1
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Mcguire JA, Huang X, Reilly SB, Iskandar DT, Wang-Claypool CY, Werning S, Chong RA, Lawalata SZS, Stubbs AL, Frederick JH, Brown RM, Evans BJ, Arifin U, Riyanto A, Hamidy A, Arida E, Koo MS, Supriatna J, Andayani N, Hall R. Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation. Syst Biol 2023; 72:885-911. [PMID: 37074804 PMCID: PMC10405571 DOI: 10.1093/sysbio/syad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/20/2023] Open
Abstract
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].
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Affiliation(s)
- Jimmy A Mcguire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Xiaoting Huang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qindao, Shandong, 266003, PR China
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Sarah Werning
- Department of Anatomy, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312-4198, USA
| | - Rebecca A Chong
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Shobi Z S Lawalata
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- United in Diversity Foundation, Jalan Hayam Wuruk, Jakarta, Indonesia
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey H Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd., University of Kansas, Lawrence, KS 66045, USA
| | - Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
- Center for Taxonomy and Morphology, Zoologisches Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, R230 20146 Hamburg, Germany
| | - Awal Riyanto
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Jatna Supriatna
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Noviar Andayani
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Robert Hall
- SE Asia Research Group (SEARG), Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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2
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Yamamoto M, Kanazawa N, Nomura M, Horie Y, Okamura H. Bisphenol A alters sexual dimorphism and gene expression in marine medaka Oryzias melastigma. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:25691-25700. [PMID: 36346516 DOI: 10.1007/s11356-022-23863-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Bisphenol A (BPA) is an endocrine disruptor that is present in freshwater and marine environments. However, conclusive evidence for the toxicity of chronic BPA exposure to marine fishes remains lacking. Therefore, we investigated the influence of BPA on male marine medaka (Oryzias melastigma). BPA exposure induced formation of testis-ova at 2610 µg/L, and male-type anal fins became more female type in a concentration-dependent manner. Some males with female-type anal fins had normal testes, indicating that anal fin shape is more sensitive to BPA. Gonadal soma-derived factor (gsdf) expression decreased after BPA exposure in the 746 and 2610 µg/L exposure groups, although the changes were not statistically significant. Additionally, liver vitellogenin (vtg) expression increased in a dose-dependent manner and was significantly higher in all exposure groups. vtg and gsdf are likely to be useful biomarkers for the impact of estrogenic endocrine disrupters in O. melastigma.
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Affiliation(s)
- Mitsushi Yamamoto
- Division of Ocean Safety Systems Science, Faculty of Maritime Sciences, Kobe University, 5-1-1 Fukaeminami, Higashinada, Kobe, 658-0022, Japan
| | - Nobuhiro Kanazawa
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan
| | - Miho Nomura
- Graduate School of Maritime Science, Kobe University, Fukaeminami-machi, Higashinada-ku, Kobe, Japan
| | - Yoshifumi Horie
- Research Center for Inland Sea (KURCIS), Kobe University, 5-1-1 Fukaeminami, Higashinada, Kobe, 658-0022, Japan.
| | - Hideo Okamura
- Research Center for Inland Sea (KURCIS), Kobe University, 5-1-1 Fukaeminami, Higashinada, Kobe, 658-0022, Japan
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3
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Sudasinghe H, Ranasinghe T, Wijesooriya K, Pethiyagoda R, Rüber L, Meegaskumbura M. Molecular phylogeny and phylogeography of ricefishes (Teleostei: Adrianichthyidae:
Oryzias
) in Sri Lanka. Ecol Evol 2022; 12:e9043. [PMID: 35784081 PMCID: PMC9219105 DOI: 10.1002/ece3.9043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/20/2022] [Accepted: 06/06/2022] [Indexed: 12/02/2022] Open
Abstract
Ricefishes of the genus Oryzias occur commonly in the fresh and brackish waters in coastal lowlands ranging from India across Southeast Asia and on to Japan. Among the three species of Oryzias recorded from peninsular India, two widespread species, O. carnaticus and O. dancena, have previously been reported from Sri Lanka based on museum specimens derived from a few scattered localities. However, members of the genus are widespread in the coastal lowlands of Sri Lanka, a continental island separated from India by the shallow Palk Strait. Although recent molecular phylogenies of Adrianichthyidae represent near‐complete taxon representation, they lack samples from Sri Lanka. Here, based on sampling at 13 locations representative of the entire geographic and climatic regions of the island's coastal lowlands, we investigate for the first time the molecular phylogenetic relationships and phylogeography of Sri Lankan Oryzias based on one nuclear and two mitochondrial markers. Sri Lankan Oryzias comprise two distinct non‐sister lineages within the javanicus species group. One of these is represented by samples exclusively from the northern parts of the island; it is recognized as O. dancena. This lineage is recovered as the sister group to the remaining species in the javanicus group. The second lineage represents a species that is widespread across the island's coastal lowlands. It is recovered as the sister group of O. javanicus and is identified as O. cf. carnaticus. Ancestral‐range estimates suggest two independent colonizations of Indian subcontinent and Sri Lanka by widespread ancestral species of Oryzias during two discrete temporal windows: late Miocene and Plio‐Pleistocene. No phylogeographic structure is apparent in Sri Lankan Oryzias, suggesting that there are no strong barriers to gene flow and dispersal along the coastal floodplains, as is the case also for other generalist freshwater fishes in the island.
