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Lupše N, Kłodawska M, Truhlářová V, Košátko P, Kašpar V, Bitja Nyom AR, Musilova Z. Developmental changes of opsin gene expression in ray-finned fishes (Actinopterygii). Proc Biol Sci 2022; 289:20221855. [DOI: 10.1098/rspb.2022.1855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Fish often change their habitat and trophic preferences during development. Dramatic functional differences between embryos, larvae, juveniles and adults also concern sensory systems, including vision. Here, we focus on the photoreceptors (rod and cone cells) in the retina and their gene expression profiles during development. Using comparative transcriptomics on 63 species, belonging to 23 actinopterygian orders, we report general developmental patterns of opsin expression, mostly suggesting an increased importance of the rod opsin (
RH1
) gene and the long-wavelength-sensitive cone opsin, and a decreasing importance of the shorter wavelength-sensitive cone opsin throughout development. Furthermore, we investigate in detail ontogenetic changes in 14 selected species (from Polypteriformes, Acipenseriformes, Cypriniformes, Aulopiformes and Cichliformes), and we report examples of expanded cone opsin repertoires, cone opsin switches (mostly within
RH2
) and increasing rod : cone ratio as evidenced by the opsin and phototransduction cascade genes. Our findings provide molecular support for developmental stage-specific visual palettes of ray-finned fishes and shifts between, which most likely arose in response to ecological, behavioural and physiological factors.
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Affiliation(s)
- Nik Lupše
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 12844 Prague, Czech Republic
| | - Monika Kłodawska
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 12844 Prague, Czech Republic
| | - Veronika Truhlářová
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 12844 Prague, Czech Republic
| | - Prokop Košátko
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 12844 Prague, Czech Republic
| | - Vojtěch Kašpar
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Arnold Roger Bitja Nyom
- Department of Management of Fisheries and Aquatic Ecosystems, University of Douala, Douala P.O. Box 7236, Cameroon
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré P.O. Box 454, Cameroon
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 12844 Prague, Czech Republic
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2
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Lupše N, Cortesi F, Freese M, Marohn L, Pohlman JD, Wysujack K, Hanel R, Musilova Z. Visual gene expression reveals a cone to rod developmental progression in deep-sea fishes. Mol Biol Evol 2021; 38:5664-5677. [PMID: 34562090 PMCID: PMC8662630 DOI: 10.1093/molbev/msab281] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Vertebrates use cone cells in the retina for colour vision and rod cells to see in dim light. Many deep-sea fishes have adapted to their environment to have only rod cells in the retina, while both rod and cone genes are still preserved in their genomes. As deep-sea fish larvae start their lives in the shallow, and only later submerge to the depth, they have to cope with diverse environmental conditions during ontogeny. Using a comparative transcriptomic approach in 20 deep-sea fish species from eight teleost orders, we report on a developmental cone-to-rod switch. While adults mostly rely on rod opsin (RH1) for vision in dim light, larvae almost exclusively express middle-wavelength-sensitive ("green") cone opsins (RH2) in their retinas. The phototransduction cascade genes follow a similar ontogenetic pattern of cone- followed by rod-specific gene expression in most species, except for the pearleye and sabretooth (Aulopiformes), in which the cone cascade remains dominant throughout development. By inspecting the whole genomes of five deep-sea species (four of them sequenced within this study: Idiacanthus fasciola, Chauliodus sloani; Stomiiformes; Coccorella atlantica, and Scopelarchus michaelsarsi; Aulopiformes), we found that deep-sea fish possess one or two copies of the rod RH1 opsin gene, and up to seven copies of the cone RH2 opsin genes in their genomes, while other cone opsin classes have been mostly lost. Our findings hence provide molecular evidence for a limited opsin gene repertoire and a conserved vertebrate pattern whereby cone photoreceptors develop first and rod photoreceptors are added only at later developmental stages.
