The first whole-body single-cell atlas of an adult vertebrate is here. Using the miniature transparent fish Danionella cerebrum, researchers generated the first whole-body single-cell transcriptomic atlas of an adult vertebrate, profiling 607,000+ cells across the entire organism and integrating scRNA-seq with MERFISH spatial transcriptomics. Beyond cataloging cell types, the atlas uncovers conserved positional memory programs, reveals how adult neurons are organized by developmental origin rather than neurotransmitter identity, and maps regenerative dynamics following brain injury. Key findings • Constructed a whole-body atlas of 607,370 cells, identifying 40 major tissue classes and nearly 100 neural cell types spanning the central and peripheral nervous systems. • Combined single-cell RNA sequencing with 500-gene MERFISH to spatially localize cell types throughout the entire adult vertebrate body. • Adult connective tissue retains embryonic positional information, including persistent HOX gene expression and conserved appendage-patterning programs (e.g., TBX5, TBX4, PITX1, LMX1B) in adult fins. • Comparative analyses reveal that neuronal transcriptomes are organized primarily by brain region/developmental origin, rather than neurotransmitter identity—an organizing principle shared with mammals. • Molecular signatures indicate mosaic paedomorphosis, with adult Danionella retaining both larval- and adult-like transcriptional programs across multiple tissues. • Time-resolved single-cell profiling after telencephalic injury defines sequential regenerative programs involving radial glial activation, immune remodeling, neurogenesis, and neuronal maturation, providing a roadmap of vertebrate brain regeneration. Why it matters This resource establishes Danionella cerebrum as a uniquely powerful vertebrate model for systems biology. Its miniature, transparent body makes organism-wide molecular mapping feasible, enabling future studies of aging, regeneration, neural circuits, disease, pharmacology, and evolution at single-cell resolution. The atlas also provides one of the most comprehensive references yet for understanding vertebrate cell diversity and tissue organization. #SingleCell #SpatialTranscriptomics #MERFISH #Danionella #CellAtlas #Neuroscience #Regeneration #StemCells #DevelopmentalBiology #Evolution