Pangenome-driven discovery and comparative genomics of glycosyltransferase genes in Camellia sinensis

The quality of tea plants is determined by the accumulation of secondary metabolites including tea polyphenols, flavonoids, theanine and terpenoids. UDP-glycosyltransferase (UGT) genes catalyze the glycosylation of UDP-sugar donors to small-molecule acceptors, which directly modulates the structure, stability and biological activity of these quality-related metabolites. We systematically identified UGT gene family members across 22 high-quality tea plant pan-genomes. Evolutionary characteristics were analyzed via duplication type, Ka/Ks ratio and structural variation (SV) analysis. The expression patterns of CsUGT genes were investigated using expression comparison and transcriptomic data under normal and abiotic stress conditions. A total of 3,210 UGT genes were identified and classified into 201 orthologous groups (OGs), including 9 core, 24 soft-core, 116 dispensable and 52 private OGs. Whole-genome duplication (WGD) dominated core and soft-core gene duplication, while non-core genes were mainly derived from transposed or proximal duplications. Fifteen CsUGT genes underwent positive selection, and most were under purifying selection. SVs significantly affected the expression, conserved domains and cis-elements of CsUGT22, CsUGT14 and CsUGT43. CsUGT genes were highly expressed in tea plant buds and young leaves; CsUGT29, CsUGT43 and CsUGT49 were markedly upregulated under drought and salt stresses. This study reports the first comprehensive pan-genomic analysis of the tea plant UGT gene family, which elucidates its evolutionary dynamics and adaptive functional diversification. These findings establish a fundamental framework for future molecular research and breeding applications of CsUGT genes in tea plants.