Objective This study aimed to comprehensively identify the key genes involved in the biosynthesis of spinosin and jujuboside A. Methods Ziziphi Spinosae Semen samples at green fruit and mature stages were selected as experimental materials to construct transcriptomic and metabolomic datasets. Key candidate genes associated with the spinosin and jujuboside A biosynthesis pathways were systematically analyzed through functional annotation and differential expression gene analysis. Results Metabolomic profiling detected 1 646 metabolites, while transcriptomic sequencing and functional annotation identified 7 316 differentially expressed genes. Results revealed that spinosin was relatively enriched during the green fruit stage of Ziziphi Spinosae Semen, whereas jujuboside A accumulated predominantly at the mature stage. Through phylogenetic and heatmap analyses, 50 key candidate genes were screened, including 33 UGTs, 12 OMTs, two OSCs, and three CYP450s, which are hypothesized to participate in the downstream biosynthesis of spinosin and jujuboside A. Conclusion This work systematically deciphers and proposes biosynthetic pathways for these components, laying a foundation for subsequent functional gene validation. It advances molecular biology research on Ziziphi Spinosae Semen bioactive compounds and provides novel insights for the development and utilization of traditional Chinese medicine resources.

Ziziphus jujube Mill. var. spinosa (Bunge) Hu ex H. F. Chou  /  metabolomics  /  transcriptomics  /  spinosin  /  jujuboside A