Abstract

not-yet-known not-yet-known not-yet-known unknown Detailed knowledge of transcriptional responses to environmental cues is impossible without single cell (SC) resolution data. We performed two SC RNAseq experiments surveying transcriptional profiles of females and males of Daphnia magna, a freshwater plankton crustacean which is both a classic and emerging new model for eco-physiology, toxicology, and evolutionary genomics. We were able to identify over 30 distinct cell types about half of which could be functionally annotated. First, we identified ovaries- and testis-related cell types by focusing on female- and male-specific clusters. Second, we compared markers between SC clusters and bulk RNAseq data on transcriptional profiles of early embryos, circulating hemocytes, midgut, heads (containing brain, eyes, muscles, and hepatic caeca), antennae II, and carapace. Finally, we compared transcriptional profiles of Daphnia cell clusters with orthologous markers of 250+ cell types annotated in Drosophila cell atlas. This allowed us to recognize striated myocites, gut enterocytes, cuticular cells, as well as 5 different neuron types, including photoreceptors. One well-defined cluster showed a significant enrichment in markers of both hemocytes and fat body of Drosophila, but not with bulk RNAseq data from circulating hemocytes, allowing us to hypothesize the existence of non-circulating, fat body-associated population of hemocytes in Daphnia. On the other hand, the circulating hemocytes express numerous cuticular proteins suggesting their role, in addition to macrophagy, in wound repair. The baseline SC resource presented here will be useful for a variety of researchers using Daphnia to answer in-depth questions in ecophysiology, toxicology and biology of adaptation to changing environment.