Genome-wide DNA methylation and transcriptome analysis of the Pacific white shrimp Penaeus vannamei post-WSSV infection

The Pacific white shrimp, Penaeus vannamei, is a globally significant aquaculture species, but it faces major threats from the white spot syndrome virus (WSSV) due to the virus's broad host range and high lethality. Although various studies have explored the molecular mechanisms of P. vannamei resistance to WSSV, the role of epigenetics, particularly DNA methylation, remains underexplored. DNA methylation, a key epigenetic modification, can influence gene expression and immune response. This study conducted genome-wide DNA methylation and transcriptome analysis at different post-infection stages. The results showed a significant decrease in genome-wide DNA methylation post-WSSV infection, corresponding with the upregulation of many differentially expressed genes (DEGs), particularly in the CG context. Early in the infection, classic immune pathways like JAK-STAT and p53 were enriched in differentially methylated region (DMR) related DEGs. However, in the later stage, immune-related pathways declined, giving way to pathways involved in cellular and metabolic processes, suggesting an adaptation phase where the shrimp's immune system adjusts to prolonged infection by managing cellular processes and metabolic demands.