Metabolomic Profiling of Pogostemon cablin Reveals Disruption of Secondary Metabolite Biosynthesis Induced by Corynespora cassiicola Infection

<i>Pogostemon cablin</i> (patchouli) is an economically important aromatic plant widely used in the fragrance and pharmaceutical industries. This study investigates the effects of Corynespora leaf spot disease (CLSD) on the metabolic profiles and patchouli alcohol content of patchouli leaves. Utilizing gas chromatography-mass spectrometry (GC-MS), real-time PCR (qPCR), and comprehensive non-targeted metabolomic analyses (HS-SPME-GC-MS and LC-MS/MS), we compared diseased (LD-TJ) and healthy (CK) leaves. Results revealed a significant 51% reduction in patchouli alcohol content in CLSD-infected leaves, which was correlated with a 94% decrease in expression of the patchoulol synthase (PTS)-encoding gene (<i>p</i> < 0.01) and a 79% reduction in farnesyl pyrophosphate synthase (FPPS)-encoding gene expression (<i>p</i> < 0.05), both critical for terpenoid biosynthesis. Metabolomic analyses identified extensive disruptions in both volatile and non-volatile compounds, with the majority of differential abundance metabolites (DAMs) being downregulated. Key metabolic pathways, including beta-alanine metabolism and nicotinate/nicotinamide metabolism, were notably affected, indicating broader metabolic instability. Additionally, crucial transcription factors involved in terpenoid biosynthesis were significantly downregulated, indicating a potential mechanism by which <i>C. cassiicola</i> may compromise patchouli quality through modulation of host metabolic processes. These findings underscore the urgent need to develop disease-resistant <i>P. cablin</i> cultivars through genetic and metabolic engineering to enhance the sustainability and productivity of this valuable industrial crop.