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

Key results

1. ShownA whole-body scRNA-seq atlas of adult Danionella cerebrum resolves cells from all major tissue classes and recovers very rare populations, supporting near-saturation coverage of the transcriptomic states that survive dissociation.

   607,370 cells passed QC across 12 samples, forming 40 broad classes; subclustering gave neural 390,222 cells/95 clusters, epithelial 92,214/47, connective 110,902/42, muscle 10,038/27. pth, rln3a, avp, galn+ neurons (30 to 150 cells CNS-wide) were detected. DESeq2 confirmed 95.7% (internal organs) and 85.4% (CNS) of top-20 Seurat markers. · Single-cell RNA sequencing and profiling cell…; Neural tissues; Non-neural tissues; 10X single-cell mRNA sequencing

2. ShownAdult connective tissue, especially fibroblasts, keeps regional Hox expression along the body axis, and fin fibroblasts persistently express fin-type-appropriate limb-identity factors, consistent with constitutive adult positional information.

   Among 31,756 trunk fibroblasts (19 clusters), Hox genes were top anterior-vs-posterior DE genes; epcam+ epithelial and myod1+ muscle cells lacked this. Pectoral (vs anal) fin enriched tbx5a, lmx1b, hoxc8a; pelvic (vs pectoral) tbx4, pitx1; caudal (vs pectoral) hoxc12a, hoxb13a, hoxc13a; dorsal (vs anal) zic1. HCR-FISH showed tbx5a, hoxc9a, lmx1b in pectoral fin. · Constitutive adult positional information and…; Figure legends

3. SuggestedAcross the adult CNS, neuronal transcriptomic similarity tracks brain region more than neurotransmitter class, and SAMap links Danionella neuron and glia clusters to mouse and zebrafish counterparts largely by regional or developmental identity.

   About 269,000 CNS neurons were collapsed into 206 metacells; hierarchical clustering on PCs of 3000 HVGs split first by region, with neurotransmitter classes nested within region blocks; batch and ARI checks also favored region, especially for glutamatergic cells. GABAergic clusters matched mouse 09-CNU-LGE and 08-CNU-MGE classes; telencephalic glutamatergic clusters matched zebrafish Dp and Dm. · Regional identity drives neuronal transcriptomic…; CNS Region and neurotransmitter class comparison…; Variance partitioning (PERMANOVA) test; Cross-species analysis

4. ShownUnilateral telencephalon injury triggers a staged program on the injured side (wound and myeloid response, radial glia proliferation, remodeling, circuit maturation) and a distinct metabolic/stress response contralaterally, with new glutamatergic neurons integrating.

   127,168 cells in 53 clusters across 5 timepoints (12 hours to 30 days); acute changes concentrated between 12 hours and 7 days, and the contralateral side lacked myeloid recruitment. HCR-FISH confirmed upregulated fabp11a, fabp7a, abcd4a and epd (n=4 for the day 3 panel); EdU labeling marked mature slc17a6a+ glutamatergic neurons in the injured hemisphere. · Regenerative dynamics in the Danionella cerebrum…; Brain injury experiments and regeneration…; Figure legends

5. SuggestedAdult Danionella cell types occupy intermediate, mosaic developmental positions between larval and adult zebrafish references, with larval-like blood and cartilage programs alongside adult-like cardiomyocytes and germ cells.

   Spearman-based developmental-position scoring against the ZMAP larval atlas (0 to 5 days post-fertilization) and 11 pooled adult zebrafish datasets placed Danionella globally between them; erythroid and Schwann cells scored larval-like, cardiomyocytes and germ cells adult-like; embryonic hemoglobins (hbbe2, hbae1.3) and cartilage genes col2a1b and matn4 persisted. · Molecular analysis of paedomorphic features…; Comparative paedomorphic comparison analysis; Developmental-position scoring (per-cell-type…; Figure legends