The rhodopsin-encoding gene of bony fish lacks introns

Diversification processes of teleost intron-less opsin genes

Opsins are universal photosensitive proteins in animals. Vertebrates have a variety of opsin genes for visual and non-visual photoreceptions. Analysis of the gene structures shows that most opsin genes have introns in their coding regions. However, teleosts exceptionally have several intron-less opsin genes which are presumed to have been duplicated by an RNA-based gene duplication mechanism, retroduplication. Among these retrogenes, we focused on the Opn4 (melanopsin) gene responsible for non-image-forming photoreception. Many teleosts have five Opn4 genes including one intron-less gene, which is speculated to have been formed from a parental intron-containing gene in the Actinopterygii. In this study, to reveal the evolutionary history of Opn4 genes, we analyzed them in teleost (zebrafish and medaka) and non-teleost (bichir, sturgeon and gar) fishes. Our synteny analysis suggests that the intron-less Opn4 gene emerged by retroduplication after branching of the bichir lineage. In addition, our biochemical and histochemical analyses showed that, in the teleost lineage, the newly acquired intron-less Opn4 gene became abundantly used without substantial changes of the molecular properties of the Opn4 protein. This stepwise evolutionary model of Opn4 genes is quite similar to that of rhodopsin genes in the Actinopterygii. The unique acquisition of rhodopsin and Opn4 retrogenes would have contributed to the diversification of the opsin gene repertoires in the Actinopterygii and the adaptation of teleosts to various aquatic environments.

Evolutionary history of teleost intron-containing and intron-less rhodopsin genes

Recent progress in whole genome sequencing has revealed that animals have various kinds of opsin genes for photoreception. Among them, most opsin genes have introns in their coding regions. However, it has been known for a long time that teleost retinas express intron-less rhodopsin genes, which are presumed to have been formed by retroduplication from an ancestral intron-containing rhodopsin gene. In addition, teleosts have an intron-containing rhodopsin gene (exo-rhodopsin) exclusively for pineal photoreception. In this study, to unravel the evolutionary origin of the two teleost rhodopsin genes, we analyzed the rhodopsin genes of non-teleost fishes in the Actinopterygii. The phylogenetic analysis of full-length sequences of bichir, sturgeon and gar rhodopsins revealed that retroduplication of the rhodopsin gene occurred after branching of the bichir lineage. In addition, analysis of the tissue distribution and the molecular properties of bichir, sturgeon and gar rhodopsins showed that the abundant and exclusive expression of intron-containing rhodopsin in the pineal gland and the short lifetime of its meta II intermediate, which leads to optimization for pineal photoreception, were achieved after branching of the gar lineage. Based on these results, we propose a stepwise evolutionary model of teleost intron-containing and intron-less rhodopsin genes.

Vision using multiple distinct rod opsins in deep-sea fishes

Vertebrate vision is accomplished through light-sensitive photopigments consisting of an opsin protein bound to a chromophore. In dim light, vertebrates generally rely on a single rod opsin [rhodopsin 1 (RH1)] for obtaining visual information. By inspecting 101 fish genomes, we found that three deep-sea teleost lineages have independently expanded their RH1 gene repertoires. Among these, the silver spinyfin (Diretmus argenteus) stands out as having the highest number of visual opsins in vertebrates (two cone opsins and 38 rod opsins). Spinyfins express up to 14 RH1s (including the most blueshifted rod photopigments known), which cover the range of the residual daylight as well as the bioluminescence spectrum present in the deep sea. Our findings present molecular and functional evidence for the recurrent evolution of multiple rod opsin-based vision in vertebrates.

Integrative approach reveals a new species of Nematocharax (Teleostei: Characidae)

An integrative approach based on morphological and multilocus genetic data was used to describe a new species of Nematocharax from the headwaters of the upper Contas River on the Diamantina Plateau, north-eastern Brazil and to infer the relationships among evolutionary lineages within this fish genus. Multispecies coalescent inference using three mitochondrial and five nuclear loci strongly supports a basal split between Nematocharax venustus and the new species, whose distinctive morphological characters include absence of filamentous rays on pelvic fins of maturing and mature males, reduced anal-fin lobe length and lower body depth. The unique morphological and genetic traits of the population from the upper Contas River were supported by previous reports based on cytogenetics, DNA barcode and geometric morphometrics, reinforcing the validation of the new species. The conservation status of this new species is discussed.

Rhodopsin gene evolution in early teleost fishes

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 molecular and cellular basis of rhodopsin retinitis pigmentosa reveals potential strategies for therapy

Inherited mutations in the rod visual pigment, rhodopsin, cause the degenerative blinding condition, retinitis pigmentosa (RP). Over 150 different mutations in rhodopsin have been identified and, collectively, they are the most common cause of autosomal dominant RP (adRP). Mutations in rhodopsin are also associated with dominant congenital stationary night blindness (adCSNB) and, less frequently, recessive RP (arRP). Recessive RP is usually associated with loss of rhodopsin function, whereas the dominant conditions are a consequence of gain of function and/or dominant negative activity. The in-depth characterisation of many rhodopsin mutations has revealed that there are distinct consequences on the protein structure and function associated with different mutations. Here we categorise rhodopsin mutations into seven discrete classes; with defects ranging from misfolding and disruption of proteostasis, through mislocalisation and disrupted intracellular traffic to instability and altered function. Rhodopsin adRP offers a unique paradigm to understand how disturbances in photoreceptor homeostasis can lead to neuronal cell death. Furthermore, a wide range of therapies have been tested in rhodopsin RP, from gene therapy and gene editing to pharmacological interventions. The understanding of the disease mechanisms associated with rhodopsin RP and the development of targeted therapies offer the potential of treatment for this currently untreatable neurodegeneration.

