Integrated transcriptomic and metabolomic analyses reveal flavonoid and lipid metabolic reprogramming in <i>Dendrobiumofficinale</i> during <i>Colletotrichum fructicola</i> -induced anthracnose

Anthracnose disease caused by <i>Colletotrichum fructicola</i> severely compromises the medicinal value and yield of <i>Dendrobium officinale</i>. To elucidate the host metabolic response to pathogen infection, we integrated transcriptomic and metabolomic analyses of <i>D. officinale</i> challenged with <i>C. fructicola</i>. Our results revealed a profound metabolic reprogramming orchestrated by the pathogen, characterized by upregulated flavonoid biosynthesis (<i>e.g.</i>, <i>DFR</i>, <i>LDOX</i> activation) and enhanced lipid catabolism (<i>e.g.</i>, β-oxidation <i>via LACS</i>, <i>DECR</i>, <i>HACL</i>). Metabolite profiling demonstrated a significant reduction in phosphatidylcholine (PC) and phosphatidylethanolamine (PE) alongside increased free fatty acids, indicating active lipid degradation. Notably, acyl-CoA intermediates linked lipid catabolism to flavonoid production, suggesting a metabolic axis where pathogen-induced lipid breakdown fuels defense-related secondary metabolite synthesis. This study identifies flavonoid and lipid metabolic reprogramming as critical axes in host-pathogen interactions, providing a foundation for developing targeted disease control strategies.