Aquaculture is the fastest growing farmed food sector in the world and is a key part of global food security. Crustacean aquaculture, while being one of the most profitable sectors, is threatened by pathogens such as white spot syndrome virus (WSSV), which results in severe stock losses and animal health and welfare problems.
Here, we employed single-nuclei RNA sequencing technology to study WSSV-infected and non-infected Pacific whiteleg shrimp (Litopenaeus vannamei) to identify genes involved in the WSSV infection process. To achieve this, we optimized disease challenge protocols in adult shrimps, developed new protocols for nuclei isolation of lymphoid organ, and compiled a cell atlas for the tissue (Figure 1), significantly improving our understanding of both the host transcriptome and the cell heterogeneity present in this tissue. Differential analyses between infected and control animals revealed key cell types and genes involved in the response to WSSV in whiteleg shrimp. The genes identified as important in infection in this study provide crucial insights for the development of effective therapeutic strategies to combat WSSV in shrimp aquaculture.