The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation

We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.

Characterization and Evolution of the Spotted Gar Retina

In this study, we characterize the retina of the spotted gar, Lepisosteus oculatus, a ray-finned fish. Gar did not undergo the whole genome duplication event that occurred at the base of the teleost fish lineage, which includes the model species zebrafish and medaka. The divergence of gars from the teleost lineage and the availability of a high-quality genome sequence make it a uniquely useful species to understand how genome duplication sculpted features of the teleost visual system, including photoreceptor diversity. We developed reagents to characterize the cellular organization of the spotted gar retina, including representative markers for all major classes of retinal neurons and Müller glia. We report that the gar has a preponderance of predicted short-wavelength shifted (SWS) opsin genes, including a duplicated set of SWS1 (ultraviolet) sensitive opsin encoding genes, a SWS2 (blue) opsin encoding gene, and two rod opsin encoding genes, all of which were expressed in retinal photoreceptors. We also report that gar SWS1 cones lack the geometric organization of photoreceptors observed in teleost fish species, consistent with the crystalline photoreceptor mosaic being a teleost innovation. Of note the spotted gar expresses both exo-rhodopsin (RH1-1) and rhodopsin (RH1-2) in rods. Exo-rhodopsin is an opsin that is not expressed in the retina of zebrafish and other teleosts, but rather is expressed in regions of the brain. This study suggests that exo-rhodopsin is an ancestral actinopterygian (ray finned fish) retinal opsin, and in teleosts its expression has possibly been subfunctionalized to the pineal gland.

A second visual rhodopsin gene, rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes

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.

Functional opsin retrogene in nocturnal moth

Background

Retrotransposed genes are different to other types of genes as they originate from a processed mRNA and are then inserted back into the genome. For a long time, the contribution of this mechanism to the origin of new genes, and hence to the evolutionary process, has been questioned as retrogenes usually lose their regulatory sequences upon insertion and generally decay into pseudogenes. In recent years, there is growing evidence, notably in mammals, that retrotransposition is an important process driving the origin of new genes, but the evidence in insects remains largely restricted to a few model species.

Findings

By sequencing the messenger RNA of three developmental stages (first and fifth instar larvae and adults) of the pest Helicoverpa armigera, we identified a second, intronless, long-wavelength sensitive opsin (that we called LWS2). We then amplified the partial CDS of LWS2 retrogenes from another six noctuid moths, and investigate the phylogenetic distribution of LWS2 in 15 complete Lepidoptera and 1 Trichoptera genomes. Our results suggests that LWS2 evolved within the noctuid. Furthermore, we found that all the LWS2 opsins have an intact ORF, and have an ω-value (ω = 0.08202) relatively higher compared to their paralog LWS1 (ω = 0.02536), suggesting that LWS2 opsins were under relaxed purifying selection. Finally, the LWS2 shows temporal compartmentalization of expression. LWS2 in H. armigera in adult is expressed at a significantly lower level compared to all other opsins in adults; while in the in 1^st instar stage larvae, it is expressed at a significantly higher level compared to other opsins.

Conclusions

Together the results of our evolutionary sequence analyses and gene expression data suggest that LWS2 is a functional gene, however, the relatively low level of expression in adults suggests that LWS2 is most likely not involved in mediating the visual process.

Electronic supplementary material

The online version of this article (doi:10.1186/s13100-016-0074-8) contains supplementary material, which is available to authorized users.

Cubozoan genome illuminates functional diversification of opsins and photoreceptor evolution

Animals sense light primarily by an opsin-based photopigment present in a photoreceptor cell. Cnidaria are arguably the most basal phylum containing a well-developed visual system. The evolutionary history of opsins in the animal kingdom has not yet been resolved. Here, we study the evolution of animal opsins by genome-wide analysis of the cubozoan jellyfish Tripedalia cystophora, a cnidarian possessing complex lens-containing eyes and minor photoreceptors. A large number of opsin genes with distinct tissue- and stage-specific expression were identified. Our phylogenetic analysis unequivocally classifies cubozoan opsins as a sister group to c-opsins and documents lineage-specific expansion of the opsin gene repertoire in the cubozoan genome. Functional analyses provided evidence for the use of the Gs-cAMP signaling pathway in a small set of cubozoan opsins, indicating the possibility that the majority of other cubozoan opsins signal via distinct pathways. Additionally, these tests uncovered subtle differences among individual opsins, suggesting possible fine-tuning for specific photoreceptor tasks. Based on phylogenetic, expression and biochemical analysis we propose that rapid lineage- and species-specific duplications of the intron-less opsin genes and their subsequent functional diversification promoted evolution of a large repertoire of both visual and extraocular photoreceptors in cubozoans.

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

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.

Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)

The genetic mechanisms underlying regressive evolution-the degeneration or loss of a derived trait--are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appears to have retained functional amino acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional constraint of rhodopsin in amblyopsid cavefishes, as at least three cave lineages have independently accumulated unique loss-of-function mutations over the last 10.3 Mya. Although several cave lineages still possess functional rhodopsin, they exhibit increased rates of nonsynonymous mutations that have greater effect on the structure and function of rhodopsin compared to those in surface lineages. These results indicate that functionality of rhodopsin has been repeatedly lost in amblyopsid cavefishes. The presence of a functional copy of rhodopsin in some cave lineages is likely explained by stochastic accumulation of mutations following recent subterranean colonization.

