scholarly journals Evolutionary ecology of the visual opsin gene sequence and its expression in turbot (Scophthalmus maximus)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yunong Wang ◽  
Li Zhou ◽  
Lele Wu ◽  
Changbin Song ◽  
Xiaona Ma ◽  
...  
Keyword(s):  
Visual System ◽  
Evolutionary Ecology ◽  
Blue Shift ◽  
Scophthalmus Maximus ◽  
Chromosome 8 ◽  
Opsin Gene ◽  
Evolutionary Analysis ◽  
Opsin Expression ◽  
Branch Site ◽  
Opsin Genes

Abstract Background As flatfish, turbot undergo metamorphosis as part of their life cycle. In the larval stage, turbot live at the ocean surface, but after metamorphosis they move to deeper water and turn to benthic life. Thus, the light environment differs greatly between life stages. The visual system plays a great role in organic evolution, but reports of the relationship between the visual system and benthic life are rare. In this study, we reported the molecular and evolutionary analysis of opsin genes in turbot, and the heterochronic shifts in opsin expression during development. Results Our gene synteny analysis showed that subtype RH2C was not on the same gene cluster as the other four green-sensitive opsin genes (RH2) in turbot. It was translocated to chromosome 8 from chromosome 6. Based on branch-site test and spectral tuning sites analyses, E122Q and M207L substitutions in RH2C, which were found to be under positive selection, are closely related to the blue shift of optimum light sensitivities. And real-time PCR results indicated the dominant opsin gene shifted from red-sensitive (LWS) to RH2B1 during turbot development, which may lead to spectral sensitivity shifts to shorter wavelengths. Conclusions This is the first report that RH2C may be an important subtype of green opsin gene that was retained by turbot and possibly other flatfish species during evolution. Moreover, E122Q and M207L substitutions in RH2C may contribute to the survival of turbot in the bluish colored ocean. And heterochronic shifts in opsin expression may be an important strategy for turbot to adapt to benthic life.

scholarly journals Evolutionary ecology of the visual opsin gene sequence and its expression in turbot (Scophthalmus maximus)

2020 ◽  
Author(s):  
Yunong Wang ◽  
Li Zhou ◽  
Lele Wu ◽  
Xiaona Ma ◽  
Shihong Xu ◽  
...  
Keyword(s):  
Evolutionary Ecology ◽  
Vision System ◽  
Blue Shift ◽  
Scophthalmus Maximus ◽  
Chromosome 8 ◽  
Opsin Gene ◽  
Evolutionary Analysis ◽  
Opsin Expression ◽  
Branch Site ◽  
Opsin Genes

Abstract Background As flatfish, turbot undergo metamorphosis as part of their life cycle. In the larval stage, turbot live at the ocean surface, but after metamorphosis they move to deeper water and turn to benthic life. Thus, the light environment differs greatly between life stages. The vision system plays a great role in organic evolution, but reports of the relationship between the visual system and benthic life are rare. In this study, we reported the molecular and evolutionary analysis of opsin genes in turbot, and the heterochronic shifts in opsin expression during development.Results Our gene synteny analysis showed that subtype RH2C was not on the same gene cluster as the other four green-sensitive opsin genes ( RH2 ) in turbot. It was translocated to chromosome 8 from chromosome 6. Based on branch-site test and spectral tuning sites analyses, E122Q and M207L substitutions in RH2C , which were found to be under positive selection, are closely related to the blue shift of optimum light sensitivities. And real-time PCR results indicated the dominant opsin gene shifted from red-sensitive ( LWS ) to RH2B1 during turbot development, which may lead to spectral sensitivity transition from red to green.Conclusions We demonstrated that RH2C may be an important subtype of green opsin gene that was retained by turbot and possibly other flatfish species during evolution. Moreover, E122Q and M207L substitutions in RH2C may contribute to the survival of turbot in the bluish colored ocean. And heterochronic shifts in opsin expression may be an important strategy for turbot to adapt to benthic life.

scholarly journals Evolution of opsin expression in birds driven by sexual selection and habitat

2015 ◽  
Vol 282 (1798) ◽  
pp. 20142321 ◽  
Author(s):  
Natasha I. Bloch
Keyword(s):  
Sexual Selection ◽  
Visual System ◽  
Sensory System ◽  
Light Environment ◽  
Opsin Gene ◽  
Light Spectrum ◽  
Opsin Expression ◽  
Cone Opsin ◽  
Gene Coding ◽  
Male Plumage

