Muller glia mediated regeneration restores neuronal diversity and retinal circuit organization in the adult zebrafish

The ability to regenerate neurons with the appropriate identities and connectivity is a major challenge in regenerative neuroscience. Unlike mammals, zebrafish can regenerate retinal neurons after injury through reprogramming of endogenous Muller glia. However, it remains unclear how closely regenerated neurons match the identities, diversity and structural features of the cells that were lost. Here, we combined inducible lineage tracing, single-cell RNA sequencing and morphological analysis to define the molecular and structural features of Muller glia-derived neurons in the adult zebrafish retina. Using light lesion and NMDA injury to selectively ablate photoreceptors or inner retinal neurons, we found that injury context biased the relative proportions of regenerated neurons, with each paradigm favoring replacement of the populations most affected by damage. Nevertheless, both injury paradigms generated all major retinal cell classes, indicating that Muller glia-derived progenitors retain broad neurogenic potential. Regenerated neurons showed substantial transcriptional similarity to endogenous counterparts, with the remaining differences primarily reflecting ongoing maturation. At subtype resolution, regenerated amacrine cells restored broad neurochemical and morphological diversity, and regenerated retinal ganglion cells re-established long-range projections to the optic tectum. Together, these findings show that Muller glia-mediated regeneration in the adult zebrafish retina restores neuronal diversity and key features of retinal circuit organization, providing insights for understanding how complex neuronal identities and connectivity can be rebuilt after injury.