Functional diversity of melanopsins and their global expression in the teleost retina

Melanopsin (OPN4) is an opsin photopigment that, in mammals, confers photosensitivity to retinal ganglion cells and regulates circadian entrainment and pupil constriction. In non-mammalian species, two forms of opn4 exist, and are classified into mammalian-like (m) and non-mammalian-like (x) clades. However, far less is understood of the function of this photopigment family. Here we identify in zebrafish five melanopsins (opn4m-1, opn4m-2, opn4m-3, opn4x-1 and opn4x-2), each encoding a full-length opsin G protein. All five genes are expressed in the adult retina in a largely non-overlapping pattern, as revealed by RNA in situ hybridisation and immunocytochemistry, with at least one melanopsin form present in all neuronal cell types, including cone photoreceptors. This raises the possibility that the teleost retina is globally light sensitive. Electrophysiological and spectrophotometric studies demonstrate that all five zebrafish melanopsins encode a functional photopigment with peak spectral sensitivities that range from 470 to 484 nm, with opn4m-1 and opn4m-3 displaying invertebrate-like bistability, where the retinal chromophore interchanges between cis- and trans-isomers in a light-dependent manner and remains within the opsin binding pocket. In contrast, opn4m-2, opn4x-1 and opn4x-2 are monostable and function more like classical vertebrate-like photopigments, where the chromophore is converted from 11-cis to all-trans retinal upon absorption of a photon, hydrolysed and exits from the binding pocket of the opsin. It is thought that all melanopsins exhibit an invertebrate-like bistability biochemistry. Our novel findings, however, reveal the presence of both invertebrate-like and vertebrate-like forms of melanopsin in the teleost retina, and indicate that photopigment bistability is not a universal property of the melanopsin family. The functional diversity of these teleost melanopsins, together with their widespread expression pattern within the retina, suggests that melanopsins confer global photosensitivity to the teleost retina and might allow for direct "fine-tuning" of retinal circuitry and physiology in the dynamic light environments found in aquatic habitats.

A novel rhodopsin-like gene expressed in zebrafish retina

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.

Adaptation of pineal expressed teleost exo-rod opsin to non-image forming photoreception through enhanced Meta II decay

Photoreception by vertebrates enables both image-forming vision and non-image-forming responses such as circadian photoentrainment. Over the recent years, distinct non-rod non-cone photopigments have been found to support circadian photoreception in diverse species. By allowing specialization to this sensory task a selective advantage is implied, but the nature of that specialization remains elusive. We have used the presence of distinct rod opsin genes specialized to either image-forming (retinal rod opsin) or non-image-forming (pineal exo-rod opsin) photoreception in ray-finned fish (Actinopterygii) to gain a unique insight into this problem. A comparison of biochemical features for these paralogous opsins in two model teleosts, Fugu pufferfish (Takifugu rubripes) and zebrafish (Danio rerio), reveals striking differences. While spectral sensitivity is largely unaltered by specialization to the pineal environment, in other aspects exo-rod opsins exhibit a behavior that is quite distinct from the cardinal features of the rod opsin family. While they display a similar thermal stability, they show a greater than tenfold reduction in the lifetime of the signaling active Meta II photoproduct. We show that these features reflect structural changes in retinal association domains of helices 3 and 5 but, interestingly, not at either of the two residues known to define these characteristics in cone opsins. Our findings suggest that the requirements of non-image-forming photoreception have lead exo-rod opsin to adopt a characteristic that seemingly favors efficient bleach recovery but not at the expense of absolute sensitivity.

Systemic splicing factor deficiency causes tissue-specific defects: a zebrafish model for retinitis pigmentosa

Retinitis pigmentosa (RP) is a common hereditary eye disease that causes blindness due to a progressive loss of photoreceptors in the retina. RP can be elicited by mutations that affect the tri-snRNP subunit of the pre-mRNA splicing machinery, but how defects in this essential macromolecular complex transform into a photoreceptor-specific phenotype is unknown. We have modeled the disease in zebrafish by silencing the RP-associated splicing factor Prpf31 and observed detrimental effects on visual function and photoreceptor morphology. Despite reducing the level of a constitutive splicing factor, no general defects in gene expression were found. Instead, retinal genes were selectively affected, providing the first in vivo link between mutations in splicing factors and the RP phenotype. Silencing of Prpf4, a splicing factor hitherto unrelated to RP, evoked the same defects in vision, photoreceptor morphology and retinal gene expression. Hence, various routes affecting the tri-snRNP can elicit tissue-specific gene expression defects and lead to the RP phenotype.

Individual variation in rod absorbance spectra correlated with opsin gene polymorphism in sand goby (Pomatoschistus minutus)

Rod absorbance spectra, characterized by the wavelength of peak absorbance(λmax) were related to the rod opsin sequences of individual sand gobies (Pomatoschistus minutus) from four allopatric populations[Adriatic Sea (A), English Channel (E), Swedish West Coast (S) and Baltic Sea(B)]. Rod λmax differed between populations in a manner correlated with differences in the spectral light transmission of the respective water bodies [λmax: (A)≈503 nm; (E and S)≈505–506 nm; (B)≈508 nm]. A distinguishing feature of B was the wide within-population variation of λmax (505.6–511.3 nm). The rod opsin gene was sequenced in marked individuals whose rod absorbance spectra had been accurately measured. Substitutions were identified using EMBL/GenBank X62405 English sand goby sequence as reference and interpreted using two related rod pigments, the spectrally similar one of the Adriatic P. marmoratus (λmax≈507 nm) and the relatively red-shifted Baltic P. microps(λmax≈515 nm) as outgroups. The opsin sequence of all E individuals was identical to that of the reference, whereas the S and B fish all had the substitution N151N/T or N151T. The B fish showed systematic within-population polymorphism, the sequence of individuals withλ max at 505.6–507.5 nm were identical to S, but those with λmax at 509–511.3 nm additionally had F261F/Y. The substitution F261Y is known to red-shift the rod pigment and was found in all P. microps. We propose that ambiguous selection pressures in the Baltic Sea and/or gene flow from the North Sea preserves polymorphism and is phenotypically evident as a wide variation in λmax.