Theories of sexual and natural selection predict coevolution of visual perception with conspecific colour and/or the light environment animals occupy. One way to test these theories is to focus on the visual system, which can be achieved by studying the opsin-based visual pigments that mediate vision. Birds vary greatly in colour, but opsin gene coding sequences and associated visual pigment spectral sensitivities are known to be rather invariant across birds. Here, I studied expression of the four cone opsin genes ( Lws, Rh2, Sws2 and Sws1 ) in 16 species of New World warblers (Parulidae). I found levels of opsin expression vary both across species and between the sexes. Across species, female, but not male Sws2 expression is associated with an index of sexual selection, plumage dichromatism. This fits predictions of classic sexual selection models, in which the sensory system changes in females, presumably impacting female preference, and co-evolves with male plumage. Expression of the opsins at the extremes of the light spectrum, Lws and Uvs, correlates with the inferred light environment occupied by the different species. Unlike opsin spectral tuning, regulation of opsin gene expression allows for fast adaptive evolution of the visual system in response to natural and sexual selection, and in particular, sex-specific selection pressures.

scholarly journals Developmental and environmental plasticity in opsin gene expression in Lake Victoria cichlid fish

2021 ◽  
Author(s):  
Lucia Irazábal-González ◽  
Daniel Shane Wright ◽  
Martine Maan
Keyword(s):  
Gene Expression ◽  
Visual System ◽  
Developmental Stages ◽  
Lake Victoria ◽  
Developmental Trajectories ◽  
Expression Profiles ◽  
Cichlid Fish ◽  
Opsin Gene ◽  
Opsin Expression ◽  
Visual Conditions

AbstractIn many organisms, sensory abilities develop and evolve according to the changing demands of navigating, foraging and communication across different environments and life stages. Teleost fish inhabit heterogeneous light environments and exhibit a large diversity in visual system properties among species. Cichlids are a classic example of this diversity, generated by different tuning mechanisms that involve both genetic factors and phenotypic plasticity. Here, we document the developmental progression of visual pigment gene expression in Lake Victoria cichlids and test if these patterns are influenced by variation in light conditions. We reared two sister species of Pundamilia to adulthood in two distinct visual conditions that resemble the two light environments that they naturally inhabit in Lake Victoria. We also included interspecific first-generation hybrids. We then quantified (using RT-qPCR) the expression of the four Pundamilia opsins (SWS2B, SWS2A, RH2A and LWS) at 14 time points. We find that opsin expression profiles progress from shorter-wavelength sensitive opsins to longer-wavelength sensitive opsins with increasing age, in both species and their hybrids. The developmental trajectories of opsin expression also responded plastically to the visual conditions. Finally, we found subtle differences between reciprocal hybrids, possibly indicating parental effects and warranting further investigation. Developmental and environmental plasticity in opsin expression may provide an important stepping stone in the evolution of cichlid visual system diversity.Research highlightsIn Lake Victoria cichlid fish, expression levels of opsin genes (encoding visual pigments) differ between developmental stages and between experimental light treatments. This plasticity may contribute to the evolution of cichlid visual system diversity.

scholarly journals Evolution of regulatory networks associated with traits under selection in cichlids

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tarang K. Mehta ◽  
Christopher Koch ◽  
Will Nash ◽  
Sara A. Knaack ◽  
Padhmanand Sudhakar ◽  
...  
Keyword(s):  
Visual System ◽  
Regulatory Sequence ◽  
Potential Candidate ◽  
East African ◽  
Regulatory Regions ◽  
A Genome ◽  
Opsin Genes ◽  
East African Cichlids ◽  
Gene Regulatory ◽  
African Cichlids

Abstract Background Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. Results To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait—the visual system—for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. Conclusions Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits.

scholarly journals Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3145 ◽  
Author(s):  
Edson Ishengoma ◽  
Morris Agaba ◽  
Douglas R. Cavener
Keyword(s):  
Positive Selection ◽  
Visual Signal ◽  
Evolutionary Analysis ◽  
Long Distance ◽  
Phenotypic Differences ◽  
Multiple Strategies ◽  
Branch Site ◽  
Signature Of Selection ◽  
Evolutionary Success ◽  
Signatures Of Selection

BackgroundThe capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with many of them. The extent to which the giraffe’s unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood.MethodsThe recent availability of giraffe and okapi genomes provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site tests of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and orthologous sequences from other mammals.ResultsSignatures of selection were identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence inCRYAAandOPN1LW. Significant selection divergence was identified inSAGwhile positive selection was detected inLUMwhen okapi is compared with ruminants and other mammals. Sequence analysis ofOPN1LWshowed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants.DiscussionBy taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and okapi vision adaptations. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and okapi habitat. We hypothesize that requirement for long distance vision associated with predation and communication with conspecifics likely played an important role in the adaptive pressure on giraffe vision genes.

