Integrative metabolomic and transcriptomic analyses reveal coordinated variation in phenolic acid metabolism and...

This study describes the enzymatic and transcriptional correlates of phenolic acid biosynthesis in Ocimum basilicum, suggesting an association between accession-specific metabolic diversity and differences in redox homeostasis under common‑garden conditions. The metabolic diversity of phenolic acids in Ocimum basilicum contributes to its distinct chemical profiles and potential nutraceutical value, but the transcriptional correlates underlying accession-specific variation remain unclear. This study employed an integrated multi-omics approach combining LC-MS/MS metabolomics, antioxidant enzyme assays, and transcriptome sequencing to profile four O. basilicum accessions (G002, G083, G082, and G122). We identified 292 phenolic acids, with 267 showing differential accumulation based on our screening criteria (VIP > 1 and fold change ≥ 2 or ≤ 0.5, used for metabolite prioritization rather than formal statistical inference). Accessions G002 and G122 exhibited distinct antioxidant profiles, characterized by lower lipid peroxidation (MDA), distinct SOD/POD activities, and elevated levels of specific metabolites including rosmarinic acid methyl ester and 5-O-caffeoylshikimic acid. Transcriptomic analysis revealed that the differential expression of key phenylpropanoid pathway genes (e.g., HCT, C3'H, RAS) is correlated with these distinct metabolic profiles. Correlation and network analyses further suggest an association between variation in phenolic acid accumulation to variations in antioxidant enzyme activities. Additionally, computational prediction suggested that the key differential metabolites are predicted to possess multi-target interactions with proteins relevant to human health, providing a basis for hypothesis generation. Our integrative analysis provides insights into the metabolic plasticity of O. basilicum under basal conditions and highlights specific genetic and metabolic signatures associated with O. basilicum redox homeostasis and phenolic acid diversity. These findings provide a basis for further investigation of metabolic variation among accessions.