Into the blue: gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii

The cartilaginous fishes reside at the base of the gnathostome lineage as the oldest extant group of jawed vertebrates. Recently, the genome of the elephant shark, Callorhinchus milii, a chimaerid holocephalan, has been sequenced and therefore becomes the first cartilaginous fish to be analyzed in this way. The chimaeras have been largely neglected and very little is known about the visual systems of these fishes. By searching the elephant shark genome, we have identified gene fragments encoding a rod visual pigment, Rh1, and three cone visual pigments, the middle wavelength-sensitive or Rh2 pigment, and two isoforms of the long wavelength-sensitive or LWS pigment, LWS1 and LWS2, but no evidence for the two short wavelength-sensitive cone classes, SWS1 and SWS2. Expression of these genes in the retina was confirmed by RT-PCR. Full-length coding sequences were used for in vitro expression and gave the following peak absorbances: Rh1 496 nm, Rh2 442 nm, LWS1 499 nm, and LWS2 548 nm. Unusually, therefore, for a deep-sea fish, the elephant shark possesses cone pigments and the potential for trichromacy. Compared with other vertebrates, the elephant shark Rh2 and LWS1 pigments are the shortest wavelength-shifted pigments of their respective classes known to date. The mechanisms for this are discussed and we provide experimental evidence that the elephant shark LWS1 pigment uses a novel tuning mechanism to achieve the short wavelength shift to 499 nm, which inactivates the chloride-binding site. Our findings have important implications for the present knowledge of color vision evolution in early vertebrates.

The visual pigments of a deep-sea teleost, the pearl eye Scopelarchus analis

The eyes of deep-sea fish have evolved to function under vastly reduced light conditions compared to those that inhabit surface waters. This has led to a bathochromatic shift in the spectral location of maximum absorbance (lambda(max)) of their rod (RH1) pigments and the loss of cone photoreceptors. There are exceptions to this, however, as demonstrated by the deep-sea pearl eye Scopelarchus analis. Here we show the presence of two RH1 pigments (termed RH1A and RH1B) and a cone RH2 pigment. This is therefore the first time that the presence of a cone pigment in a deep-sea fish has been confirmed by molecular analysis. The lambda(max) values of the RH1A and RH1B pigments at 486 and 479 nm, respectively, have been determined by in vitro expression of the recombinant opsins and show the typical short-wave shifts of fish that live in deep water compared to surface dwellers. RH1B, however, is expressed only in more adult fish and lacks key residues for phosphorylation, indicating that it may not be involved in image formation. In contrast, the RH2 pigment has additional residues near the C terminus that may be involved in phosphorylation and does not show temporal changes in expression. The distribution of these pigments within the multiple retinae of S. analis is discussed.

Evolutionarily conserved and divergent regulatory sequences in the fish rod opsin promoter

Fish have multiple types and subtypes of opsin genes that are expressed in a highly regulated manner in retinal photoreceptor cells. In the rod opsin proximal promoter region (RPPR) of zebrafish (Danio rerio), the BAT 1 regulatory region contains highly conserved OTX (GATTA) and OTX-like (TATTA) sequences that can be recognized by the mammalian cone-rod homeobox (CRX) protein. However, binding of zebrafish crx to the OTX sequence has remained elusive. In contrast to the BAT 1 region, the Ret 1 region, located approximately 20 bp upstream of the BAT 1 region in mammals, is not conserved in zebrafish. In the Ret 1 region, even the core OTX-like sequence (AATTA sequence in mammals) is destructed. We show in this study that a region between Ret 1 and BAT 1 (denoted IRB, Inter-Ret 1-BAT 1) is highly conserved among fish species. Using electrophoretic mobility shift assay (EMSA), we show that zebrafish crx binds to the conserved OTX sequence and that the fish-specific IRB region specifically binds elements present in both retinal and brain nuclear extracts of zebrafish. These results imply that the regulatory mechanisms of opsin gene expression consist not only of evolutionarily conserved but also of divergent machinery among different animal taxa.

Structure and evolution of the teleost extraretinal rod-like opsin (errlo) and ocular rod opsin (rho) genes: is teleost rho a retrogene?

In Teleost fish examined to date the ocular rod opsin gene, rho, is intronless, unlike the rod opsin genes of other vertebrate classes which possess a five exon/four intron structure. We have examined in silico the structure of rho (which is expressed uniquely in the retina) and the closely related extraretinal rod-like opsin (exo-rhodopsin) gene, errlo (which is expressed uniquely in the pineal), in the puffer-fish, Fugu rubripes (Takifugu rubripes). Whilst the ocular rho is intronless in common with other Teleosts, the pineal errlo has the five exon/four intron structure common to the rod opsin gene of other vertebraes. A comparison of the sequence surrounding the errlo and rho loci indicates that the errlo locus is syntenic with RHO, the human rod opsin gene, rather than rho. We suggest that the intronless rho may have arisen through an ancient retrotransposition of a mature mRNA originating from errlo. This duplication event has occurred early in the evolution of the Actinopterygii (ray-finned fish) since the rho of the primitive Actinopterygians such as sturgeon, bowfin, and gar is also intronless. Since it appears that the intron containing errlo is the ancestral opsin gene that gave rise to the intronless rho in the Teleostei, errlo is therefore the true orthologue of the rod opsin gene in other vertebrate classes. We suggest that loss of expression of errlo in the retina could be related to the metabolic and physiological advantages, such as a reduction in splicing events during RNA processing, that may be conferred through possession of an additional, intronless rod opsin gene in the form of rho.