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

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Zuzana Musilova ◽  
Walter Salzburger ◽  
Fabio Cortesi
Keyword(s):  
Sensory System ◽  
Photoreceptor Cells ◽  
Opsin Gene ◽  
Annual Review ◽  
Specific Gene ◽  
Publication Date ◽  
Teleost Fishes ◽  
Opsin Genes ◽  
The Rich ◽  
Species Specific

Visual opsin genes expressed in the rod and cone photoreceptor cells of the retina are core components of the visual sensory system of vertebrates. Here, we provide an overview of the dynamic evolution of visual opsin genes in the most species-rich group of vertebrates, teleost fishes. The examination of the rich genomic resources now available for this group reveals that fish genomes contain more copies of visual opsin genes than are present in the genomes of amphibians, reptiles, birds, and mammals. The expansion of opsin genes in fishes is due primarily to a combination of ancestral and lineage-specific gene duplications. Following their duplication, the visual opsin genes of fishes repeatedly diversified at the same key spectral-tuning sites, generating arrays of visual pigments sensitive from the ultraviolet to the red spectrum of the light. Species-specific opsin gene repertoires correlate strongly with underwater light habitats, ecology, and color-based sexual selection. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Interspecific Variation in Rx1 Expression Controls Opsin Expression and Causes Visual System Diversity in African Cichlid Fishes

2014 ◽  
Vol 31 (9) ◽  
pp. 2297-2308 ◽  
Author(s):  
Jane E. Schulte ◽  
Conor S. O’Brien ◽  
Matthew A. Conte ◽  
Kelly E. O’Quin ◽  
Karen L. Carleton
Keyword(s):  
Visual System ◽  
Interspecific Variation ◽  
Cichlid Fishes ◽  
Opsin Expression ◽  
African Cichlid

scholarly journals Opsin gene repertoires in northern archaic hominids

Genome ◽  
2016 ◽  
Vol 59 (8) ◽  
pp. 541-549 ◽  
Author(s):  
John S. Taylor ◽  
Thomas E. Reimchen
Keyword(s):  
Colour Vision ◽  
Modern Human ◽  
Active Species ◽  
Opsin Gene ◽  
Human Reference Genome ◽  
Northern Latitudes ◽  
Opsin Genes ◽  
Northern Distribution ◽  
Dim Light ◽  
Additional Support

The Neanderthals’ northern distribution, hunting techniques, and orbit breadths suggest that they were more active in dim light than modern humans. We surveyed visual opsin genes from four Neanderthals and two other archaic hominids to see if they provided additional support for this hypothesis. This analysis was motivated by the observation that alleles responsible for anomalous trichromacy in humans are more common in northern latitudes, by data suggesting that these variants might enhance vision in mesopic conditions, and by the observation that dim light active species often have fewer opsin genes than diurnal relatives. We also looked for evidence of convergent amino acid substitutions in Neanderthal opsins and orthologs from crepuscular or nocturnal species. The Altai Neanderthal, the Denisovan, and the Ust’-Ishim early modern human had opsin genes that encoded proteins identical to orthologs in the human reference genome. Opsins from the Vindija Cave Neanderthals (three females) had many nonsynonymous substitutions, including several predicted to influence colour vision (e.g., stop codons). However, the functional implications of these observations were difficult to assess, given that “control” loci, where no substitutions were expected, differed from humans to the same extent. This left unresolved the test for colour vision deficiencies in Vindija Cave Neanderthals.

scholarly journals Molecular evolution and expression of opsin genes in Hydra vulgaris

2019 ◽  
Author(s):  
Aide Macias Munoz ◽  
Rabi Murad ◽  
Ali Mortazavi
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Tree ◽  
Opsin Gene ◽  
Expression Data ◽  
Rna Seq ◽  
Light Detection ◽  
Hydra Vulgaris ◽  
Visual Diversity ◽  
Opsin Genes ◽  
Insight Into

Abstract Background: The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris (H. vulgaris) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris. We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions. Results: We identified 45 opsin genes in H. vulgaris, many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes (HvOpA1 and HvOpB1) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris. We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades. Conclusions: This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgarisopsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.

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