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bioRxiv · 10.64898/2026.02.03.703562

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

Atabay, K. D.·Aoude, P.·Park, C.·Kadobianskyi, M.·Paugois, O. H.·Judkewitz, B.·Reddien, P.
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Abstract

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 based on their regional gene expression signatures. The body-wide atlas elucidated cell types harboring adult positional information, 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.

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Atabay, K. D., Aoude, P., Park, C., Kadobianskyi, M., Paugois, O. H., Judkewitz, B., Reddien, P.. 2026-02-05. Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration. https://doi.org/10.64898/2026.02.03.703562

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