The regulation of retina specific expression of rhodopsin gene in vertebrates

Rhodopsin genes in most vertebrate species, with the exception of teleost fishes, contain introns. Despite differences in the gene structure, similar regulatory motifs have been identified in fish, amphibian and mammalian rhodopsin promoters, suggesting that rhodopsin gene regulation may be conserved in vertebrates. However, there is no direct evidence to support this notion. To address this, the rhodopsin promoter from the pufferfish, Fugu rubripes, was isolated and tested in transgenic mice and frogs. A 6.5 kb Fugu genomic fragment containing the rhodopsin gene and 4.5 kb 5' flanking region was able to direct expression of the Fugu rhodopsin gene to the retina of transgenic mice. In transgenic tadpoles, photoreceptor rod cell-specific expression of a reporter gene was achieved using only 500 bp Fugu rhodopsin promoter fragment. Mutagenesis of this promoter fragment revealed that a conserved NRE-like motif is crucial for the retina-specific expression. Our investigation suggests that the regulation of retinal specific expression is conserved in the pufferfish, frog and mouse and that the ancestral intron-containing rhodopsin gene has been displaced by an intronless copy in teleosts.

Molecular structure and developmental expression of three muscle-type troponin T genes in zebrafish

Troponin T (Tnnt), a troponin component, interacts with tropomyosin and is crucial to the regulation of striated muscle contraction. To gain insight into the molecular evolution and developmental regulation of Tnnt gene (Tnnt) in lower vertebrates, zebrafish Tnnt1 (slow Tnnt), Tnnt2 (cardiac Tnnt), and Tnnt3b (fast Tnnt isoform b) were characterized. The polypeptides of zebrafish Tnnt1, Tnnt2, and Tnnt3b were conserved in the central tropomyosin- and C-terminal troponin I-binding domains. However, the N-terminal hypervariable regions were highly extended and rich in glutamic acid in polypeptides of Tnnt1 and Tnnt2, but not Tnnt3b. The Tnnt2 and Tnnt3b contain introns, whereas Tnnt1 is intron-free. During development, large to small, alternatively spliced variants were detected in Tnnt2, but not in Tnnt1 or Tnnt3. Whole-mount in situ hybridization showed zebrafish Tnnt1 and Tnnt2 are activated during early somitogenesis (10 hr postfertilization, hpf) and cardiogenesis (14 hpf), respectively, but Tnnt3b is not activated until middle somitogenesis (18 hpf). Tnnt2 and Tnnt3b expression was cardiac- and fast-muscle specific, but Tnnt1 was expressed in both slow and fast muscles. We propose that three, distinct, muscle-type Tnnt evolved after the divergence of fish and deuterostome invertebrates. In zebrafish, the developmental regulation of Tnnt during somitogenesis and cardiogenesis is more restricted and simpler than in tetrapods. These new findings may provide insight into the developmental regulation and molecular evolution of vertebrate Tnnt.

Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa

Although much progress has been made recently in teleostean phylogeny, relationships among the main lineages of the higher teleosts (Acanthomorpha), containing more than 60% of all fish species, remain poorly defined. This study represents the most extensive taxonomic sampling effort to date to collect new molecular characters for phylogenetic analysis of acanthomorph fishes. We compiled and analyzed three independent data sets, including: (i) mitochondrial ribosomal fragments from 12S and 16s (814bp for 97 taxa); (ii) nuclear ribosomal 28S sequences (847bp for 74 taxa); and (iii) a nuclear protein-coding gene, rhodopsin (759bp for 86 taxa). Detailed analyses were conducted on each data set separately and the principle of taxonomic congruence without consensus trees was used to assess confidence in the results as follows. Repeatability of clades from separate analyses was considered the primary criterion to establish reliability, rather than bootstrap proportions from a single combined (total evidence) data matrix. The new and reliable clades emerging from this study of the acanthomorph radiation were: Gadiformes (cods) with Zeioids (dories); Beloniformes (needlefishes) with Atheriniformes (silversides); blenioids (blennies) with Gobiesocoidei (clingfishes); Channoidei (snakeheads) with Anabantoidei (climbing gouramies); Mastacembeloidei (spiny eels) with Synbranchioidei (swamp-eels); the last two pairs of taxa grouping together, Syngnathoidei (aulostomids, macroramphosids) with Dactylopteridae (flying gurnards); Scombroidei (mackerels) plus Stromatoidei plus Chiasmodontidae; Ammodytidae (sand lances) with Cheimarrhichthyidae (torrentfish); Zoarcoidei (eelpouts) with Cottoidei; Percidae (perches) with Notothenioidei (Antarctic fishes); and a clade grouping Carangidae (jacks), Echeneidae (remoras), Sphyraenidae (barracudas), Menidae (moonfish), Polynemidae (threadfins), Centropomidae (snooks), and Pleuronectiformes (flatfishes).

