Transcriptome and metabolome profiling of Macrobrachium rosenbergii reveals immune defense mechanisms against decapod iridescent virus 1

Abstract

The giant freshwater prawn Macrobrachium rosenbergii is a globally vital aquaculture species threatened by decapod iridescent virus 1 (DIV1), which causes severe economic losses. This study integrated transcriptomic and metabolomic profiling to elucidate immune defense mechanisms in M. rosenbergii against DIV1. Transmission electron microscopy revealed viral proliferation in hepatopancreatic and gill tissues, with higher virion density in gills. Artificial infection experiments classified individuals into susceptible (S) and resistant (R) groups. Transcriptome analysis identified 768 unique differentially expressed genes (DEGs) in S-vs-R comparisons, enriched in oxidative phosphorylation, HIF-1 signaling, and PI3K-Akt pathways. Metabolomics highlighted perturbations in arginine biosynthesis, with elevated N-α-acetylcitrulline, citrulline, and L-arginine in resistant prawn, suggesting enhanced nitric oxide-mediated antiviral responses. Integrated multi-omics analysis revealed coordinated regulation of MAPK, calcium signaling, and mTOR pathways, alongside ABC transporters linked to metabolite detoxification. Key genes (JNK, RHOA, TAB1, AKT, PI3K, STAT) were validated via qRT-PCR, showing upregulated expression in resistant individuals. These findings uncover metabolic reprogramming and immune signaling adaptations critical for DIV1 resistance, providing insights for breeding disease-resistant prawn varieties and informing targeted therapeutic strategies to mitigate aquaculture losses.