Abstract

Lipids play multifaceted roles beyond structure and storage, yet their diversity within medicinally important genera like Isatis is poorly characterized. This study conducted the integrated lipidomic and transcriptomic analysis of three Isatis species, namely, I. oblongata , I. tinctoria , and I. indigotica . Lipidomics identified 324 metabolites, with isoprene lipids being most abundant. Analysis revealed a conserved core lipidome (301 metabolites) alongside species-unique compounds. Statistical and machine-learning screening of 215 differential lipids identified six key metabolites with strong species-specific patterns, serving as potential chemical markers. Transcriptomics uncovered thousands of differentially expressed genes, including a conserved core set. Integrated analysis established a plausible transcriptional basis for the gradient accumulation of LysoPE 18:1, linked to differential expression of PLA2 and LPEAT genes. This multi-omics resource elucidates the regulatory basis of lipid metabolic divergence in Isatis , establishing a foundational framework for chemotaxonomy and future metabolic engineering in this genus.