Integrated transcriptome and metabolome analysis reveals the accumulation of secondary metabolites in Camphora glanduliferum ‘Honganzhang’ at different harvest times

Background Camphora glanduliferum ‘Honganzhang’ is an economically important woody plant valued for its eucalyptol-rich essential oils. The yield and composition of its secondary metabolites are highly dynamic and sensitive to harvest timing. However, the molecular mechanisms governing the seasonal reprogramming of terpenoid and flavonoid biosynthesis in this species remain largely unexplored. To elucidate these regulatory networks, we performed an integrated metabolomic and transcriptomic analysis of leaves collected at three distinct harvest times: June (H1), August (H2), and October (H3). Results Metabolomic profiling identified 2,704 metabolites, with terpenoids (33.17%) and flavonoids (31.52%) being the predominant classes. A clear temporal divergence was observed: total terpenoid accumulation peaked in H1 and declined in H3, whereas flavonoid content increased significantly from H1 to H2. Transcriptomic analysis identified 9,824 − 13,513 differentially expressed genes (DEGs) across comparisons. Notably, we observed a transcript-metabolite discordance in terpenoid biosynthesis; key genes (e.g., DXS , GPPS , TPS04 ) were upregulated in H2 and H3 despite lower total terpenoid accumulation, suggesting a compensatory mechanism driven by high volatilization or metabolic flux diversion towards gibberellin biosynthesis. Conversely, flavonoid biosynthesis exhibited a strictly coordinated stage-specific flux redirection: H1 and H3 favored flavonol accumulation via the upregulation of FLS and CYP75B1 , while H2 prioritized proanthocyanidin synthesis through the specific upregulation of LAR . Furthermore, a co-expression regulatory network was constructed to link key metabolites and structural genes to transcription factors from the MYB, bHLH, NAC, and WRKY families, highlighting their roles as central hubs in orchestrating these metabolic shifts. Conclusions This study reveals the dynamic transcriptional reprogramming that drives the seasonal accumulation of secondary metabolites in C. glanduliferum ‘Honganzhang’. It investigates the specific regulatory modules controlling the trade-off between flavonol and proanthocyanidin pathways and proposes a mechanism for the seasonal fluctuation of terpenoids. These findings provide a theoretical foundation for determining optimal harvest windows to maximize specific bioactive compounds and facilitate the molecular breeding of elite Lauraceae varieties.