Genome-Wide Identification of the TRAF Gene Family in Common Carp (Cyprinus carpio) and Analysis of Their Expression in Response to CyHV-3 Challenge

Tumor necrosis factor receptor-associated factors (TRAFs) are key signal transduction molecules in innate immunity and are involved in multiple immune pathways, such as TNF receptor and Toll-like receptor signaling. In this study, 16 CcTRAFs were identified from the common carp genome, assigned to six subfamilies (TRAF1/2/3/4/6/7), with no TRAF5 found. Significant paralogous expansion was observed in the TRAF2/4 subfamilies. All CcTRAF proteins were predicted to be unstable and hydrophilic by ProtParam analysis; most contain conserved RING, TRAF and MATH domains, whereas CcTRAF7 carries seven WD40 domains. Gene structure and conserved motif analysis revealed high conservation of exon numbers and motif compositions within each subfamily, while the TRAF7 subfamily displayed distinct characteristics. Collinearity analysis further indicated that segmental duplication promotes CcTRAF family expansion. qRT-PCR showed that CcTRAF genes have tissue-specific expression patterns and are preferentially expressed in the liver, spleen, and kidney. Under CyHV-3 infection, the expression levels of CcTRAF3/6/7 in these tissues first increased and then decreased, peaking at 48 h post-challenge. In summary, CcTRAF genes, especially CcTRAF3/6/7, play important roles in the immune response of common carp against CyHV-3. This study provides a molecular basis for understanding innate immune regulation in teleost fish and the functional roles of TRAF genes.