Integrated multiomics profiling elucidates the spatiotemporal metabolic dynamics and regulatory networks of the bioactive components of

Introduction: Methods: An integrated multiomics strategy (LC-MS/MS metabolomics and Illumina transcriptomics) was employed to elucidate the metabolic and transcriptional landscapes across three pivotal fruit ripening stages (initial, color-changing, and mature) and four tissues (roots, pericarp, fruits, and seeds). Weighted gene coexpression network analysis (WGCNA) was used to identify core modules associated with medicinal compound biosynthesis and hub transcription factors. Results: A total of 1,558 metabolites were identified via metabolomic profiling, which revealed pronounced tissue-specific accumulation: fruits and pericarps were enriched in amino acids, flavonoids, and organic acids, seeds accumulated terpenoids, flavonoids, and fatty acids, roots served as the predominant reservoir for pharmacologically active terpenoids, such as the antitumor cucurbitacin B. Transcriptome analysis revealed tissue- and stage-specific expression patterns of genes involved in terpenoid, phenylpropanoid, and flavonoid biosynthetic pathways, which were strongly correlated with metabolite abundance. WGCNA identified three core modules (MEturquoise, MEblack, and MEbrown) and pinpointed the transcription factor Discussion: Collectively, our findings provide a comprehensive molecular blueprint for the spatiotemporal biosynthesis of medicinal compounds in