Single-cell transcriptome defines cell-type repertoire of adult Daphnia magna

Detailed knowledge of transcriptional responses to environmental cues or developmental stimuli requires single-cell resolution. We performed 2 single-cell RNAseq experiments of adult 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 >25 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 cell 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 200+ cell types annotated in Drosophila cell atlas. This allowed us to recognize striated myocytes, enterocytes, cuticular cells, as well as 9 different neuron types, including photoreceptors. Several well-defined clusters showed a significant enrichment in markers of both hemocytes and either fat body, or ovaries, or certain neuron types of Drosophila, but not with bulk RNAseq data from circulating hemocytes. This allowed us to hypothesize the existence of noncirculating, fat body-, ovary-, or neuron-associated populations of hemocytes in Daphnia. The circulating hemocytes express numerous cuticular proteins suggesting their role, in addition to macrophagy, in wound repair. Our data will be useful as a baseline resource for researchers using Daphnia to answer questions in ecophysiology, toxicology and biology of adaptation to changing environment.