Identification of neuronal lineages in the Drosophila peripheral nervous system with a novel multi-spectral lineage tracing system

Elucidating cell lineages provides crucial understanding of development. Recently developed sequencing-based techniques enhance the scale of lineage tracing but eliminate the spatial information offered by conventional approaches. Multispectral labeling techniques, such as Brainbow, have the potential to identify lineage-related cells in situ. Here, we report Lineage Tracker Bitbow, a \"digital\" version of Brainbow that greatly expands the color diversity, and a suite of statistical methods for quantifying the lineage relationship of any two cells. Applying these tools to Drosophila peripheral nervous system, we determined lineage relationship between all neuronal pairs. Based on the refined lineage map, we explored whether distinct cis-regulatory elements are used in controlling the expression of a terminal selector gene in distinct lineage patterns. This study demonstrates LT-Bitbow as an efficient tool for in-situ lineage mapping and its potential in studying molecular mechanisms in the lineage context.