Vision Res 2024 Sep 20;222:108447. doi: 10.1016/j.visres.2024.108447.

The genomic evolution of visual opsin genes in amphibians.

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Among tetrapod (terrestrial) vertebrates, amphibians remain more closely tied to an amphibious lifestyle than amniotes, and their visual opsin genes may be adapted to this lifestyle. Previous studies have discussed physiological, morphological, and molecular changes in the evolution of amphibian vision. We predicted the locations of the visual opsin genes, their neighboring genes, and the tuning sites of the visual opsins, in 39 amphibian genomes. We found that all of the examined genomes lacked the Rh2 gene. The caecilian genomes have further lost the SWS1 and SWS2 genes; only the Rh1 and LWS genes were retained. The loss of the SWS1 and SWS2 genes in caecilians may be correlated with their cryptic lifestyles. The opsin gene syntenies were predicted to be highly similar to those of other bony vertebrates. Moreover, dual syntenies were identified in allotetraploid Xenopus laevis and X. borealis. Tuning site analysis showed that only some Caudata species might have UV vision. In addition, the S164A that occurred several times in LWS evolution might either functionally compensate for the Rh2 gene loss or fine-tuning visual adaptation. Our study provides the first genomic evidence for a caecilian LWS gene and a genomic viewpoint of visual opsin genes by reviewing the gains and losses of visual opsin genes, the rearrangement of syntenies, and the alteration of spectral tuning in the course of amphibians' evolution.

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Species referenced: Xenopus tropicalis Xenopus laevis Xenopus borealis
Genes referenced: apobec2 arf5 atp6v1f bak1 bicd2 calu cand2 ccdc136 cdhr5 dennd6b drd4 efcab12 fgd1 flnc ftsj1 gcc1 gnl3l grm4 gtf3c6 h1-8 hcfc1 ift122 irak1 itpr3 kcp lep nt5dc2 opn1sw pax4 plxnd1 ppp6r2 prdm4 prrt4 rbm28 rbsn rho rpl32 sbf1 syce1 tmcc1 tmem116 tmem187 tmem53 tnpo3 trh tspan33