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Ceratocystis fimbriata, a widespread plant pathogenic fungus, causes symptoms such as black spots, wilting, and death on various plants. Pomegranate wilt, caused by this fungus, is a devastating disease in which chlamydospores play a key role in the disease cycle. In this study, we performed transcriptomic and metabolic analyses on three C. fimbriata strains (A4, F1, and D1) obtained from the Plant Pathology Laboratory of Xichang University. We compared mycelia samples collected before and after chla-mydospore formation. Our analysis identified 3,395 differentially accumulated metab-olites and 4,268 differentially expressed genes. By integrating the transcriptome and metabolome data, we found 63, 44 and 57 metabolic pathways enriched in each strain, respectively. Notably, 29 pathways were shared across all three strains, predominantly those associated with amino acid biosynthesis, cofactor biosynthesis, carbon metabo-lism and 2-oxocarboxylic acid metabolism. Furthermore, genes related to branched-chain transaminase and citrate synthase-related genes were enriched in these core pathways. These findings suggest that branched-chain transaminase and citrate synthase play important roles in chlamydospore formation.