Expression Profile of Transfer RNA-Derived Fragments in Chinese Mitten Crab (Eriocheir sinensis) After Challenge with Aeromonas hydrophila

The Chinese mitten crab (Eriocheir sinensis) is an important cultured crab in China; however, its aquaculture productivity is severely limited by bacterial pathogens, including Aeromonas hydrophila. Transfer RNA-derived fragments (tRFs) are an emerging class of functional small non-coding RNAs that have been implicated in host–pathogen interactions and immune regulation; yet, their roles in the antibacterial defense of crustaceans remain poorly understood. To investigate the immune response of the Chinese mitten crab to A. hydrophila infection, we employed high-throughput sequencing to characterize the expression profiles and functional features of tRFs in crab hemocytes following a bacterial challenge. The results revealed that tRFs exhibited a conserved length distribution (15–20 nt) and subtype composition, with 5′-tRFs representing the dominant subtype in both control and infected groups. Notably, infection specifically induced the abundance of tRF fragments of 35-nt tRF fragments and slightly altered the proportion of tRF subtypes. Differential expression analysis identified 415 significantly upregulated and 3 downregulated tRFs upon A. hydrophila infection, suggesting widespread changes in tRF abundance during infection. Target prediction and functional enrichment analyses were performed for the top 30 differentially expressed tRFs; the predicted targets were significantly associated with VEGF signaling pathway, DNA replication proteins, FoxO signaling pathway, and NF-kappa B signaling pathway. The reliability of the sequencing data was confirmed by stem-loop RT-qPCR validation. Collectively, our findings advance the understanding of tRF expression in crustacean immunity and suggest that tRFs may be associated with the immune response of crabs against bacterial infection, pending functional validation.