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.