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 nonalcoholic 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 flavonol 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.

Acknowledgements

This work was supported by Central Public-interest Scientific Institution Basal Research Fund (No. 1610212024002), the China Agricultural Research System of MOF and MARA (CARS-019), and the Chinese Academy of Agricultural Sciences through the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2021-TRICAAS), Zhejiang Provincial Natural Science Foundation of China, under Grant No. LZ22C160008, and Jiangxi Province Talent Plan (jxsq2023102020) to L.C.

Authors contributions

X.Z, W.C., M.Y., and L.C. planned and designed the research; X.Z., X.X., Y.L., N.C., C.M., J.M., and J.J. performed experiments and analyzed data; X.Z., W.C., M.Y., and L.C. wrote and revised the article.

Data availability

The data that support the findings of this study are available in the supplementary material of this article.

Conflicts of interest statement

The authors declare no conflict of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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