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Affiliation(s)
- Nik Lupše
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 12844 Prague, Czech Republic
| | - Fabio Cortesi
- Queensland Brain Institute, University of Queensland, Brisbane 4072 QLD, Australia
| | - Marko Freese
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Lasse Marohn
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Jan-Dag Pohlman
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Klaus Wysujack
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Reinhold Hanel
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 12844 Prague, Czech Republic
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3
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Chen JN, Samadi S, Chen WJ. Rhodopsin gene evolution in early teleost fishes. PLoS One 2018; 13:e0206918. [PMID: 30395593 PMCID: PMC6218077 DOI: 10.1371/journal.pone.0206918] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/22/2018] [Indexed: 01/03/2023] Open
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.
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Affiliation(s)
- Jhen-Nien Chen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Sarah Samadi
- Institute de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle–CNRS, Sorbonne Université, EPHE, Paris, France
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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4
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Mark MD, Donner M, Eickelbeck D, Stepien J, Nowrousian M, Kück U, Paris F, Hellinger J, Herlitze S. Visual tuning in the flashlight fish Anomalops katoptron to detect blue, bioluminescent light. PLoS One 2018; 13:e0198765. [PMID: 29995896 PMCID: PMC6040694 DOI: 10.1371/journal.pone.0198765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/24/2018] [Indexed: 01/23/2023] Open
Abstract
Bioluminescence is a fascinating phenomenon and can be found in many different organisms including fish. It has been suggested that bioluminescence is used for example for defense, prey attraction, and for intraspecific communication to attract for example sexual partners. The flashlight fish, Anomalops katoptron (A. katoptron), is a nocturnal fish that produces bioluminescence and lives in shallow waters, which makes it ideal for laboratory studies. In order to understand A. katoptron's ability to detect bioluminescent light (480 to 490 nm) at night, we characterized the visual system adaptation of A. katoptron using phylogenetic, electrophysiological and behavioral studies. We found that the retinae of A. katoptron contain rods and sparse cones. A. katoptron retinae express two main visual pigments, rhodopsin (RH1), and to a lesser extent, rhodopsin-like opsin (RH2). Interestingly, recombinant RH1 and RH2 are maximally sensitive to a wavelength of approximately 490 nm light (λmax), which correspond to the spectral peak of in vivo electroretinogram (ERG) measurements. In addition, behavioral assays revealed that A. katoptron is attracted by low intensity blue but not red light. Collectively, our results suggest that the A. katoptron visual system is optimized to detect blue light in the frequency range of its own bioluminescence and residual starlight.
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Affiliation(s)
- Melanie D. Mark
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
- * E-mail:
| | - Marcel Donner
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Dennis Eickelbeck
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Jennifer Stepien
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Minou Nowrousian
- Department of General and Molecular Botany, Ruhr-University Bochum, Bochum, Germany
| | - Ulrich Kück
- Department of General and Molecular Botany, Ruhr-University Bochum, Bochum, Germany
| | - Frank Paris
- Department of Animal Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Jens Hellinger
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Stefan Herlitze
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
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5
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Karagic N, Härer A, Meyer A, Torres‐Dowdall J. Heterochronic opsin expression due to early light deprivation results in drastically shifted visual sensitivity in a cichlid fish: Possible role of thyroid hormone signaling. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:202-214. [DOI: 10.1002/jez.b.22806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Nidal Karagic
- Zoology and Evolutionary BiologyDepartment of BiologyUniversity of Konstanz Konstanz Germany
| | - Andreas Härer
- Zoology and Evolutionary BiologyDepartment of BiologyUniversity of Konstanz Konstanz Germany
| | - Axel Meyer
- Zoology and Evolutionary BiologyDepartment of BiologyUniversity of Konstanz Konstanz Germany
- Radcliffe Institute for Advanced StudyHarvard University Cambridge Massachusetts
| | - Julián Torres‐Dowdall
- Zoology and Evolutionary BiologyDepartment of BiologyUniversity of Konstanz Konstanz Germany
- ZukunftskollegUniversity of Konstanz Konstanz Germany
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6
