Cellular heterogeneity in the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis. Honey bee development cell atlas

It is estimated that animals pollinate 87.5% of flowering plants worldwide and that managed honey bees (Apis mellifera) account for 30-50% of this ecosystem service to agriculture. In addition to their important role as pollinators, honey bees are well established models for studying learning and memory, behaviour, caste differentiation, epigenetic mechanisms, olfactory biology, sex determination and eusociality. Despite their importance to agriculture, knowledge of honey bee genomics lags behind many other livestock species. In this study we have used scRNA-Seq to map cell types to different developmental stages of the worker honey bee (prepupa at day 11 and pupa at day 15), determined their gene signatures and accordingly provide potential functional annotations for genes. To identify cell type populations we examined the cell-to-cell network based on the similarity of the single-cells’ transcriptomic profiles. Grouping similar cells together we identified 63 different cell clusters of which 15 clusters were identifiable at both stages. To determine genes associated with specific cell populations or with a particular biological process involved in honey bee development, we used gene coexpression analysis. We combined this analysis with literature mining, the honey bee protein atlas and Gene Ontology analysis to determine cell cluster identity. Of the cell clusters identified, 9 were related to the nervous system, 7 to the fat body, 14 to the cuticle, 5 to muscle, 4 to compound eye, 2 to midgut, 2 to hemocytes and 1 to malpighian tubule/pericardial nephrocyte. To the best of our knowledge, this is the first reported use of scRNA-Seq within the order Hymenoptera and demonstrates the potential for further work to investigate the biology of honey bees at the single cell level.