First Whole-Body Single-Cell Atlas of Adult Vertebrate Generated in Danionella cerebrum

Whitehead Institute researchers have generated the first comprehensive whole-body single-cell atlas of an adult vertebrate, Danionella cerebrum, a tiny, transparent fish. The team analyzed over 600,000 cells from various parts of the fish to create a complete transcriptome atlas, detailing the active genes in each cell. This atlas provides a molecular reference for the fish's cell types, their activity patterns, and their locations.

The atlas offers a new resource for studying brain regeneration, cellular diversity, and tissue function coordination. It also serves as a baseline for investigating how injury, aging, drugs, or changes affect cells throughout the entire animal. The atlas is publicly available through DigiFish, an interactive resource for exploring cell types and gene activity.

The team's findings, published in Science, highlight the potential of this atlas in identifying specific cells and genes for study or manipulation and following their activity in the animal. Danionella cerebrum is one of the smallest vertebrates, with an adult size of around 12 mm and the smallest vertebrate brain, containing approximately 650,000 neurons in a 0.6 mm³ brain.

Its transparent body allows for real-time, single-cell imaging of the entire brain and body. This unique feature, combined with its small size and close genetic relationship to zebrafish, makes Danionella cerebrum an ideal candidate for whole-animal single-cell profiling.