In silico characterisation and chromosomal localisation of human RRH (peropsin)--implications for opsin evolution

BACKGROUND

The vertebrate opsins are proteins which utilise a retinaldehyde chromophore in their photosensory or photoisomerase roles in the visual/irradiance detection cycle. The majority of the opsins, such as rod and cone opsins, have a very highly conserved gene structure suggesting a common lineage. Exceptions to this are RGR-opsin and melanopsin, whose genes have very different intron insertion positions. The gene structure of another opsin, peropsin (retinal pigment epithelium-derived rhodopsin homologue, RRH) is unknown.

RESULTS

By in silico analysis of the GenBank database we have determined that the human RRH comprises 7 exons spanning approximately 16.5 kb and is localised to chromosome 4q25 in the following gene sequence: cen-EGF-RRH-IF-qter - a position that excludes this gene as a candidate for the RP29 autosomal recessive retinitis pigmentosa locus. A comparison of opsin gene structures reveals that RRH and RGR share two common intron (introns 1 and 4) insertion positions which may reflect a shared ancestral gene.

CONCLUSION

The opsins comprise a diverse group of genes which appear to have arisen from three different lineages. These lineages comprise the "classical opsin superfamily" which includes the rod and cone opsins, pinopsin, VA-opsin, parapinopsin and encephalopsin; the RRH and RGR group; and the melanopsin line. A common lineage for RRH and RGR, together with their sites of expression in the RPE, indicates that peropsin may act as a retinal isomerase.

Visualization of rod photoreceptor development using GFP-transgenic zebrafish

Zebrafish retina contains five morphologically distinct classes of photoreceptors, each expressing a distinct type of opsin gene. Molecular mechanisms underlying specification of opsin expression and differentiation among the cell types are largely unknown. This is partly because mutants affected with expression of a particular class of opsin gene are difficult to find. In this study we established the transgenic lines of zebrafish carrying green fluorescent protein (GFP) gene under the 1.1-kb and 3.7-kb upstream regions of the rod-opsin gene. In transgenic fish, GFP expression initiated and proceeded in the same spatiotemporal pattern with rod-opsin gene. The retinal section from adult transgenic fish showed GFP expression throughout the rod cell layer. These results indicate that the proximal 1.1-kb region is sufficient to drive gene expression in all rod photoreceptor cells. These transgenic fish should facilitate screening of mutants affected specifically with rod-opsin expression or rod cell development by visualization of rod cells by GFP.

Retina-specific cis-elements and binding nuclear proteins of carp rhodopsin gene

The upstream cis-elements controlling the retina-specific expression of carp rhodopsin gene were fully characterized in vivo. Transgenic studies demonstrated that both carp neural retina leucine zipper response-like element (cNRE, within nucleotides (nt) -63 to -75) and carp-specific element (CSE, nt -46 to -52) were crucial to reporter gene expression in medaka retinae. The retina-specific expression rates of embryos injected with nt -1 to -641 and longer fragments were much higher than those of embryos injected with nt -1 to -138 and shorter fragments, indicating that an enhancer is located in the nt -138 to -641 region. Retinal extracts and the probe BAT-1 (nt -90 to -120) formed two DNA-protein complexes, B1 and B2. Retinal extracts and the probes cNRE and CSE formed the complexes N1 and C1, respectively. The protein factors in B1 and C1 were mammal-like cone-rod homeobox proteins.

The molecular basis for spectral tuning of rod visual pigments in deep-sea fish

Most species of deep-sea fish possess of a rod-only retina with a pigment that is generally shortwave shifted in λmax towards the blue region of the spectrum. In addition, the λmax values of different species tend to cluster at particular points in the spectrum. In this study, the rod opsin gene sequences from 28 deep-sea fish species drawn from seven different Orders are compared. The λmax values of the rod pigments vary from approximately 520 nm to <470 nm, with the majority lying between 490 nm and 477 nm. The 520 nm pigment in two species of dragon fish is associated with a Phe261Tyr substitution, whereas the shortwave shifts of the pigments in the other 26 species are accountable by substitutions at a further eight sites (83, 122, 124, 132, 208, 292, 299 and 300). Clustering of λmax values does not, however, involve a common subset of these substitutions in the different species. A phylogenetic analysis predicts that the pigment in the ancestral species would have had a λmax of approximately 480 nm. A total of 27 changes is required to generate the pattern of substitutions seen in the different species, with many sites undergoing multiple changes.

Intron loss in the SART1 genes of Fugu rubripes and Tetraodon nigroviridis

The human SART1 gene was initially identified in a screen for proteins recognised by IgE, which may be implicated in atopic disease. We have examined the genomic structure and cDNA sequence of the SART1 gene in the compact genomes of the pufferfish Fugu rubripes and Tetraodon nigroviridis. The entire coding regions of both the Fugu and Tetraodon SART1 genes are contained within single exons. The Fugu gene contains only one intron located in the 5' untranslated region. Southern blot hybridisation of Fugu genomic DNA confirmed the SART1 gene to be single copy. Partial genomic structures were also determined for the human, mouse, Drosophila and C. elegans SART1 homologues. The human and mouse genes both contain many introns in the coding region, the human gene possessing at least 20 exons. The Drosophila and C. elegans homologues contain 6 and 12 exons, respectively. This is only the second time such a difference in the organization of homologous Fugu and human genes has been reported. The Fugu and Tetraodon SART1 genes encode putative proteins of 772 and 774 aa, respectively, each having 65% amino acid identity to human SART1. Leucine zipper and basic motifs are conserved in the predicted Fugu and Tetraodon proteins.

