Single-cell RNA sequencing of Pacific white shrimp hepatopancreas infected with Vibrio parahaemolyticus

The shrimp aquaculture industry is vulnerable to large losses due to acute hepatopancreatic necrosis disease (AHPND), caused by the bacterium Vibrio parahaemolyticus. The mechanism by which the pathogen causes disease, and the host immune response, is not completely understood. The shrimp hepatopancreas is a multi-functional organ with roles in digestion, immunity, molting and reproduction. Therefore, we set out to characterize the cells of the hepatopancreas and the host response to Vibrio parahaemolyticus infection at single-cell resolution. The hepatopancreas from three individual shrimp were processed to create a single-cell transcriptomic atlas. Then the hepatopancreas from three Vibrio parahaemolyticus infected and two mocked treated shrimp were sampled for infection study. All single-cell libraries were generated using the 10X Genomics platform and sequenced on an Illumina sequencer. Data were aligned to the Litopenaeus vannamei reference genome using Cell Ranger. Seurat and clusterProfiler were used for downstream analyses. Cells of the hepatopancreas were characterized and the transcriptomic response to AHPND-causing V. parahaemolyticus was examined. Data will inform further functional studies and has the potential to aid in the development of novel preventative measures or treatments. Overall design: Atlas: shrimp (average 13 g) were housed in 50 L tanks (23°C, 16.5 ppt salinity). Prior to sampling, the shrimp were not fed for 18 hours. Infection: 70 shrimp (average 19 g) were dispersed evenly between seven 50 L tanks (28°C, 4 ppt salinity). The shrimp were not fed for 24 hours prior to the infection. Mock (n = 30) and infection (n = 40) treatments were randomly assigned to the tank groups. The control shrimp were treated via reverse gavage with 100 µl of media, while the shrimp in the treatment group were infected with 100 µl of V. parahaemolyticus (6.90 x 10^5 cfu/ml). A total of 2 mock and 3 infected shrimp hepatopancreas samples were collected one hour after treatment.