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Luehrmann M, Stieb SM, Carleton KL, Pietzker A, Cheney KL, Marshall NJ. Short term colour vision plasticity on the reef: Changes in opsin expression under varying light conditions differ between ecologically distinct reef fish species. J Exp Biol 2018; 221:jeb.175281. [DOI: 10.1242/jeb.175281] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 08/21/2018] [Indexed: 12/17/2022]
Abstract
Vision mediates important behavioural tasks such as mate choice, escape from predators and foraging. In fish, photoreceptors are generally tuned to specific visual tasks and/or to their light environment according to depth or water colour to ensure optimal performance. Evolutionary mechanisms acting on opsin genes, the protein component of the photopigment, can influence the spectral sensitivity of photoreceptors. Opsin genes are known to respond to environmental conditions on a number of time scales including shorter time frames due to seasonal variation, or through longer term evolutionary tuning. There is also evidence for ‘on-the-fly’ adaptations in adult fish in response to rapidly changing environmental conditions, however, results are contradictory. Here we investigated the ability of three reef fish species that belong to two ecologically distinct families, Yellow-striped cardinalfish, Ostorhinchus cyanosoma, Ambon damselfish, Pomacentrus amboinensis, and Lemon damselfish, Pomacentrus moluccensis, to alter opsin-gene expression as an adaptation to short-term (weeks to months) changes of environmental light conditions, and attempted to characterize the underlying expression regulation principles. We report the ability for all species to alter opsin gene expression within months and even a few weeks, suggesting that opsin expression in adult reef fish is not static. Furthermore, we found that opsin expression changes in single cones generally occurred more rapidly than in double cones, and identified different responses of RH2 opsin gene expression between the ecologically distinct reef fish families. Quantum catch correlation analysis suggested different regulation mechanisms for opsin expression dependent on gene class.
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Affiliation(s)
- Martin Luehrmann
- Queensland Brain Institute, The University of Queensland, Sensory Neurobiology Group, 4072, Brisbane, QLD, Australia
| | - Sara M. Stieb
- Queensland Brain Institute, The University of Queensland, Sensory Neurobiology Group, 4072, Brisbane, QLD, Australia
| | - Karen L. Carleton
- Department of Biology, The University of Maryland, College Park, MD, 20742, USA
| | - Alisa Pietzker
- Queensland Brain Institute, The University of Queensland, Sensory Neurobiology Group, 4072, Brisbane, QLD, Australia
| | - Karen L. Cheney
- Queensland Brain Institute, The University of Queensland, Sensory Neurobiology Group, 4072, Brisbane, QLD, Australia
- School of Biological Sciences, The University of Queensland, 4072, Brisbane, QLD, Australia
| | - N. Justin Marshall
- Queensland Brain Institute, The University of Queensland, Sensory Neurobiology Group, 4072, Brisbane, QLD, Australia
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7
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de Busserolles F, Cortesi F, Helvik JV, Davies WIL, Templin RM, Sullivan RKP, Michell CT, Mountford JK, Collin SP, Irigoien X, Kaartvedt S, Marshall J. Pushing the limits of photoreception in twilight conditions: The rod-like cone retina of the deep-sea pearlsides. SCIENCE ADVANCES 2017; 3:eaao4709. [PMID: 29134201 PMCID: PMC5677336 DOI: 10.1126/sciadv.aao4709] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
Most vertebrates have a duplex retina comprising two photoreceptor types, rods for dim-light (scotopic) vision and cones for bright-light (photopic) and color vision. However, deep-sea fishes are only active in dim-light conditions; hence, most species have lost their cones in favor of a simplex retina composed exclusively of rods. Although the pearlsides, Maurolicus spp., have such a pure rod retina, their behavior is at odds with this simplex visual system. Contrary to other deep-sea fishes, pearlsides are mostly active during dusk and dawn close to the surface, where light levels are intermediate (twilight or mesopic) and require the use of both rod and cone photoreceptors. This study elucidates this paradox by demonstrating that the pearlside retina does not have rod photoreceptors only; instead, it is composed almost exclusively of transmuted cone photoreceptors. These transmuted cells combine the morphological characteristics of a rod photoreceptor with a cone opsin and a cone phototransduction cascade to form a unique photoreceptor type, a rod-like cone, specifically tuned to the light conditions of the pearlsides' habitat (blue-shifted light at mesopic intensities). Combining properties of both rods and cones into a single cell type, instead of using two photoreceptor types that do not function at their full potential under mesopic conditions, is likely to be the most efficient and economical solution to optimize visual performance. These results challenge the standing paradigm of the function and evolution of the vertebrate duplex retina and emphasize the need for a more comprehensive evaluation of visual systems in general.
