The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and a multi-informatic analysis paradigm

The Drosophila type-II neuroblast (NB) lineages present an attractive model to investigate the neural differentiation process. With only 16 stem cells, the type-II NB lineages generate many intermediate neural progenitors (INPs) to rapidly expand the neuron and glia pool, similar to those in the human outer subventricular zone (OSVZ). We performed targeted single-cell mRNA sequencing (scRNA-seq) in 3rd instar larval brains and created MiCV, an scRNA-seq data visualization web tool to integrate results from multiple bioinformatics analyses, display co-expression patterns of multiple genes simultaneously, and retrieve gene function and ortholog annotations. We identified novel markers that label distinct neural subsets using MiCV and subsequently in situ profiled them to recover the spatial information lacking in the scRNA-seq data. These new markers further enabled us to build novel neural developmental trajectories that lead to unique neuronal cell fates. Combining prior knowledge, in silico analyses, and in situ evidence, this multi-informatic investigation describes the molecular landscape of neural differentiation from a single developmental snapshot in Drosophila , and provides an experimental and analytical roadmap for navigating the differentiation process of more complex brains. ### Competing Interest Statement NSM is the founder of MiOmics Inc. (MI, USA). All other authors declare no conflicts of interest.