A Single Cell Genomics Atlas of the Drosophila Larval Eye Reveals Distinct Developmental Timelines and Novel Markers for All Photoreceptor Subtypes
The Drosophila eye is a powerful model system to study the dynamics of cell differentiation, cell state transitions, cell maturation, and pattern formation. However, a high-resolution single cell genomics resource that accurately profiles all major cell types of the larval eye disc and their spatiotemporal relationships is lacking. Here, we report transcriptomic and chromatin accessibility data for all known cell types in the developing eye. Photoreceptors appear as strands of cells that represent dynamic developmental timelines. Photoreceptor subtypes are transcriptionally distinct when they begin to differentiate, but then appear to assume a common transcriptome as they mature. We identify novel cell type maturation genes, enhancers, and potential regulators, as well as genes with distinct R3 or R4 photoreceptor specific expression. Finally, we observe that photoreceptor chromatin accessibility is more permissive than non-neuronal lens-secreting cone cells, which show a more restrictive chromatin profile. These single cell genomics atlases will greatly enhance the power of the Drosophila eye as a model system. Overall design: The Drosophila larval eye disc was dissected and dissociated into single cells using collagensae and dispase.