2.14 Identification of opsin genes
The zebrafish genome annotation file (Zv10) was downloaded from NCBI RefSeq, and zebrafish opsin genes were subtracted (Table S1) and used as reference sequences. For each of the other 13 fish genomes, the opsin genes were identified as follows: 1) The zebrafish and 13 fish protein sequences were aligned with Pfam database using Hmmer (http://hmmer.org/ download.html) to find conserved motifs of opsin protein sequences. 2) The opsin genes with conserved motifs in 13 fishes were BLASTed against the zebrafish protein sequences (e-value < 1×10-5). Only the protein sequences with the best hits to annotated zebrafish opsins were retained. 3) To reduce false negatives, the coding sequences of these protein sequences and the genomic locations of opsin genes were retrieved from their genome annotation files (Table S2), and only genes annotated as opsin genes/light sensitive genes were retained (Table S1), while the coding sequences were used for follow-up studies.