Analysis of metabolomics and transcriptomics of Camellia drupifera seeds during maturation provides new insights into bioactive compound biosynthesis

• Profiling identified 1,559 metabolites and 5,971 DEGs across seed maturation. • Flavonoid, sugar, and lipid metabolism displayed stage-dependent shifts. • Carbohydrates transitioned from glycosylation donors to lipid precursors in late stages. • Key genes exhibited cross-pathway regulation of metabolite accumulation. • Multi-omics integration revealed networks underlying bioactive compound biosynthesis. Camellia drupifera , an understudied tea-oil camellia species, is valued for its seeds, which contain abundant bioactive compounds. To elucidate the dynamics of these compounds during seed maturation, an integrated analysis was conducted by combining metabolomic, transcriptomic, and physiological analyses at five developmental stages. A total of 1,559 metabolites and 5,971 differentially expressed genes were identified, with flavonoids, phenolic acids, and amino acid derivatives being the predominant metabolite classes. Physiological indicators, including flavonoid, vitamin E, carotenoid, and polysaccharide contents, demonstrated strong correlations with other bioactive metabolites and antioxidant capacity. Key pathways, such as flavonoid biosynthesis, fructose and mannose metabolism, carotenoid biosynthesis, and α-linolenic acid metabolism, exhibited distinct stage-specific metabolic shifts. Notably, the fructose and mannose metabolism pathways appeared to transition from supplying sugar donors for flavonoid glycosylation to potentially supporting lipid biosynthesis. Furthermore, co-expression analysis revealed several hub genes involved in sugar, lipid, and carotenoid metabolism, indicating coordinated cross-pathway regulatory mechanisms. Collectively, these findings provide a comprehensive framework for understanding the mechanisms underlying carbon allocation during seed development in C. drupifera .