Integrated Metabolomic and Transcriptomic Analysis Reveals the Response Mechanisms of Phallus rubrovolvatus to Yeast Pathogen Infection

Phallus rubrovolvatus is a valuable edible and medicinal mushroom, but its cultivation is severely hindered by yellow rot disease caused by Saccharomycopsis phalli , which shows a 60 to 80% incidence and causes severe fruiting body rot, yield loss, and quality decline. The molecular mechanisms, particularly the dynamic transcriptional and metabolic responses, underlying the defense of P. rubrovolvatus against S. phalli remain poorly understood, limiting the development of targeted control strategies. To address this gap, we conducted an integrated transcriptomic and metabolomic analysis, identifying differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) at 8, 16, 32, and 48 hours post-inoculation (hpi). Results showed significant changes in the pentose and glucuronate interconversion pathway, with reduced expression of related genes (e.g., ARD1, XR ) and decreased accumulation of metabolites (e.g., D-glucuronic acid). Conversely, the arginine biosynthesis pathway was significantly enriched, with accumulated intermediates (e.g., citrulline, argininosuccinic acid) and upregulated biosynthesis genes (e.g., glnA, rocF ). Alanine, aspartate and glutamate metabolism was also implicated in the infection response, mediating carbon-nitrogen skeleton flux and energy allocation to meet physiological demands. Additionally, glutathione metabolism was significantly enriched, accompanied by upregulated glutathione S-transferase ( GST ) genes. Overall, this study reveals a multi-pathway defense response in P. rubrovolvatus against S. phalli across the infection time course, involving coordinated carbon–nitrogen metabolic reprogramming and antioxidant defense activation, offering theoretical insight into its disease resistance mechanisms and supporting breeding of yellow rot-resistant varieties.