Multi-omics analysis provides insights into the mechanisms of flavonoid and phenolic acid biosynthesis in harvested Camellia pubipetala

Camellia pubipetala Y. Wan & S. Z. Huang, known for its high polyphenol content, particularly flavonoids with potent antioxidant properties, has garnered significant scientific attention. Nonetheless, the biosynthetic genes associated with these metabolites in C. pubipetala are still insufficiently understood. This study addresses this gap through transcriptomic and targeted metabolomic analyses of five developmental stages of C. pubipetala flowers: young bud, early bud, turning yellow, semi-blooming, and full bloom. The analysis showed fluctuating levels of total flavonoids, phenolics, and antioxidant activities, that peaked at the semi-blooming stage before declining. A total of 739 differentially accumulated metabolites (DAMs) and 42,252 differentially expressed genes (DEGs) were identified, primarily enriched in pathways related to flavonoid and phenylpropanone biosynthesis. The study also enabled the construction of a comprehensive biosynthetic pathway for phenolic acids and flavonoids. The consistency between qRT-PCR analysis of 16 genes and transcriptomic data was validated. Furthermore, a gene co-expression network was built using Cytoscape, which revealed nine essential transcription factors (CpMYB1, CpMYB3, CpbHLH5, CpC2H29, CpGRAS5, CpGARP-G2-like1, CpB3-ARF, CpB31, CpB33) and eight key structural genes (F3'H, CHI.2, FAH.3, FLS.2, PAL.2, CCR.1, CCR.2, LAR) active in these pathways. Although further functional characterization is needed, these findings enhance the understanding of flavonoid and phenolic acid biosynthetic in C. pubipetala and offer a theoretical foundation for its future medicinal and nutritional exploitation.