Rhodopsin gene evolution in early teleost fishes

Abstract

Rhodopsin mediates an essential step in image capture and is tightly associated with visual adaptations of aquatic organisms, especially species that live in dim light environments (e.g., the deep sea). The rh1 gene encoding rhodopsin was formerly considered a single-copy gene in genomes of vertebrates, but increasing exceptional cases have been found in teleost fish species. The main objective of this study was to determine to what extent the visual adaptation of teleosts might have been shaped by the duplication and loss of rh1 genes. For that purpose, homologous rh1/rh1-like sequences in genomes of ray-finned fishes from a wide taxonomic range were explored using a PCR-based method, data mining of public genetic/genomic databases, and subsequent phylogenomic analyses of the retrieved sequences. We show that a second copy of the fish-specific intron-less rh1 is present in the genomes of most anguillids (Elopomorpha), Hiodon alosoides (Osteoglossomorpha), and several clupeocephalan lineages. The phylogenetic analysis and comparisons of alternative scenarios for putative events of gene duplication and loss suggested that fish rh1 was likely duplicated twice during the early evolutionary history of teleosts, with one event coinciding with the hypothesized fish-specific genome duplication and the other in the common ancestor of the Clupeocephala. After these gene duplication events, duplicated genes were maintained in several teleost lineages, whereas some were secondarily lost in specific lineages. Alternative evolutionary schemes of rh1 and comparison with previous studies of gene evolution are also reviewed.

The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function

“…This teleostspecific genome duplication is also traceable in the visual opsin genes of some fishes. For example, Elopomorpha (eels) and Osteoglossomorpha have retained their two ancestral rod opsins (RH1s) (Chen et al 2018), and characins, bony tongues, and gobies have two ancestral types of the red-sensitive LWS opsin (Adrian-Kalchhauser et al 2020;Cortesi et al unpublished;Liu et al 2019) (Figure 2).…”

Multiple ancestral and a plethora of recent gene duplications during the evolution of the green sensitive opsin genes (RH2) in teleost fishes

“…Hence, the onset of the RH2 duplications, or more likely the surviving ancestral duplicates are from a different evolutionary time point compared to the other visual opsins (Musilova et al, 2021). Both, the ancestral duplicates of RH1 (Chen et al, 2018;Musilova et al, 2019) and LWS (Cortesi et al, 2021) can be dated back to the teleost ancestor or even earlier. On the contrary, the surviving ancestral SWS2 duplicates first occurred later during the teleost evolution, in the neoteleost and percomorph ancestors (Cortesi et al, 2015).…”

Decoupled spectral tuning and eye size diversification patterns in an Antarctic adaptive radiation

“…As several available notothenioid genomes were sequenced with low (10x) coverage, instances of fragmented opsin genes within scaffolds were excluded from analysis as meaningful tuning site comparisons would not be possible. Additionally, non-visual extra-ocular rhodopsin, (exo-rh1) sequences, which are similar to Rh1 but expressed in the pineal gland (Chen et al 2018; Fujiyabu et al 2019), were excluded from this study.…”