Grass Carp Reovirus (GCRV) and Aeromonas hydrophila (Ah) are the causative agents of haemorrhagic disease in grass carp. The study aimed to investigate the molecular mechanisms and immune responses at the miRNA, mRNA and protein levels in grass carp kidney cells (CIK) infected by Grass Carp Reovirus (GCRV, NV) and Aeromonas hydrophilus (Bacteria, NB) to gain insight into their pathogenesis. Within 48h of infection with Grass Carp Reovirus (GCRV), 99 differentially expressed microRNA (DEMs), 2,132 differentially expressed genes (DEGs), and 627 differentially expressed proteins (DEPs) were identified by sequencing; a total of 92 DEMs, 3,162 DEGs, and 712 DEPs were identified within 48h of infection with Aeromonas hydrophila. It is worth noting that most of the DEGs in the NV group were primarily involved in cellular pro-cesses, while most of the DEGs in the NB group were associated with metabolic path-ways based on KEGG enrichment analysis. This study revealed that the mechanism of grass carp hemorrhage caused by GCRV infection differs from that caused by Aeromonas hydrophila infection. An important miRNA-mRNA-protein regulatory network was es-tablished based on comprehensive transcriptome and proteome analysis. Furthermore, 14 DEGs and 6 DEMs were randomly selected for verification of RNA/small RNA-seq data by RT-qPCR. Our study not only contributes to understanding of the pathogenesis of grass carp CIK cells infected with GCRV and Aeromonas hydrophila but also serves as a significant reference value for other aquatic animal haemorrhagic diseases.
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