Integrative Multi-Omics Analysis Reveals Nutritional Metabolite Diversity and Regulatory Mechanisms in Ocimum basilicum

Ocimum basilicum is widely used as both a culinary and medicinal plant; however, its nutritional metabolite composition, functional relevance, and underlying regulatory mechanisms remain incompletely characterized. To systematically profile nutritional metabolites and explore their potential biological relevance in O. basilicum, an integrative multi-omics strategy that combined UPLC-MS/MS-based metabolomics, transcriptomics, network pharmacology, and molecular docking was deployed herein. A total of 443 nutritional metabolites across four accessions were identified, including vitamins, saccharides, amino acids and lipids. Of these, Vitamin A1 (retinol) and N-acetyl-L-tryptophan were found to be important metabolites that could have functional significance. Predictive network pharmacology and molecular docking analyses suggested potential in silico interactions between these metabolites and disease-associated targets, including ESR2 and MAPK1; these findings await experimental validation. Transcriptomic analysis also showed that genes involved in Vitamin A1 biosynthesis (PSY, LCYB) were expressed, and the expression patterns of the genes were validated by the qPCR analysis, in which expression level was largely consistent with the transcriptome results. Specifically, the accessions G083 and G082 showed high values of Vitamin A1 and N-acetyl-L-tryptophan, respectively, suggesting that they may also be interesting germplasm for functional food innovation and the development of nutraceuticals. Overall, this study offers a comprehensive multi-omics dataset and mechanistic insights that can help in the targeted use of O. basilicum for nutritional and functional applications.