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Affiliation(s)
- Fanny de Busserolles
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jon Vidar Helvik
- Department of Biology, University of Bergen, Bergen 5020, Norway
| | - Wayne I. L. Davies
- The Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
- School of Biological Science, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Lions Eye Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Rachel M. Templin
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert K. P. Sullivan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Craig T. Michell
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistokatu 7, FI-80101 Joensuu, Finland
| | - Jessica K. Mountford
- The Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
- School of Biological Science, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Lions Eye Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Shaun P. Collin
- The Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
- School of Biological Science, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Lions Eye Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Xabier Irigoien
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Marine Research, AZTI - Tecnalia, Herrera Kaia, Portualdea z/g, 20110 Pasaia (Gipuzkoa), Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Stein Kaartvedt
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | - Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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8
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Nakamura Y, Yasuike M, Mekuchi M, Iwasaki Y, Ojima N, Fujiwara A, Chow S, Saitoh K. Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication. ZOOLOGICAL LETTERS 2017; 3:18. [PMID: 29075512 PMCID: PMC5645911 DOI: 10.1186/s40851-017-0079-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/11/2017] [Indexed: 06/16/2023]
Abstract
BACKGROUND Gene duplication is considered important to increasing the genetic diversity in animals. In fish, visual pigment genes are often independently duplicated, and the evolutionary significance of such duplications has long been of interest. Eels have two rhodopsin genes (rho), one of which (freshwater type, fw-rho) functions in freshwater and the other (deep-sea type, ds-rho) in marine environments. Hence, switching of rho expression in retinal cells is tightly linked with eels' unique life cycle, in which they migrate from rivers or lakes to the sea. These rho genes are apparently paralogous, but the timing of their duplication is unclear due to the deep-branching phylogeny. The aim of the present study is to elucidate the evolutionary origin of the two rho copies in eels using comparative genomics methods. RESULTS In the present study, we sequenced the genome of Japanese eel Anguilla japonica and reconstructed two regions containing rho by de novo assembly. We found a single corresponding region in a non-teleostean primitive ray-finned fish (spotted gar) and two regions in a primitive teleost (Asian arowana). The order of ds-rho and the neighboring genes was highly conserved among the three species. With respect to fw-rho, which was lost in Asian arowana, the neighboring genes were also syntenic between Japanese eel and Asian arowana. In particular, the pattern of gene losses in ds-rho and fw-rho regions was the same as that in Asian arowana, and no discrepancy was found in any of the teleost genomes examined. Phylogenetic analysis supports mutual monophyly of these two teleostean synteny groups, which correspond to the ds-rho and fw-rho regions. CONCLUSIONS Syntenic and phylogenetic analyses suggest that the duplication of rhodopsin gene in Japanese eel predated the divergence of eel (Elopomorpha) and arowana (Osteoglossomorpha). Thus, based on the principle of parsimony, it is most likely that the rhodopsin paralogs were generated through a whole genome duplication in the ancestor of teleosts, and have remained till the present in eels with distinct functional roles. Our result indicates, for the first time, that teleost-specific genome duplication may have contributed to a gene innovation involved in eel-specific migratory life cycle.
