Multi-omics profiling provides new insight into HQT and HCT involved in regulating 5-caffeoylquinic acid and lignin biosynthesis in Tetrastigma hemsleyanum

Tetrastigma hemsleyanum Diels et Gilg, a perennial herb in the Vitaceae family, produces 5-caffeoylquinic acid (also known as chlorogenic acid, CGA). A CGA-enriched variety was identified, but its genomic sequences and resources for its accelerated breeding remain unavailable. Here its high-quality genome (2 n = 52) was assembled at the chromosome level. Transcriptome and metabolome analyses provided a high-level overview of the network of genes associated with CGA biosynthesis and leaf development. A hydroxycinnamoyl-CoA shikimic/quinate transferase (ThHCT) and hydroxycinnamoyl-CoA quinate transferase (ThHQT) were found to specifically expresse in leaves but not in roots. Heterologously overexpressing ThHQT and ThHCT led to increased CGA and lignin monomer levels, respectively. UHPLC-MS/MS analysis of recombinant enzymes showed that ThHQT efficiently catalyzes CGA formation from caffeoyl-CoA and quinic acid, confirming ThHQT's primary role in CGA production. In contrast, ThHCT was less active in CGA synthesis but can catalyze the reverse reaction, converting CGA (with acetyl-CoA) into quinic acid, highlighting ThHCT's possible role in lignin biosynthesis. A new ThHD-ZIP1 was determined to be capable of binding the ThHQT promoter to promote its mRNA level significantly. In summary, this study provides valuable genomic resources for enhancing CGA content in T. hemsleyanum and offers insight into lignin biosynthesis, laying a foundation for future molecular breeding. • Tetrastigma hemsleyanum high-quality genome from Jiande city is firstly assembled. • Identified HCT and HQT have vital effects on lignin and CGA synthesis respectively. • HQT exhibits the strongest catalytic activity under acidic conditions (pH 6.5). • nCGA and cCGA can be detected but CGA remains undetectable (≥pH7.0). • HD-ZIP1 contributes to HQT expression as to influence CGA synthesis.