For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae , that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type–related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

The developing Drosophila heart consists of cardioblasts that differentiate into different types of cardiomyocytes and pericardial cells. A large body of work has identified numerous genes and pathways involved in heart specification and differentiation, downstream of cardiac transcription factors, such as Tinman (NKX2-5) and Dorsocross1/2/3 (TBX5). The advent of single-cell RNA sequencing (scRNAseq) technology allowed us for the first time to describe the transcriptome of different cardiac cell types in the Drosophila model at high resolution. Here, we applied scRNAseq on sorted cells of late-stage Drosophila embryos expressing a cardiac GFP reporter. We find distinct expression profiles of cardioblasts as they mature to cardiomyocytes, as well as discretely clustering pericardial cells, including a set expressing Tinman that potentially assist in heart morphogenesis. In addition, we describe other cell types that were sequenced as by-catch due to low but distinct extracardiac expression of the GFP reporter. Our studies on wildtype cardioblasts will be the foundation for investigating developmental profiles in mutant backgrounds and for generating gene regulatory networks at single-cell resolution during cardiogenesis.