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Affiliation(s)
- Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Miyuki Mekuchi
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Nobuhiko Ojima
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Japan Fisheries Research and Education Agency, 2-3-3 Minatomirai, Nishi, Yokohama, Kanagawa 220-6115 Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Seinen Chow
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Kenji Saitoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama, Shiogama, Miyagi 985-0001 Japan
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9
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Morrow JM, Lazic S, Dixon Fox M, Kuo C, Schott RK, de A Gutierrez E, Santini F, Tropepe V, Chang BSW. A second visual rhodopsin gene, rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes. ACTA ACUST UNITED AC 2016; 220:294-303. [PMID: 27811293 DOI: 10.1242/jeb.145953] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022]
Abstract
Rhodopsin (rh1) is the visual pigment expressed in rod photoreceptors of vertebrates that is responsible for initiating the critical first step of dim-light vision. Rhodopsin is usually a single copy gene; however, we previously discovered a novel rhodopsin-like gene expressed in the zebrafish retina, rh1-2, which we identified as a functional photosensitive pigment that binds 11-cis retinal and activates in response to light. Here, we localized expression of rh1-2 in the zebrafish retina to a subset of peripheral photoreceptor cells, which indicates a partially overlapping expression pattern with rh1 We also expressed, purified and characterized Rh1-2, including investigation of the stability of the biologically active intermediate. Using fluorescence spectroscopy, we found the half-life of the rate of retinal release of Rh1-2 following photoactivation to be more similar to that of the visual pigment rhodopsin than to the non-visual pigment exo-rhodopsin (exorh), which releases retinal around 5 times faster. Phylogenetic and molecular evolutionary analyses show that rh1-2 has ancient origins within teleost fishes, is under similar selective pressure to rh1, and likely experienced a burst of positive selection following its duplication and divergence from rh1 These findings indicate that rh1-2 is another functional visual rhodopsin gene, which contradicts the prevailing notion that visual rhodopsin is primarily found as a single copy gene within ray-finned fishes. The reasons for retention of this duplicate gene, as well as possible functional consequences for the visual system, are discussed.
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Affiliation(s)
- James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Savo Lazic
- Department of Molecular Genetics, University of Toronto, Toronto, Canada, M5S 1A8
| | - Monica Dixon Fox
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Claire Kuo
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Francesco Santini
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada, M5T 3A9.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5 .,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
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10
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Biagioni LM, Hunt DM, Collin SP. Morphological Characterization and Topographic Analysis of Multiple Photoreceptor Types in the Retinae of Mesopelagic Hatchetfishes with Tubular Eyes. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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de Busserolles F, Hart NS, Hunt DM, Davies WI, Marshall NJ, Clarke MW, Hahne D, Collin SP. Spectral Tuning in the Eyes of Deep-Sea Lanternfishes (Myctophidae): A Novel Sexually Dimorphic Intra-Ocular Filter. BRAIN, BEHAVIOR AND EVOLUTION 2015; 85:77-93. [DOI: 10.1159/000371652] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/15/2014] [Indexed: 11/19/2022]
Abstract
Deep-sea fishes possess several adaptations to facilitate vision where light detection is pushed to its limit. Lanternfishes (Myctophidae), one of the world's most abundant groups of mesopelagic fishes, possess a novel and unique visual specialisation, a sexually dimorphic photostable yellow pigmentation, constituting the first record of a visual sexual dimorphism in any non-primate vertebrate. The topographic distribution of the yellow pigmentation across the retina is species specific, varying in location, shape and size. Spectrophotometric analyses reveal that this new retinal specialisation differs between species in terms of composition and acts as a filter, absorbing maximally between 356 and 443 nm. Microspectrophotometry and molecular analyses indicate that the species containing this pigmentation also possess at least 2 spectrally distinct rod visual pigments as a result of a duplication of the Rh1 opsin gene. After modelling the effect of the yellow pigmentation on photoreceptor spectral sensitivity, we suggest that this unique specialisation acts as a filter to enhance contrast, thereby improving the detection of bioluminescent emissions and possibly fluorescence in the extreme environment of the deep sea. The fact that this yellow pigmentation is species specific, sexually dimorphic and isolated within specific parts of the retina indicates an evolutionary pressure to visualise prey/predators/mates in a particular part of each species' visual field.
