Genomic and Metabolomic Insights into Volatile and Nonvolatile Metabolite Variation from Fresh Leaves to the Turning Stages in Wuyi Rock Tea “Rougui”

Wuyi rock tea is renowned for its distinctive ″rock flavor,″ largely formed during the turning stage through mechanical stress and enzymatic changes.To investigate its molecular basis, we assembled the most contiguous tea genome to date from the representative cultivar “Rougui” and identified structural variations distributed across flavor-related genes and pathways. Metabolomic profiling highlighted the fourth and fifth turning stages as critical, showing surges in volatiles and nucleotides, rapid catechin and amino acid degradation, and a striking 180-fold rise in theaflavins. Leveraging transcriptome data with >97% mapping rate to the “Rougui” genome, we identified 1248 genes forming key coexpression modules associated with volatiles and theaflavins biosynthesis. These modules include 10 TPSs, PPO, POD, and multiple upstream structural genes that were coordinately activated during the sequential turning stages. The results offer genomic resources and insights into the regulation of flavor formation in Wuyi rock tea.