| Summary: | <i>Aeromonas veronii</i> is a major pathogen threatening freshwater aquaculture, yet the molecular mechanisms of <i>Pelteobagrus vachellii</i>’s immune response to this infection remain unclear. This study integrated histopathology, mRNA-seq and small RNA-seq to investigate <i>P. vachellii</i>’s response to <i>A. veronii</i> at 48 h post-challenge. Histopathologically, infection induced gill epithelial detachment, hepatocyte swelling with cytoplasmic vacuolation, and melanomacrophage centers (MMCs) in the mid-kidney (histological assessment of the head kidney was not feasible due to sampling limitations associated with its small size). Transcriptomic analysis identified 1210 differentially expressed genes (DEGs) in the head kidney (819 downregulated, 391 upregulated), significantly enriched in 11 immune pathways (e.g., NF-κB, Th17 cell differentiation, Complement and coagulation cascades), with key immune genes (e.g., <i>IL-1β</i>, <i>TCRα</i>, <i>CCL4</i>) upregulated. Gene Set Enrichment Analysis (GSEA) revealed activation of the proteasome, ribosome and oxidative phosphorylation pathways, and suppression of the autophagy-animal, FoxO and AMPK pathways. Small RNA-seq identified 544 known and 958 novel miRNAs in the head kidney, with 42 downregulated and 36 upregulated differentially expressed miRNAs (DE miRNAs). The miRNA-mRNA network showed that DE miRNAs (e.g., miR-101-y/z, miR-132-z, miR-3167-y) negatively regulated immune-related target genes (<i>IL-1R1</i>, <i>IRF4</i>, <i>IκBα</i>) in core immune pathways. Collectively, this study clarifies the pathological and miRNA-mRNA regulatory modules of <i>P. vachellii</i> head kidney against <i>A. veronii</i> infection, providing valuable information that enables the further analyses of the defense mechanisms of <i>P. vachellii</i> against <i>A. veronii</i> infection.
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