Background: Lonicera macranthoides (L. macranthoides) is a traditional Chinese medicinal plant, the flower buds of which are rich in bioactive compounds, such as chlorogenic acids (CGAs) and flavonoids, and exhibit diverse pharmacological activities. Methods: Integrated transcriptomic and metabolomic analyses were conducted across three floral developmental stages: flower bud (FB), white flower (WF), and golden flower (GF). Results: Clustering analysis revealed distinct molecular profiles, with the WF and GF stages clustering together and clearly separating from the FB stage. The most significant metabolomic variation was observed between the GF and FB stages. KEGG enrichment analysis consistently highlighted the phenylpropanoid biosynthesis pathway as a key hub. Stage-specific accumulation patterns were identified for critical metabolites: caffeoylquinic acid peaked at the WF stage, while ferulic acid, sinapic acid, cinnamic acid, and p-coumaric acid reached their highest levels at the GF stage. Within this pathway, we identified 11 DEGs encoding the core enzymes, alongside 15 associated DAMs. The expression trends of four PAL genes were fully consistent with the accumulation of related precursors, and F5H expression correlated with its downstream product, sinapic acid. WGCNA identified a key module highly correlated with key phenolic acids, containing 71 transcription factors, including MYB, bHLH, WRKY, and AP2/ERF families, potentially forming a complex regulatory network for phenylpropanoid biosynthesis. Conclusions: This study deciphers the stage-specific regulatory network of CGA biosynthesis, providing critical insights and genetic resources for cultivating high-medicinal-content varieties of L. macranthoides.

Background: Lonicera macranthoides is a valuable traditional Chinese medicinal plant, enriched in secondary metabolites that exert significant therapeutic effects against specific diseases. However, the differences in the accumulation of key metabolites across various tissues of this plant remain poorly understood. Methods: This study analyzed the transcriptomes and metabolomes of three key tissues (flowers, leaves, and fruits) in Lonicera macranthoides. Results: Transcriptome sequencing identified 7321 differentially expressed genes (DEGs) common to flowers, fruits, and leaves. Among the top 20 KEGG pathways enriched by these DEGs, metabolic pathways and biosynthesis of secondary metabolites were prominently represented. At least 70 CYP genes and 12 UGT genes were differentially expressed, with a greater proportion of these genes being up-regulated in flowers or fruits. DEGs involved in flavonoid biosynthesis include CHI, CHS, and FLS, with most of these genes being up-regulated in fruits. Metabolomics analysis identified 4961 metabolites across the three tissues. KEGG pathway classification of these DAMs showed that a large proportion are involved in metabolic pathways and secondary metabolite biosynthesis. Conjoint analysis of the transcriptomic and metabolomic data revealed that the most significantly enriched were metabolic pathways and biosynthesis of secondary metabolites. Integrative analysis of DEGs and DAMs indicated that flowers and fruits are likely key tissues for the biosynthesis of hederagenin-based saponins, while fruits may serve as critical organs for flavonoid biosynthesis. Conclusions: This study provides novel insights into the tissue-specific differential accumulation of metabolites in Lonicera macranthoides, and lays a crucial foundation for further investigating the underlying molecular regulatory mechanisms.