Whole-body single-cell atlas of an adult vertebrate, Danionella cerebrum

A complete cell type transcriptome atlas of a vertebrate could promote understanding of animal cell type composition, organization, and evolution. The miniaturized, transparent, and regenerative teleost Danionella cerebrum brings whole-vertebrate single-cell profiling experiments within reach. We performed region-stratified single-cell RNA sequencing across the adult Danionella body and mapped cell types and gene expression at single-cell resolution using spatial transcriptomics. We delineated spatially distinct neural cell types on the basis of their regional gene expression signatures. The body-wide atlas elucidated cell types harboring adult molecular positional memory, uncovered paedomorphic features, and revealed conserved body-region and appendage-specification programs in adult connective tissue. Comparative analyses revealed conserved neural cell types, and regeneration datasets uncovered expression dynamics during telencephalon regeneration. This whole-vertebrate transcriptome atlas yields a comprehensive resource for myriad questions in biology and neuroscience.