Cross-species single-cell transcriptomic atlas of retinal photoreceptors reveals molecular signatures underlying color vision adaptation
The retina exhibits conserved structural and functional features across species, yet the evolutionary mechanisms underlying color vision remain unclear. Here, we employ a single-cell prediction (scPred) model to construct a cross-species single-cell retinal atlas from 24 species. We identify conserved retinal cell types and expression patterns, with photoreceptor cells, especially rods, showing evolutionary shifts. Opsin expression and transcriptional programs in rods and cones display species-specific patterns. Cone subtypes exhibit distinct metabolic features, with fatty acid biosynthesis enriched in OPN1SW<sup>+</sup> and OPN1MW<sup>+</sup> cones and FOXO3 specifically linked to OPN1LW<sup>+</sup> cones. Fluorescence in situ hybridization (FISH) and quantitative real-time PCR validate cone subtype-specific transcription factors and metabolic genes in representative species. This work provides a valuable resource for understanding the transcriptional and metabolic basis of color vision and guides the selection of model organisms for studying color-vision-related diseases.
Authors
- Yanhui Lu (ORCID: https://orcid.org/0000-0002-7905-2561)
- Dongchang Xiao (ORCID: https://orcid.org/0000-0003-0093-0323)
- Yaqing Shu (ORCID: https://orcid.org/0000-0003-2768-1654)
- Liangming Zhang (ORCID: https://orcid.org/0000-0003-2282-4687)
- Gang Cao
- Chengkai Yan
- Wei Qiu (ORCID: https://orcid.org/0000-0001-8102-8192)
- Jianping Ji (ORCID: https://orcid.org/0009-0006-9596-5447)
- Hui Yang (ORCID: https://orcid.org/0000-0002-9138-1325)
- Shishi Shen
- Shasha Li (ORCID: https://orcid.org/0000-0002-2166-950X)
- Jian Sun (ORCID: https://orcid.org/0000-0003-1569-0334)
- Xi Cheng (ORCID: https://orcid.org/0000-0002-0838-5094)
- Zhibin Li (ORCID: https://orcid.org/0000-0002-3869-3397)
- Shuilin Wu (ORCID: https://orcid.org/0000-0001-6957-7498)
- Yuge Wang (ORCID: https://orcid.org/0000-0003-3005-6163)
Institutions
- South China Agricultural University (CN)
- Sun Yat-sen University (CN)
- Shenzhen Institute of Information Technology (CN)
- Shenzhen Institutes of Advanced Technology (CN)
- Third Affiliated Hospital of Sun Yat-sen University (CN)
Publication Details
- Journal
- Cell Reports
- Published
- 2025-08-21
- DOI
- https://doi.org/10.1016/j.celrep.2025.116164
- Citations
- 1
- Primary Topic
- Retinal Development and Disorders
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- National Natural Science Foundation of China-Guangdong Joint Fund