Molecular evolution of vertebrate visual pigments

Dramatic improvement of our understanding of the genetic basis of vision was brought by the molecular characterization of the bovine rhodopsin gene and the human rhodopsin and color opsin genes (Nathans and Hogness, 1983; Nathans et al., 1984, 1986a,b). The availability of cDNA clones from these studies has facilitated the isolation of retinal and nonretinal opsin genes and cDNA clones from a large variety of species. Today, the number of genomic and cDNA clones of opsin genes isolated from different vertebrate species exceeds 100 and is increasing rapidly. The opsin gene sequences reveal the importance of the origin and differentiation of various opsins and visual pigments. To understand the molecular genetic basis of spectral tuning of visual pigments, it is essential to establish correlations between a series of the sequences of visual pigments and their lambda(max) values. The potentially important amino acid changes identified in this way have to be tested whether they are in fact responsible for the lambda(max)-shifts using site-directed mutagenesis and cultured cells. A major goal of molecular evolutionary genetics is to understand the molecular mechanisms involved in functional adaptations of organisms to different environments, including the mechanisms of the regulation of the spectral absorption. Therefore, both molecular evolutionary analyses of visual pigments and vision science have an important common goal.

Molecular cloning of fresh water and deep-sea rod opsin genes from Japanese eel Anguilla japonica and expressional analyses during sexual maturation

We have determined the complete cDNA sequences of fresh water rod opsin gene (fwo) and deep-sea rod opsin gene (dso) from Japanese eel Anguilla japonica. The cDNA clones of fwo and dso consisted of 1437 and 1497 nucleotides, respectively. The predicted opsins of both genes consisted of 352 amino acid residues. Southern blot and PCR analyses of genomic DNA indicated that the Japanese eel genome contains only one fwo and one dso and they are intronless. Quantitative RT-PCR analyses revealed that the expression of fwo decreases with sexual maturation while that of dso increases.

Structural characterization and transcriptional pattern of two types of carp rhodopsin gene

This work characterizes the genomic structures of two types of carp (Cyprinus carpio) rhodopsin (cRh) gene, i.e. type I (cRh-I) and type II (cRh-II). Two types of cRh gene share only 45.6% polynucleotide identity in the upstream region from nucleotide -3436 to +97. However, three conserved regions are found. Homologies to the consensus recognition sites for transcription factors, Crx and Nrl, which are involved in photoreceptor-specific expression, are also observed in cRh genes. With specific polymerase chain reaction (PCR) primers, the two types of cRh gene can be clearly discriminated from each carp genome. Most carps exhibit both types of cRh gene, however, there are still carps possessing either cRh-I or cRh-II. Both cRh-I and cRh-II mRNAs are expressed at an approximately equal level in both eyes extracted from a carp carrying both types of cRh gene.

RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements

While the significance of middle repetitive elements had been neglected for a long time, there are again tendencies to ascribe most members of a given middle repetitive sequence family a functional role--as if the discussion of SINE (short interspersed repetitive elements) function only can occupy extreme positions. In this article, I argue that differences between the various classes of retrosequences concern mainly their copy numbers. Consequently, the function of SINEs should be viewed as pragmatic such as, for example, mRNA-derived retrosequences, without underestimating the impact of retroposition for generation of novel protein coding genes or parts thereof (exon shuffling by retroposition) and in particular of SINEs (and retroelements) in modulating genes and their expression. Rapid genomic change by accumulating retrosequences may even facilitate speciation [McDonald, J.F., 1995. Transposable elements: possible catalysts of organismic evolution. Trends Ecol. Evol. 10, 123-126.] In addition to providing mobile regulatory elements, small RNA-derived retrosequences including SINEs can, in analogy to mRNA-derived retrosequences, also give rise to novel small RNA genes. Perhaps not representative for all SINE/master gene relationships, we gained significant knowledge by studying the small neuronal non-messenger RNAs, namely BC1 RNA in rodents and BC200 RNA in primates. BC1 is the first identified master gene generating a subclass of ID repetitive elements, and BC200 is the only known Alu element (monomeric) that was exapted as a novel small RNA encoding gene.

Late changes in spliceosomal introns define clades in vertebrate evolution

The evolutionary origin of spliceosomal introns has been the subject of much controversy. Introns are proposed to have been both lost and gained during evolution. If the gain or loss of introns are unique events in evolution, they can serve as markers for phylogenetic analysis. We have made an extensive survey of the phylogenetic distribution of seven spliceosomal introns that are present in Fugu genes, but not in their mammalian homologues; we show that these introns were acquired by actinopterygian (ray-finned) fishes at various stages of evolution. We have also investigated the intron pattern of the rhodopsin gene in fishes, and show that the four introns found in the ancestral chordate rhodopsin gene were simultaneously lost in a common ancestor of ray-finned fishes. These changes in introns serve as excellent markers for phylogenetic analysis because they reliably define clades. Our intron-based cladogram establishes the difficult-to-ascertain phylogenetic relationships of some ray-finned fishes. For example, it shows that bichirs (Polypterus) are the sister group of all other extant ray-finned fishes.

