2.15 Synteny and phylogenetic analyses of opsin genes
To examine opsin duplications by both gene synteny and gene trees, we
first observed the locations of opsin genes in the studied genome
annotations. The gene order and orientation in the syntenic region were
defined based on the original genome annotation. We used a sliding
window approach to check adjacent genes that appeared in nearby regions.
The size of the sliding window was set as the opsin gene plus three
upstream and three downstream genes. If none of the adjacent genes on
the same chromosome/contig could be found, we reported no adjacent
upstream/ downstream gene of the opsin genes. Second, we extracted the
coding sequences of opsin genes, and single-exon coding sequences were
aligned using Muscle, and gene trees were constructed using MEGAX v10
(Kumar et al. 2018) for maximum likelihood methods, and the model
GTR was chosen for the likelihood ratio. The reliability of the clades
in the gene trees was assessed by bootstrap probabilities computed using
1000 replicates.