influence of DNA methylation on secondary metabolism during leaf development in the tea plant (Camellia sinensis). In this study, we combined the methylome, transcriptome, and metabolome to investigate the dynamic changes in DNA methylation and its potential regulatory roles in secondary metabolite biosynthesis. In this study, the level of genomic DNA methylation increased as leaf development progressed from tender to old leaf. It additionally exhibited a similar distribution across the genomic background at the two distinct developmental stages studied. Notably, integrated analysis of transcriptomic and methylomic data showed that DNA hypermethylation primarily occurred in genes of the phenylpropanoid, flavonoid, and terpenoid biosynthesis pathways. The effect of methylation on transcription of these secondary metabolite biosynthesis genes was dependent on the location of methylation (i.e., in the promoter, gene or intergenic regions) and the sequence context (i.e., CpG, CHG, or CHH). Changes in the content of catechins and terpenoids were consistent with the changes in gene transcription and the methylation state of structural genes, such as serine carboxypeptidase-like acyltransferases 1A (SCPL1A), leucoanthocyanidin reductase (LAR), and nerolidol synthase (NES). Our study provides valuable information for dissecting the effects of DNA methylation on regulation of genes involved in secondary metabolism during tea leaf development.