Enhanced retinal longwave sensitivity using a chlorophyll-derived photosensitiser in Malacosteus niger, a deep-sea dragon fish with far red bioluminescence

Through partial bleaching of both visual pigment extracts and cell suspensions we show that the deep-sea stomiid Malacosteus niger, which produces far red bioluminescence, has two visual pigments within its retina which form a rhodopsin/porphyropsin pigment pair with lambda max values around 520 and 540 nm, but lacks the very longwave sensitive visual pigments (lambda max > 550 nm) observed in two other red light producing stomiids. The presence of only a single opsin gene in the M. niger genome was confirmed by molecular and cladistic analysis. To compensate for its apparently reduced longwave sensitivity compared to related species, the outer segments of M. niger contain additional pigments, which we identify as a mixture of defarnesylated and demetallated derivatives of bacteriochlorophylls c and d, that are used as a photosensitiser to enhance its sensitivity to longwave radiation.

cDNA cloning, genomic organization and chromosomal localization of human heparan glucosaminyl N-deacetylase/N-sulphotransferase-2

The cDNA and gene encoding human heparan glucosaminyl N-deacetylase/N-sulphotransferase-2 have been cloned. The cDNA encoded a protein of 883 amino acids that was 94% similar to heparan N-sulphotransferase-2 from mouse mast cells. Comparison of the deduced amino acid sequences of human heparan N-sulphotransferase-1 and -2 showed that the enzymes were 70% similar; greater than 90% of the amino acids between residues 418 and 543 were identical. The least conserved amino acids were found in the N-terminus/putative transmembrane regions of the two enzymes. The human heparan N-sulphotransferase-2 gene was localized to chromosome arm 10q (band 10q22) by in situ fluorescent hybridization. The gene contains 13 exons spanning 6.5 kb, ranging in size from 88 bp (exon 2) to >1 kb (exon 1), and 12 introns, which were found to occur at similar sites within the coding sequence of the human heparan N-sulphotransferase-1 gene. The structure of the two genes differed in that the heparan N-sulphotransferase-1 gene contained one additional intron. The similarity of the heparan N-sulphotransferase-1 and -2 proteins and their similar exon-intron organization suggest that they derive from a common ancestral gene.

Switch in rod opsin gene expression in the European eel, Anguilla anguilla (L.)

The rod photoreceptors of the European eel, Anguilla anguilla (L.), alter their wavelength of maximum sensitivity (lambda max) from c.a. 523 nm to c.a. 482 nm at maturation, a switch involving the synthesis of a new visual pigment protein (opsin) that is inserted into the outer segments of existing rods. We artificially induced the switch in rod opsin production by the administration of hormones, and monitored the switch at the level of mRNA accumulation using radiolabelled oligonuleotides that hybridized differently to the two forms of eel rod opsin. The production of the deep-sea form of rod opsin was detected 6 h after the first hormone injection, and the switch in rod opsin expression was complete within four weeks, at which time only the mRNA for the deep-sea opsin was detectable in the retinal cells. It is suggested that this system could be used as a tractable model for studying the regulatory control of opsin gene expression.

Molecular genetic basis of adaptive selection: examples from color vision in vertebrates

A central unanswered question in phototransduction is how photosensitive molecules, visual pigments, regulate their absorption spectra. In nature, there exist various types of visual pigments that are adapted to diverse photic environments. To elucidate the molecular mechanisms involved in the adaptive selection of these pigments, we have to identify amino acid changes of pigments that are potentially important in changing the wavelength of maximal absorption (lambda max) and then determine the effects of these mutations on the shift in lambda max. The desired mutants can be constructed using site-directed mutagenesis, expressed in tissue culture cells, and the functional effect of virtually any such mutant can be rigorously determined. The availability of these cell/molecular methods makes vision an ideal model system in studying adaptive mechanisms at the molecular level. The identification of potentially important amino acid changes using evolutionary biological means is an indispensable step in elucidating the molecular mechanisms that underlie the spectral tuning of visual pigments.

Molecular evolution of the cottoid fish endemic to Lake Baikal deduced from nuclear DNA evidence

Lake Baikal in Eastern Siberia contains a remarkable flock of 29 species of teleost fishes of the suborder Cottoidei (sculpins, bullheads) that are endemic to the lake and its associated rivers and occupy all depth habitats down to over 1500 m. The species are divided into three families, the Cottidae with 7 species, the Abyssocottidae with 20 species, and the Comephoridae with 2 species. Nucleotide sequences of the rod opsin gene from 12 of these species, plus a non-Baikal marine species, have been used to examine the evolutionary relations and the divergence time of the flock. Phylogenetic trees, generated by neighbor-joining and maximum parsimony, indicate that the unique Comephoridae family with its viviparity and unusual appearance is closely related to the Cottidae and Abyssocottidae, whereas the genus Cottocomephorus, at present placed in the Cottidae, was the first to diverge from the ancestral species and forms a separate lineage. The major adaptation to deep water would appear to be of relatively recent origin, and there is evidence that the ancestral species occupied a shallow-water-marine or brackish habitat. Estimates of antiquity obtained from synonymous substitutions place the origin of the species flock at around 4.9 million years ago.

Parapinopsin, a novel catfish opsin localized to the parapineal organ, defines a new gene family

Multiple sites of extraretinal photoreception are present in vertebrates, but the molecular basis of extraretinal phototransduction is poorly understood. This study reports the cloning of the first opsin specifically expressed in the directly photosensitive pineal and parapineal of cold-blooded vertebrates. This opsin, identified in channel catfish and termed parapinopsin, defines a new gene family of vertebrate photopigments and is expressed in a majority of parapinealocytes and a subset of pineal photoreceptor cells. Parapinopsin shows a caudal-rostral gradient of expression within the pineal organ. This study also reports the cloning of partial cDNAs encoding the channel catfish orthologues of rhodopsin and the red cone pigment-the full complement of retinal opsins in the species. In situ hybridization studies using probes derived from these retinal opsins, together with parapinopsin, reveal no expression of retinal opsins in pineal and parapineal organ and no expression of any opsin tested in the "deep brain," iris, or dermal melanophores. These data imply that phototransduction in these sites of extraretinal photoreception must be mediated by novel opsins.