Integrated Multi-Omics Reveals Variation in Organic Acid Regulation Among Four Ocimum Species

Ocimum species are widely recognised for their diverse metabolic profiles, and recent multi-omics studies have substantially advanced the characterisation of their non-volatile metabolites. However, organic acids have not been systematically compared across Ocimum species using integrated metabolomic and transcriptomic approaches. Here, widely targeted metabolomics was used to profile organic acids across 10 accessions of four Ocimum species, identifying 70 compounds, 52 of which were common to all examined accessions. Leaf trait variation was observed among accessions, but morphological clustering diverged from species taxonomy, indicating phenotypic plasticity, whereas organic acid profiles showed clearer species- and accession-level differentiation. The two O. gratissimum accessions examined here lacked α-ketoglutaric and chelidonic acids and accumulated unique metabolites, while the two O. × africanum accessions showed hybrid-specific enrichment of Subclass 2 metabolites. Transcriptomic integration revealed jasmonic acid pathway expression differences generally associated with the accumulation of tuberonic acid glucoside and 12-hydroxyjasmonic acid glucoside. Notably, accession G144 showed high tuberonic acid glucoside accumulation despite low expression of core pathway genes, indicating that transcript abundance alone cannot fully explain metabolite levels and that additional post-transcriptional or enzyme-level regulation may be involved, a possibility requiring further experimental validation. This work provides a comprehensive organic acid profile of Ocimum, highlighting jasmonate derivatives as candidate species- or accession-level markers and offering a framework for understanding organic acid diversification, while broader genus-wide validation is required.