Transcriptomic study of WSSV infection in Litopenaeus vannamei lymphoid organ via single nuclei RNA sequencing

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 pathogenic diseases such as white spot disease (WSD), which results in severe stock losses and animal health and welfare.In this study, we used novel techniques to study the impact of white spot syndrome virus (WSSV), the causative agent of WSD, on Pacific whiteleg shrimp (Litopenaeus vannamei), and uncover additional information that may be used in creating WSSV-resistant shrimp stocks. We set up a pathogen challenge comprising of 32 adult whiteleg shrimp infected by either feed or injection of WSSV. Mid to late-stage infected individuals were sacrificed and their lymphoid organs were collected. We then developed new protocols for TST-based nuclei isolation and used them to prepare our samples for single nuclei RNA-sequencing.We constructed a cell atlas for the lymphoid organ to improve our understanding of the characteristics of this immune organ, constructed the UMAPs and investigated the role of the gene markers to determine the identity of our clusters. By comparing gene expression between the control and WSSV-infected samples we uncovered multiple genes of interest that that have the potential to be used as targets for CRISPR gene editing for WSSV-resistance in Pacific whiteleg shrimp. These genes have the potential to be valuable assets for future gene editing studies in commercially important penaeid shrimp species.