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      Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication

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          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.

          Electronic supplementary material

          The online version of this article (10.1186/s40851-017-0079-2) contains supplementary material, which is available to authorized users.

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          Most cited references 56

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          Toward almost closed genomes with GapFiller

          De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.
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            Evolution by Gene Duplication.

             S. OHNO,  S Ohno,  Susumu Ohno (1970)
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              Multiple alignment of DNA sequences with MAFFT.

              Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE.
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                Author and article information

                Contributors
                yojnakam@affrc.go.jp
                yasuike@affrc.go.jp
                mekuchim@affrc.go.jp
                yiwasaki@nig.ac.jp
                nobuhiko.ojima.t2a@cao.go.jp
                jiwara@affrc.go.jp
                chow@affrc.go.jp
                ksaitoh@affrc.go.jp
                Journal
                Zoological Lett
                Zoological Lett
                Zoological Letters
                BioMed Central (London )
                2056-306X
                17 October 2017
                17 October 2017
                2017
                : 3
                Affiliations
                [1 ]ISNI 0000 0004 1764 1824, GRID grid.410851.9, 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
                [2 ]Present address: National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
                [3 ]Present address: Japan Fisheries Research and Education Agency, 2-3-3 Minatomirai, Nishi, Yokohama, Kanagawa 220-6115 Japan
                [4 ]Present address: Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama, Shiogama, Miyagi 985-0001 Japan
                Article
                79
                10.1186/s40851-017-0079-2
                5645911
                © The Author(s). 2017

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Funding
                Funded by: Molecular genetic research project for developing stock management and breeding technologies of the Japanese eel
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

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