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

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 or states 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 populations in the 5 day larval eye, representing either RPE subtypes or states, that exhibit different localization within the eye. Specifically, we find potential proliferative, iris-associated, dorso-ventral differentiating, and mature RPE subpopulations. These populations appear to emerge via separate developmental trajectories and may be distinct from the transcriptomic RPE subpopulations of the adult eye.