Decoding eggplant fruit: Multi-omics profiling of caffeoyl-CoA-3-OMT expression

•Eggplant is a rich source of health-promoting phenolic acids, mainly chlorogenic acid (CGA).•CGA has various health benefits.•Study identified and analyzed key genes involved in the CGA biosynthesis pathway of eggplant.•This study highlights the potential of engineering the CGA biosynthesis pathway of eggplant. Eggplant (Solanum melongena L.) is a rich source of health-promoting phenolic acids, mainly chlorogenic acid (CGA), and trace elements. CGA has been shown to have antioxidant, anti-inflammatory, neuroprotective, cardioprotective, anticancer, and antidiabetic properties. The natural genome of eggplants contains essential genes for beneficial traits like drought tolerance, disease resistance, and high concentrations of medicinal substances. Transcriptomic analysis of eggplant overexpressing the hydroxycinnamoyl CoA quinate hydroxycinnamoyl transferase (HQT) gene revealed upregulation of 2165 genes, including three similar to HQT and cinnamate-4-hydroxylase (C4H). Sequence similarity analysis showed homology to caffeoyl-CoA O-methyltransferases, key enzymes in the phenylpropanoid pathway leading to CGA biosynthesis. Gene ontology and KEGG pathway analysis identified 5 highly upregulated glycosyltransferase family 43 genes (650.3-fold change). Glycosyltransferases like UDP-glucose:cinnamate glucosyltransferase and cinnamate-glucose 4′-O-glucosyltransferase are crucial for CGA production in eggplant. qRT-PCR validated the potential upregulation of HQT and C4H in transgenic eggplants. Comparative analysis revealed eggplant has the highest CGA content (5–8.1 g/kg dry weight) among vegetables, with foliar CGA acting as a natural insecticide. CGA offers antioxidant, hypoglycemic, antiviral, and hepatoprotective benefits to humans. This study highlights the role of HQT and C4H in elevating the medicinal properties of eggplant through CGA biosynthesis pathway engineering.