Fig. 2: Classification of lamprey PR types and their comparison with mouse PR types.

a UMAP visualization of two lamprey PR types. b Stacked violin plot showing distinct gene-expression patterns in the phototransduction cascade between PR1 (S-PR) and PR2 (L-PR). S-PR, short-photoreceptor (rod); L-PR, long-photoreceptor (cone). c FISH validations showing exclusive expression of rhodopsin (RHO, green in the merged image) and red-opsin (magenta in the merged image) between PR1 and PR2 (upper panel), co-expression of RHO (green in the merged image) and GNAT1 (magenta in the merged image) in PR1 (middle panel), and co-expression of red-opsin (green in the merged image) and GNAT2 (magenta in the merged image) in PR2 (bottom panel). Nuclei stained with DAPI are in blue. Scale bar, 20 μm. Each experiment was performed independently three times with similar results. d Integration of lamprey and mouse PRs visualized with UMAP, with both integrated and species-specific clusters presented in separated UMAP plots. e Confusion matrix demonstrating the transcriptomic correspondence of PR types between lamprey and mouse (Mus musculus, Mm). Mouse PRs were used as the training dataset, while lamprey PRs were used as the testing dataset. Circles and color gradients present the percentage of cells from a lamprey PR cluster assigned to a corresponding mouse PR type. See Source Data. f Violin plots showing the expression of conserved transcription factors enriched in both lamprey PR1 and mouse rods.