Single-nucleus profiling highlights the all-brain echinoderm nervous system

Metazoans comprise diverse tissues and cell types, each essential for the survival of the organism. Most of these types are established early in embryogenesis and persist into adulthood. In indirectly developing sea urchins, however, the continuity between embryonic and adult stages is interrupted by a planktonic larval stage that undergoes complete metamorphosis. While gene regulatory networks controlling embryonic and larval lineages are well studied, the molecular and morphological identities of post-metamorphic cell types remain poorly understood. Here, we reconstructed the cell type atlas of post-metamorphic Paracentrotus lividus juveniles using single-nucleus transcriptomics, revealing conservation of regulatory mechanisms. We identified signatures of eight distinct cell type groups and analyzed 29 neuronal families, including 15 unique photoreceptor types. By combining transcriptomics, spatial analysis, and ultrastructure, we identified vertebrate neuronal and opsin homologues expressed across the sea urchin juvenile. These findings show the echinoderm body plan is predominantly head-like and exhibits an “all-brain” organization.