scRNA-seq analysis of hemocytes of penaeid shrimp under virus infection

Abstract

The classification of cells in non-model organisms has lagged behind that of model organisms using established cluster of differentiation marker sets. To reduce fish diseases, research is needed to better understand immune-related cells, or hemocytes, in non-model organisms like shrimp and other marine invertebrates. In this study, we used Drop-seq to examine how virus infection affected the populations of hemocytes in kuruma shrimp,Penaeus japonicus, which had been artificially infected with a virus. The findings demonstrated that virus infection reduced particular cell populations in circulating hemolymph and inhibited the expression of antimicrobial peptides. We also identified the gene sets that are likely to be responsible for this reduction. Additionally, we identified functionally unknown genes as novel antimicrobial peptides, and we supported this assumption by the fact that these genes were expressed in the population of hemocytes that expressed other antimicrobial peptides. In addition, we aimed to improve the operability of the experiment by conducting Drop-seq with fixed cells as a template and discussed the impact of methanol fixation on Drop-seq data in comparison to previous results obtained without fixation. These results not only deepen our understanding of the immune system of crustaceans but also demonstrate that single-cell analysis can accelerate research on non-model organisms.

Single Cell Sequencing Provides Clues about the Developmental Genetic Basis of Evolutionary Adaptations in Syngnathid Fishes

“…In less traditional models, the majority of scRNAseq atlases are produced from adult tissues, allowing investigations into cell types, population differences, and genetic networks (e.g. Chari et al, 2021; Fuess & Bolnick, 2023; Hain et al, 2022; Hong et al, 2023; Koiwai et al, 2023; Parker et al, 2022; Potts et al, 2022; Royan et al, 2021; Songco-Casey et al, 2022; Vonk et al, 2023; Woych et al, 2022). Creation of developmental scRNA-seq atlases in non-model organisms is just beginning to accelerate, but many emerging models still lack such a resource, limiting our understanding of their development (e.g.…”