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Francke M, Kreysing M, Mack A, Engelmann J, Karl A, Makarov F, Guck J, Kolle M, Wolburg H, Pusch R, von der Emde G, Schuster S, Wagner HJ, Reichenbach A. Grouped retinae and tapetal cups in some Teleostian fish: Occurrence, structure, and function. Prog Retin Eye Res 2014; 38:43-69. [DOI: 10.1016/j.preteyeres.2013.10.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 11/27/2022]
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Lagman D, Ocampo Daza D, Widmark J, Abalo XM, Sundström G, Larhammar D. The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications. BMC Evol Biol 2013; 13:238. [PMID: 24180662 PMCID: PMC3826523 DOI: 10.1186/1471-2148-13-238] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/29/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vertebrate color vision is dependent on four major color opsin subtypes: RH2 (green opsin), SWS1 (ultraviolet opsin), SWS2 (blue opsin), and LWS (red opsin). Together with the dim-light receptor rhodopsin (RH1), these form the family of vertebrate visual opsins. Vertebrate genomes contain many multi-membered gene families that can largely be explained by the two rounds of whole genome duplication (WGD) in the vertebrate ancestor (2R) followed by a third round in the teleost ancestor (3R). Related chromosome regions resulting from WGD or block duplications are said to form a paralogon. We describe here a paralogon containing the genes for visual opsins, the G-protein alpha subunit families for transducin (GNAT) and adenylyl cyclase inhibition (GNAI), the oxytocin and vasopressin receptors (OT/VP-R), and the L-type voltage-gated calcium channels (CACNA1-L). RESULTS Sequence-based phylogenies and analyses of conserved synteny show that the above-mentioned gene families, and many neighboring gene families, expanded in the early vertebrate WGDs. This allows us to deduce the following evolutionary scenario: The vertebrate ancestor had a chromosome containing the genes for two visual opsins, one GNAT, one GNAI, two OT/VP-Rs and one CACNA1-L gene. This chromosome was quadrupled in 2R. Subsequent gene losses resulted in a set of five visual opsin genes, three GNAT and GNAI genes, six OT/VP-R genes and four CACNA1-L genes. These regions were duplicated again in 3R resulting in additional teleost genes for some of the families. Major chromosomal rearrangements have taken place in the teleost genomes. By comparison with the corresponding chromosomal regions in the spotted gar, which diverged prior to 3R, we could time these rearrangements to post-3R. CONCLUSIONS We present an extensive analysis of the paralogon housing the visual opsin, GNAT and GNAI, OT/VP-R, and CACNA1-L gene families. The combined data imply that the early vertebrate WGD events contributed to the evolution of vision and the other neuronal and neuroendocrine functions exerted by the proteins encoded by these gene families. In pouched lamprey all five visual opsin genes have previously been identified, suggesting that lampreys diverged from the jawed vertebrates after 2R.
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Affiliation(s)
- David Lagman
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Daniel Ocampo Daza
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Jenny Widmark
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Xesús M Abalo
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Görel Sundström
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
- Present address: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-75123 Uppsala, Sweden
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
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Yokoyama S, Starmer WT, Liu Y, Tada T, Britt L. Extraordinarily low evolutionary rates of short wavelength-sensitive opsin pseudogenes. Gene 2013; 534:93-9. [PMID: 24125953 DOI: 10.1016/j.gene.2013.09.114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 09/24/2013] [Accepted: 09/26/2013] [Indexed: 01/08/2023]
Abstract
Aquatic organisms such as cichlids, coelacanths, seals, and cetaceans are active in UV-blue color environments, but many of them mysteriously lost their abilities to detect these colors. The loss of these functions is a consequence of the pseudogenization of their short wavelength-sensitive (SWS1) opsin genes without gene duplication. We show that the SWS1 gene (BdenS1ψ) of the deep-sea fish, pearleye (Benthalbella dentata), became a pseudogene in a similar fashion about 130 million years ago (Mya) yet it is still transcribed. The rates of nucleotide substitution (~1.4 × 10(-9)/site/year) of the pseudogenes of these aquatic species as well as some prosimian and bat species are much smaller than the previous estimates for the globin and immunoglobulin pseudogenes.
