Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly

Abstract

The ability to obtain single cell transcriptomes for stable cell types and dynamic cell states is ushering in a new era for biology. We created the Tabula Drosophilae, a single cell atlas of the adult fruit fly which includes 580k cells from 15 individually dissected sexed tissues as well as the entire head and body. Over 100 researchers from the fly community contributed annotations to >250 distinct cell types across all tissues. 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 that are shared between tissues, such as blood and muscle cells, allowed the discovery of rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the entire Drosophila community and serves as a comprehensive reference to study genetic perturbations and disease models at single-cell resolution.

TM2D genes regulate Notch signaling and neuronal function in Drosophila

“…According to large-scale transcriptomic studies, mRNA of amx , amrt and bisc are expressed relatively ubiquitously with some enrichment found in the female ovary [ 37 , 38 ]. Within the ovary, these three genes are likely to be expressed in similar cell types including germline cells and follicle cells according to a large single cell RNA-sequence database that have recently been released on the bioRxiv preprint server [ 39 ]. To further test whether amx , amrt and bisc do not have overlapping functions, we assessed whether genomic rescue transgenes for amrt or bisc can rescue amx mutants.…”

Sex determination gene transformer regulates the male-female difference in Drosophila fat storage via the adipokinetic hormone pathway

“…Because some, but not all, of these studies identify a cell type in which Tra function influences these diverse phenotypes, future studies will need to determine which cell types and tissues require Tra expression to establish a female metabolic and physiological state. Indeed, recent single-cell analyses reveal widespread gene expression differences in shared cell types between the sexes ( Li et al, 2021 ).…”

The cell as a bag of RNA

“…This is the power of single-cell transcriptomics, which provides vast, multidimensional information regarding a cell's identity and physiology. My colleagues and I have spent a substantial amount of effort creating whole organism cell atlasesof flies [31], mice [32,33], lemurs (https://tabula-microcebus.ds.czbiohub. org/about) and humans [34] as have others in the community [35][36][37][38].…”

“…For example, the Tabula Muris Senis has helped us understand at a global level how gene expression changes with age, which cell types are most affected, and which of these aspects are reversible via rejuvenation approaches such as parabiosis [33,39]. As another example, the Tabula Drosophila has helped reveal how gene expression depends on sex, and has identified which cell types have the highest levels of sex-biased gene expressionthis is a launching pad to help understand how these differences meet the distinct developmental and physiological needs of males and females [31]. I view them as phenotypic companions to the genome: the genome is most accurately described as the parts list but not the blueprint of the organism.…”