Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration

A complete transcriptome atlas of every cell type of a vertebrate could promote understanding of animal cell-type composition, organization, and evolution. The miniaturized, transparent, and regenerative teleost Danionella cerebrum brings whole-organism single-cell profiling experiments within experimental reach for adult vertebrate biology. We performed regionally stratified single-cell RNA sequencing experiments in adult Danionella to profile cells across the whole body and mapped cell types and gene expression spatially at single-cell resolution using whole-animal spatial transcriptomics. We delineated spatially distinct neural progenitor and neuronal cell types across the adult nervous system based on their regional gene expression signatures. The body-wide atlas uncovered paedomorphic features, allowed elucidation of cell types likely to harbor adult positional information, and revealed constitutive expression of conserved body region and appendage specification programs in adult connective tissue. Comparative analyses revealed conserved neural cell types over a large evolutionary distance, and neural regeneration datasets uncovered temporally resolved expression dynamics in neural progenitors for telencephalon regeneration. This whole-vertebrate transcriptome atlas yields a comprehensive resource for myriad questions in biology and neuroscience.