Temporal changes in the transcriptome profile of Macrobrachium rosenbergii in response to decapod iridescent virus 1...

The farming of Macrobrachium rosenbergii faces significant challenges due to infections caused by Decapod iridovirus 1 (DIV1). To gain deeper insights into the dynamic immune regulatory processes of M. rosenbergii in response to DIV1 infection, RNA sequencing (RNA-seq) was employed to profile the transcriptome in the hepatopancreas at 24, 48, 72, and 96 hours post-infection (hpi). Time-course analysis revealed 3,339 differentially expressed genes (DEGs), which exhibited distinct expression patterns across various stages of infection. At 24 hpi and 48 hpi, the top 20 enriched pathways included 3 immunity-related pathways (Lysosome, Phagosome, C-type lectin receptor signaling) and 7 metabolism-related pathways at 24 hpi, and 5 metabolism-related pathways at 48 hpi. In contrast, in the later stages of infection (72 hpi), 13 of the top 17 enriched pathways associated with DEGs were metabolism-related, including those involved in antioxidant defense, such as the Peroxisome, Cysteine and methionine metabolism, and Glutathione metabolism. At 96 hpi, pathways related to ECM-receptor interaction, Purine metabolism, and Lysosome were significantly enriched. Among the DEGs, a total of 16 genes were consistently identified across all time points, with 14 of these genes, including alpha-2-macroglobulin-like, alpha-amylase 1-like, putative aldolase class 2 protein PA3430, platelet-derived growth factor subunit B-like, serum amyloid A-5 protein-like, phenoloxidase-activating enzyme-like, pantetheinase-like, and perlucin-like protein, demonstrating sustained upregulation at all time points. In contrast, the gene encoding rhodanese domain-containing protein CG4456-like was consistantly downregulated. Additionally, weighted gene co-expression network analysis (WGCNA) indicated several hub genes that were tightly connected to intercellular communication, such as innexin shaking-B-like and innexin inx3-like, and endochitinase A1-like. The gene expression changes varied over time, exhibiting a dynamic, time-dependent pattern that underscores the complexity of host-pathogen interactions. These results provide new insights into the cellular mechanisms influenced by DIV1 throughout the infection process, offering valuable knowledge for developing virus control strategies in shrimp aquaculture.