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Affiliation(s)
- Shozo Yokoyama
- Department of Biology, Emory University, Atlanta, GA 30322, USA.
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DAVIES WAYNEIL, COLLIN SHAUNP, HUNT DAVIDM. Molecular ecology and adaptation of visual photopigments in craniates. Mol Ecol 2012; 21:3121-58. [DOI: 10.1111/j.1365-294x.2012.05617.x] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
The visual pigment rhodopsin (rh1) constitutes the first step in the sensory transduction cascade in the rod photoreceptors of the vertebrate eye, forming the basis of vision at low light levels. In most vertebrates, rhodopsin is a single-copy gene whose function in rod photoreceptors is highly conserved. We found evidence for a second rhodopsin-like gene (rh1-2) in the zebrafish genome. This novel gene was not the product of a zebrafish-specific gene duplication event and contains a number of unique amino acid substitutions. Despite these differences, expression of rh1-2 in vitro yielded a protein that not only bound chromophore, producing an absorption spectrum in the visible range (λmax ≈ 500 nm), but also activated in response to light. Unlike rh1, rh1-2 is not expressed during the first 4 days of embryonic development; it is expressed in the retina of adult fish but not the brain or muscle. Similar rh1-2 sequences were found in two other Danio species, as well as a more distantly related cyprinid, Epalzeorhynchos bicolor. While sequences were only identified in cyprinid fish, phylogenetic analyses suggest an older origin for this gene family. Our study suggests that rh1-2 is a functional opsin gene that is expressed in the retina later in development. The discovery of a new previously uncharacterized opsin gene in zebrafish retina is surprising given its status as a model system for studies of vertebrate vision and visual development.
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Morrow JM, Chang BSW. The p1D4-hrGFP II expression vector: a tool for expressing and purifying visual pigments and other G protein-coupled receptors. Plasmid 2010; 64:162-9. [PMID: 20627111 DOI: 10.1016/j.plasmid.2010.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/29/2010] [Accepted: 07/05/2010] [Indexed: 11/19/2022]
Abstract
The heterologous expression of membrane proteins such as G protein-coupled receptors can be a notoriously difficult task. We have engineered an expression vector, p1D4-hrGFP II, in order to efficiently express visual pigments in mammalian cell culture. This expression vector is based on pIRES-hrGFP II (Stratagene), with the addition of a C-terminal 1D4 epitope tag for immunoblotting and immunoaffinity purification. This vector employs the CMV promoter and hrGFP II, a co-translated reporter gene. We measured the effectiveness of pIRES-hrGFP II in expressing bovine rhodopsin, and showed a 3.9- to 5.7-fold increase in expression as measured by absorbance spectroscopy as compared with the pMT vector, a common choice for visual pigment expression. We then expressed zebrafish RH2-1 using p1D4-hrGFP II in order to assess its utility in expressing cone opsins, known to be less stable and more difficult to express than bovine rhodopsin. We show a λ(280)/λ(MAX) value of 3.3, one third of that reported in previous studies, suggesting increased expression levels and decreased levels of misfolded, non-functional visual pigment. Finally, we monitored HEK293T cell growth following transfection with pIRES-hrGFP II using fluorescence microscopy to illustrate the benefits of having a co-translated reporter during heterologous expression studies.
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Affiliation(s)
- James M Morrow
- Department of Cell & Systems Biology, University of Toronto, Room 501, Toronto, Ontario, Canada
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Faschinger C. Zur Evolution der Linse in verschiedenen Augen: Erstaunliches. SPEKTRUM DER AUGENHEILKUNDE 2010. [DOI: 10.1007/s00717-010-0403-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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