Comparative single-cell transcriptomics of complete insect nervous systems

Molecular profiles of neurons influence information processing, but bridging the gap between genes, circuits and behavior has been very difficult. Furthermore, the behavioral state of an animal continuously changes across development and as a result of sensory experience. How behavioral state influences molecular cell state is poorly understood. Here we present a complete atlas of the Drosophila larval nervous system. We develop polyseq, a python analysis package, and use single molecule RNA-FISH to validate our scRNAseq findings. To investigate how internal state affects cell state, we altered internal state with high-throughput behaviour protocols designed to mimic wasp sting and over activation of the memory system. We found nervous system-wide gene expression changes related to cell state. This work advances our understanding of how genes, neurons, and circuits generate behavior. Single cell genomics and modulation of internal state reveal how genes, neurons, and circuits produce behavior.