Comparative Transcriptomics Reveals the microRNA-Mediated Immune Response of Large Yellow Croaker (Larimichthys crocea) to Pseudomonas plecoglossicida Infection

Visceral white nodules disease (VWND), caused by Pseudomonas plecoglossicida, is a common disease among cage-farmed large yellow croaker (Larimichthys crocea) in China. However, comprehensive investigations of the molecular defensive mechanisms used by L. crocea in response to P. plecoglossicida infection remain relatively rare. Here, we constructed transcriptomes of the L. crocea spleen at 12 h and 24 h after P. plecoglossicida challenge. We identified 518 novel miRNAs and 823 known miRNAs in the spleen of L. crocea. Between the challenge and control groups, 32 differentially expressed miRNAs (DEmiRNAs), predicted to target 356 genes, and 1152 differentially expressed mRNAs (DEmRNAs) were identified at 12 h post-infection, while 33 DEmiRNAs, predicted to target 278 genes, and 1067 DEmRNAs were identified at 24 h post-infection. Gene ontology (GO) analysis showed that 146 and 126 GO terms were significantly enriched in the target genes at 12 h and 24 h, respectively. Twenty-eight and four immune-associated Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched in the target genes at 12 h and 24 h, respectively. Three immune-associated pathways were among those most enriched in the target genes: Toll-like receptor signaling, endocytosis, and C-type lectin receptor signaling. Network analysis identified 47 DEmRNA-DEmiRNA pairs. In particular, the immune-related genes TLR5S and PIGR were targeted by the miRNAs lcr-miR-7132c and dre-miR-183-5p, respectively. Dual-luciferase assays verified that lcr-miR-7132c downregulated TLR5S, suggesting that this miRNA may participate in regulating the immune response of L. crocea to P. plecoglossicida infection through the TLR5S-mediated signaling pathway. Our results help to clarify the miRNA-mediated immune response of L. crocea to P. plecoglossicida infection.