The emergence of retinal pigment epithelial cell heterogeneity in the larval zebrafish retina

Abstract: Vision depends on the function of retinal circuits, supported by the retinal pigment epithelium (RPE) that lines the back of the eye. This single-cell layer thick epithelium provides growth factors and nutrients for the underlying photoreceptors, phagocytoses shed photoreceptor outer segment debris, and contributes to the blood-retinal barrier. Whether the cells of the RPE represent a single homogeneous population or represent distinct functional entities is poorly understood. Here, we use single cell RNA sequencing (scRNAseq) data from our mature 5-day post-fertilization zebrafish retina dataset and a publicly available adult zebrafish eye dataset, alongside in situ hybridization, to explore the transcriptomic diversity of RPE cells, its emergence over development, and its persistence into the adult. We identify 6 transcriptomically distinct RPE subtypes in the 5 day larval eye that exhibit different localization within the eye. Specifically, we find potential progenitor, iris-associated, dorso-ventral differentiating, and mature RPE subpopulations. These populations appear to emerge via separate developmental trajectories and are largely distinct from the transcriptomic RPE subpopulations of the adult eye.Notes: The dataset source from the original authors for farre_2023_adult_rpe.h5ad can be found at: [Farre AA, Sun C, Starostik MR, Hunter SS et al. Long wavelength-sensing cones of zebrafish retina exhibit multiple layers of transcriptional heterogeneity. Front Cell Neurosci 2023;17:1214084. PMID: 37519633. NCBI GEO GSE234661] The dataset source from the original authors for hehr_2026_5dpf_rpe.h5ad can be found at: 1) Preprint: https://doi.org/10.64898/2026.03.22.713558, 2) Zenodo: https://doi.org/10.5281/zenodo.18677159, 3) NCBI GEO: GSE319514. [Storey, S. S., Hehr, C. L., Standing, S., & McFarlane, S. (2026). Müller glia subtypes define neuro-glial associations and spatial morphogen axes in the zebrafish retina. bioRxiv, 2026-03.] [Storey, S. S. (2026). Müller glia subtypes define neuro-glial associations and spatial morphogen axes in the zebrafish retina [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.18677159]