Comparative Genomics of Crucian Carp-Isolated Flavobacterium psychrophilum: A Foundation for the Prevention and Control of Overwintering Mortality Syndrome in Freshwater Fish in China

Hucheng jiang¹zhe Zhao²Yanhua Zhao¹Kai Hao²Runbo Li³Aijun Xia^1*Hui Xue^1*

• ¹Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
• ²Hohai University College of Oceanography, Nanjing, China
• ³Jiangsu Marine Fisheries Research Institute, Nantong, China

Flavobacterium psychrophilum is a Gram-negative bacterium that acts as a primary etiological agent of bacterial cold-water disease (BCWD) in salmonid fish. In the past five years, this pathogen has also been isolated from multiple freshwater fish species in China, including crucian carp (Carassius auratus gibelio), grass carp (Ctenopharyngodon idellus) and silver carp (Hypophthalmichthys molitrix), and identified as the causal agent of overwintering mortality syndrome. We report the whole-genome sequencing and analysis of F. psychrophilum strain NJ01, the first isolate from crucian carp, a cyprinid host. The NJ01 genome consists of a circular chromosome of approximately 2.85 Mb with a GC content of 32.5%, encoding about 2,300 predicted proteins. Comparative genomic analysis with reference strains revealed that NJ01 retains the core genomic features of F. psychrophilum while harboring unique genetic elements that may contribute to host specificity and environmental adaptation. NJ01 also harbors genes associated with antibiotic resistance and stress response, suggesting adaptation to aquaculture conditions. Phylogenomic analysis placed NJ01 within a distinct lineage, consistent with CH46 strains isolated from rainbow trout in china. Notably, NJ01 encodes a unique combination of virulence-associated factors such as adhesion proteins, secreted enzymes, and membrane transporters, which may facilitate infection in crucian carp. This study provides novel insights into the genomic basis of F. psychrophilum pathogenicity in a cyprinid host. The distinct virulence gene repertoire of NJ01 highlights potential host-specific pathogenic strategies and broadens current understanding of F. psychrophilum evolution. These findings may support the development of targeted measures for managing emerging F. psychrophilum infections in carp aquaculture.