Integrated single-nucleus transcriptomic and metabolomic insights into bud-to-leaf development and metabolite synthesis in tea plant

Abstract The tea plant is an important non-alcoholic beverage crop known for its abundant secondary metabolites, particularly in buds and leaves. However, the coordinated regulation of bud-to-leaf development and metabolism remains poorly understood. Here, we applied single-nucleus RNA sequencing (snRNA-Seq), bulk RNA sequencing (RNA-Seq), and metabolomics to comprehensively profile the developmental trajectory and metabolic characteristics of tea plant buds and leaves. The snRNA-Seq analysis revealed 17 cell clusters and 8 cell types in buds and leaves, respectively. Notably, the proportion of palisade mesophyll (PM) cells increased progressively during development, while proliferating cells (PC) decreased. Interestingly, key enzymes in the flavonoid biosynthetic pathway were specifically localized to PM cells. Metabolomic analyses demonstrated dynamic accumulation patterns of various metabolites, including phytohormones, flavonoids, and amino acids, as the buds transitioned to mature leaves. Using multi-omics profiling, we identified CsmiRNA396b, CsUGT94P1, CsTCP3, and CsTCP14 as critical regulatory components. Enzyme activity assays confirmed that CsUGT94P1 catalyzes the conversion of flavonols into flavonols-glycosides in vitro. Furthermore, CsmiRNA396b was found to regulate leaf development by inhibiting CsGRF3 expression, while CsTCP3 and CsTCP14 played antagonistic roles in leaf development and flavonoid biosynthesis. Our findings provide novel insights into the regulatory mechanisms underlying bud-to-leaf development and metabolite production in tea plants.