Functional characterization of visual opsin repertoire in Medaka (Oryzias latipes)

Matsumoto, Yoshihisa; Fukamachi, Shoji; Mikami, Hiroshi; Kawamura, Shoji

doi:10.1016/j.gene.2005.12.005

Cited by 132 publications

(172 citation statements)

References 33 publications

Supporting

Mentioning

158

Contrasting

Unclassified

Order By: Relevance

“…estimated for visual pigments of juvenile Pacific bluefin tuna, corresponding to at least one SWS2 and two RH2 genes, respectively (16), but such a color sensitivity in tuna may be explained by the combinatorial function of more opsin genes. In particular, five green pigment genes are present in the tuna genome, whereas the other six teleost genomes sequenced to date have only one to four genes (8,21,22,30). This number is the highest among the sequenced fish species, and three of the five genes are identified in this study.…”

Section: Resultsmentioning

confidence: 69%

“…The fish visual system includes five opsin genes attributed to gene duplication: rhodopsin (RH1) in rod cells and four in cone cells: red-sensitive (middle/longwavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), and green-sensitive (RH2). Fish species often have multiple copies of opsin genes (6, 7); for example, medaka has three RH2 genes (8), and guppy has four M/LWS genes (9). In addition, many fish species have two copies of SWS2 genes, consistent with the concept that an ancient duplication occurred and each copy has been retained for a long time.…”

mentioning

confidence: 83%

See 1 more Smart Citation

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Nakamura

Mori

Saitoh

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

110

112

View full text Add to dashboard Cite

Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.tuna genome | visual system | animal opsin

show abstract

Section: Resultsmentioning

confidence: 69%

mentioning

confidence: 83%

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Nakamura

Mori

Saitoh

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

110

112

View full text Add to dashboard Cite

show abstract

“…In bony fishes, the opsin repertoire differs among species (Gojobori & Innan, 2009; Yokoyama, 2000). Generally, the surface‐dwelling species, which habit the luminous superficial area of water, have a large cone opsin repertoire, as seen in zebrafish ( Danio rerio ) (Chinen, Hamaoka, Yamada, & Kawamura, 2003), medaka ( Oryzias latipes ) (Matsumoto, Fukamachi, Mitani, & Kawamura, 2006), and guppy ( Poecilia reticulata ) (Kawamura et al., 2016). Conversely, dark deep‐sea fish tend to lose cone cells and corresponding opsins, whereas they possess a high proportion of rod cells, which contribute to dim light vision as in the case of lizardfish (Hope, Partridge, Dulai, & Hunt, 1997).…”

Section: Introductionmentioning

confidence: 99%

“…This value was close to those of RH2‐B (506 nm) and RH2‐C (490 nm), but far from that of SWS2B (416 nm). The λ max range of SWS2A in other vertebrates falls within 430–460 nm (Matsumoto et al., 2006; Spady et al., 2006). It was therefore conceivable that λ max of SWS2A shifted from the original wavelength to a longer wavelength during the evolution of the barfin flounder (Kasagi et al., 2015).…”

Section: Introductionmentioning

confidence: 99%

“…In addition to the seven functional opsins, we found an RH2‐A pseudogene in barfin flounder. The λ max range of the functional RH2‐A in other vertebrates is 450–480 nm (Matsumoto et al., 2006; Spady et al., 2006). Taken together, the pseudogenization of RH2‐A appeared to be related to a functional change caused by a long‐wavelength shift in SWS2A (Kasagi et al., 2015).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Green‐shifting ofSWS2A opsin sensitivity and loss of function ofRH2‐A opsin in flounders, genusVerasper

Kasagi

Mizusawa

Takahashi

2017

Ecology and Evolution

View full text Add to dashboard Cite

We identified visual opsin genes for three flounder species, including the spotted halibut (Verasper variegatus), slime flounder (Microstomus achne), and Japanese flounder (Paralichthys olivaceus). Structure and function of opsins for the three species were characterized together with those of the barfin flounder (V. moseri) that we previously reported. All four flounder species possessed five basic opsin genes, including lws, sws1, sws2, rh1, and rh2. Specific features were observed in rh2 and sws2. The rh2‐a, one of the three subtypes of rh2, was absent in the genome of V. variegatus and pseudogenized in V. moseri. Moreover, rh2‐a mRNA was not detected in M. achne and P. olivaceus, despite the presence of a functional reading frame. Analyses of the maximum absorption spectra (λmax) estimated by in vitro reconstitution indicated that SWS2A of M. achne (451.9 nm) and P. olivaceus (465.6 nm) were blue‐sensitive, whereas in V. variegatus (485.4 nm), it was green‐sensitive and comparable to V. moseri (482.3 nm). Our results indicate that although the four flounder species possess a similar opsin gene repertoire, the SWS2A opsin of the genus Verasper is functionally green‐sensitive, while its overall structure remains conserved as a blue‐sensitive opsin. Further, the rh2‐a function seems to have been reduced during the evolution of flounders. λmax values of predicted ancestral SWS2A of Pleuronectiformes and Pleuronectidae was 465.4 and 462.4 nm, respectively, indicating that these were blue‐sensitive. Thus, the green‐sensitive SWS2A is estimated to be arisen in ancestral Verasper genus. It is suggested that the sensitivity shift of SWS2A from blue to green may have compensated functional reduction in RH2‐A.

show abstract

Origin and adaptation of green‐sensitive (RH2) pigments in vertebrates

Yokoyama

Jia

2020

FEBS Open Bio

View full text Add to dashboard Cite

One of the critical times for the survival of animals is twilight where the most abundant visible lights are between 400 and 550 nanometres (nm). Green‐sensitive RH2 pigments help nonmammalian vertebrate species to better discriminate wavelengths in this blue‐green region. Here, evaluation of the wavelengths of maximal absorption (λmaxs) of genetically engineered RH2 pigments representing 13 critical stages of vertebrate evolution revealed that the RH2 pigment of the most recent common ancestor of vertebrates had a λmax of 503 nm, while the 12 ancestral pigments exhibited an expanded range in λmaxs between 474 and 524 nm, and present‐day RH2 pigments have further expanded the range to ~ 450–530 nm. During vertebrate evolution, eight out of the 16 significant λmax shifts (or |Δλmax| ≥ 10 nm) of RH2 pigments identified were fully explained by the repeated mutations E122Q (twice), Q122E (thrice) and M207L (twice), and A292S (once). Our data indicated that the highly variable λmaxs of teleost RH2 pigments arose from gene duplications followed by accelerated amino acid substitution.

show abstract

Functional characterization of visual opsin repertoire in Medaka (Oryzias latipes)

Cited by 132 publications

References 33 publications

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Green‐shifting ofSWS2A opsin sensitivity and loss of function ofRH2‐A opsin in flounders, genusVerasper

Origin and adaptation of green‐sensitive (RH2) pigments in vertebrates

Contact Info

Product

Resources

About