PROJECT ID: GSE175929

Data source GEO: GSE175929
Description Vertebrate vision is mediated by two kinds of photoreceptors, rods and cones, responsible for dim- and bright-light vision, respectively. Gene expression differences among cone subtypes remain poorly understood compared with rods. We generated single-cell transcriptome data using a droplet-based approach to reveal the extent of gene expression diversity among adult zebrafish photoreceptor subtypes. Populations of photoreceptor cells were enriched by using the transgenic zebrafish lines, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg, which express GFP in rods and all cone subtypes, respectively. By analyzing the single-cell transcriptomes, we found that in addition to the four canonical zebrafish cone types (ultraviolet, blue, green and red), there exist subpopulations of green and red cones in the ventral retina that express red-shifted opsin paralogs (opn1mw4 and opn1lw1). This work lays a foundation for future studies aimed at understanding how molecular differences among cone subtypes affect photoreceptor function.
Key word cone visual pigments; hormone-receptor; vertebrate eye; color-vision; opsin genes; rod; evolution; retina; identification;specification
Publication Ogawa Y, Corbo JC. Partitioning of gene expression among zebrafish photoreceptor subtypes. Sci Rep 2021 Aug 30;11(1):17340. PMID: 34462505
Abstract Vertebrate photoreceptors are categorized into two broad classes, rods and cones, responsible for dim- and bright-light vision, respectively. While many molecular features that distinguish rods and cones are known, gene expression differences among cone subtypes remain poorly understood. Teleost fishes are renowned for the diversity of their photoreceptor systems. Here, we used single-cell RNA-seq to profile adult photoreceptors in zebrafish, a teleost. We found that in addition to the four canonical zebrafish cone types, there exist subpopulations of green and red cones (previously shown to be located in the ventral retina) that express red-shifted opsin paralogs (opn1mw4 or opn1lw1) as well as a unique combination of cone phototransduction genes. Furthermore, the expression of many paralogous phototransduction genes is partitioned among cone subtypes, analogous to the partitioning of the phototransduction paralogs between rods and cones seen across vertebrates. The partitioned cone-gene pairs arose via the teleost-specific whole-genome duplication or later clade-specific gene duplications. We also discovered that cone subtypes express distinct transcriptional regulators, including many factors not previously implicated in photoreceptor development or differentiation. Overall, our work suggests that partitioning of paralogous gene expression via the action of differentially expressed transcriptional regulators enables diversification of cone subtypes in teleosts.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE175929 (5mpf) Danio rerio retina baseline 5mpf, GFP-positive cells collected from two transgenic zebrafish, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg GEO: GSM5351368

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Blue cone opsin ENSDARG00000017274 (opn1sw2) marker DOI:10.1038/s41598-021-96837-z
2 Rod opsin ENSDARG00000002193 (rho) marker DOI:10.1038/s41598-021-96837-z
3 Blue cone opsin ENSDARG00000017274 (opn1sw2) marker DOI:10.1038/s41598-021-96837-z
4 Rod opsin ENSDARG00000021113 (ptmaa) marker DOI:10.1038/s41598-021-96837-z
5 Bipolar cells ENSDARG00000002576 (cabp5a) marker DOI:10.1186/1749-8104-4-14, DOI:10.1016/j.cell.2016.07.054, DOI:10.1038/s41598-021-96837-z
5 Bipolar cells ENSDARG00000056292 (vsx1) marker DOI:10.1186/1749-8104-4-14, DOI:10.1016/j.cell.2016.07.054, DOI:10.1038/s41598-021-96837-z
5 Bipolar cells ENSDARG00000036058 (gnao1b) marker DOI:10.1186/1749-8104-4-14, DOI:10.1016/j.cell.2016.07.054, DOI:10.1038/s41598-021-96837-z
5 Bipolar cells ENSDARG00000004358 (gnb3a) marker DOI:10.1186/1749-8104-4-14, DOI:10.1016/j.cell.2016.07.054, DOI:10.1038/s41598-021-96837-z
7 Red cones ENSDARG00000044861 (opn1lw2) marker DOI:10.1038/s41598-021-96837-z
8 Green cone opsin ENSDARG00000097008 (opn1mw1) marker DOI:10.1038/s41598-021-96837-z
8 Green cone opsin ENSDARG00000044280 (opn1mw2) marker DOI:10.1038/s41598-021-96837-z
9 Rod opsin ENSDARG00000002193 (rho) marker DOI:10.1038/s41598-021-96837-z
11 Rod opsin ENSDARG00000002193 (rho) marker DOI:10.1038/s41598-021-96837-z
13 Bipolar cells ENSDARG00000004023 (isl1) marker DOI:10.1016/j.cell.2016.07.054, DOI:10.1038/s41598-021-96837-z