Integrated Metabolomic and Transcriptomic Analyses Elucidate Phenolic Acid Diversity and Their Antioxidant and Functional Associations in Ocimum Species

An integrated approach combining UPLC-MS/MS metabolomics, transcriptomics, and antioxidant enzyme assays was employed to investigate six accessions of three Ocimum species (O. × africanum, O. tenuiflorum, O. gratissimum). We identified 296 phenolic acid metabolites, with O. tenuiflorum exhibiting the highest abundance and showing pronounced interspecific variation. Correlation analyses linked specific phenolic acids to enhanced activities of SOD and POD enzymes, indicating a synergistic role in antioxidant defense. Transcriptomic analysis revealed differentially expressed genes (including HCT, C3'H, and CSE) in the phenylpropanoid pathway, underpinning the metabolic diversity. Network pharmacology and molecular docking predicted stable binding of key phenolic acids (e.g., Clinopodic acid B) to core targets like AKT1 and EGFR, implicating pathways related to cancer and inflammation. Our findings elucidate the link between phenolic acid metabolism and stress resilience in Ocimum, highlighting its potential for functional food and crop improvement.