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How flies develop sight: Scientists use single-cell sequencing to identify cell types in the visual system

Researchers discover new types of cells in the brain of developing flies thanks to a new method that creates cell-type-specific genetic tools
August 1, 2023

New York University researchers have discovered new cell types in the visual system of flies, made possible by their creation of a tool that finds and labels neurons during development.

The study, published in the journal Proceedings of the National Academy of Sciences (PNAS), combines single-cell sequencing data with a novel algorithm to identify pairs of genes that point to previously unknown cells in the brains of fruit flies.

Scientists could identify roughly half of the 200 cell types in the developing fly’s visual system based on their gene expression and prior studies, but they lacked a way to more easily study and label the other 100 cell types. Existing tools that allowed precise manipulation of neural circuits of adult fruit flies often failed to label the same neurons during development, rendering these tools unfit to study cells in the developing brain.

In this study, the scientists created a tool that takes advantage of the extensive single-cell sequencing data for the developing fly visual system to identify genes—and combinations of genes—that are exclusively expressed in certain cell types. The researchers systematically identified pairs of genes that are uniquely expressed in the majority of cell types in the fruit fly’s visual system at multiple stages of development. One such gene pair led to the discovery of MeSps, a brand-new cell type.

The researchers note that their tools can also be used to study other systems beyond vision in the developing fly, as long as single-cell data are available.