Chromosome‐level genome and methylome of vine tea suggest roles for tandem duplication and CHH hypomethylation in high dihydromyricetin accumulation

A chromosome-level genome assembly and single-base resolution methylome of vine tea (Nekemias grossedentata) reveal that lineage-specific tandem duplications of dihydromyricetin (DHM) biosynthetic genes (NgCHS and NgF3′5′ H) have expanded their copy numbers, providing the genetic basis for high DHM flux. Tissue-specific CHH hypomethylation in young leaves, associated with downregulation of RNA-directed DNA methylation (RdDM)-related methyltransferases and upregulation of the demethylase NgDML1, correlates with the selective high expression of these duplicated genes, while competing pathway branches (e.g., STS for stilbene synthase, HCT for shikimate hydroxycinnamoyl transferase, DFR for dihydroflavonol 4-reductase) maintain hypermethylation and low expression. Candidate v-myb avian myeloblastosis viral oncogene homolog (MYB) and basic helix-loop-helix (bHLH) transcription factors co-expressed with DHM pathway genes are identified. These findings suggest a “duplication-associated activation” model integrating genomic, epigenomic, and transcriptomic layers for high DHM accumulation.