Transcriptomics studies are more likely to achieve predictive results when they rely on tissue- and cell-specific transcriptional data. Identification of cell types in novel model organisms by their transcriptional profiles is difficult without data on transcriptional differences among major tissues and anatomical features. Here we report the first dataset on tissue- and organ-specific transcriptomics in freshwater plankton crustacean Daphnia magna, reporting markers of embryos, hemocytes, gut, carapace, antennae-2 and head, as well as the remaining carcass. Embryos are the most transcriptionally different from adults' features and antennae and the carapace are the most differentiated among them. We demonstrate that transcriptional markers of embryos vs. adults and of various adult anatomy features can be used to provide validation and functional explanation to published differential expression in response to environmental factors like infection, hypoxia, toxicants, or kairomones, to annotate Daphnia single cell data, and to ask questions about transcriptional diversification within extended gene families.

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.

Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Both effects are likely to depend on prior selection on phenotypic and transcriptional plasticity in response to hypoxia, and may therefore show signs of local adaptation. Here we report the lifespan effects of chronic, mild, intermittent hypoxia (CMIH) and short-term survival in acute severe hypoxia (ASH) in four clones of Daphnia magna originating from either permanent or intermittent habitats, the latter regularly drying up with frequent hypoxic conditions. We show that CMIH extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to ASH. Exposure to CMIH did not protect against ASH; to the contrary, Daphnia from the CMIH treatment had lower ASH tolerance than normoxic controls. Few transcripts changed their abundance in response to the CMIH treatment in any of the clones. After 12 hours of ASH treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in mitochondrial and respiratory metabolism, oxygen transport, and, unexpectedly, gluconeogenesis showing up-regulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to ASH than those from permanent habitats, there were no significant hypoxia-by-habitat of origin or CMIH-by-ASH interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through up-regulation of cuticular proteins and neurotrophins, respectively.