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Affiliation(s)
- Hiranya Sudasinghe
- Evolutionary Ecology and Systematics Laboratory, Department of Molecular Biology and Biotechnology University of Peradeniya Peradeniya Sri Lanka
- Postgraduate Institute of Science University of Peradeniya Peradeniya Sri Lanka
- Evolutionary Ecology, Institute of Ecology and Evolution University of Bern Bern Switzerland
- Naturhistorisches Museum Bern Bern Switzerland
| | | | - Kumudu Wijesooriya
- Department of Zoology, Faculty of Science University of Peradeniya Peradeniya Sri Lanka
| | - Rohan Pethiyagoda
- Ichthyology Section Australian Museum Sydney New South Wales Australia
| | - Lukas Rüber
- Naturhistorisches Museum Bern Bern Switzerland
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution Bern Switzerland
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry Guangxi University Nanning China
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4
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Deeply divergent freshwater fish species within a single river system in central Sulawesi. Mol Phylogenet Evol 2022; 173:107519. [DOI: 10.1016/j.ympev.2022.107519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 01/02/2023]
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5
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Seleit A, Ansai S, Yamahira K, Masengi KWA, Naruse K, Centanin L. Diversity of lateral line patterns and neuromast numbers in the genus Oryzias. J Exp Biol 2021; 224:273715. [PMID: 34897518 DOI: 10.1242/jeb.242490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 11/19/2021] [Indexed: 11/20/2022]
Abstract
A remarkable diversity of lateral line patterns exists in adult teleost fishes, the basis of which is largely unknown. By analysing the lateral line patterns and organ numbers in 29 Oryzias species and strains we report a rapid diversification of the lateral line system within this genus. We show a strong dependence of lateral line elaboration (number of neuromasts per cluster, number of parallel lateral lines) on adult species body size irrespective of phylogenetic relationships. In addition, we report that the degree of elaboration of the anterior lateral line, posterior lateral line and caudal neuromast clusters is tightly linked within species, arguing for a globally coordinated mechanism controlling lateral line organ numbers and patterns. We provide evidence for a polygenic control over neuromast numbers and positioning in the genus Oryzias. Our data also indicate that the diversity in lateral lines can arise as a result of differences in patterning both during embryonic development and post-embryonically, where simpler embryonic patterns generate less complex adult patterns and organ numbers, arguing for a linkage between the two processes.
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Affiliation(s)
- Ali Seleit
- Laboratory of Clonal Analysis of Post-Embryonic Stem Cells, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg Universität, 69120 Heidelberg, Germany.,The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, 69120Heidelberg, Germany
| | - Satoshi Ansai
- Laboratory of Bioresources, National Institute for Basic Biology Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Kawilarang W A Masengi
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, 95115 Manado, Indonesia
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Lázaro Centanin
- Laboratory of Clonal Analysis of Post-Embryonic Stem Cells, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg Universität, 69120 Heidelberg, Germany
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6
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Downer-Bartholomew BMB, Rodd FH. Female preference for color-enhanced males: a test of the sensory bias model in medaka, a drab fish. Behav Ecol 2021. [DOI: 10.1093/beheco/arab131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Sexual selection research has long focused on the evolution of female mate preferences. Most of the models that have been developed posit that mate preferences evolve in a mating context. In contrast, the sensory bias model proposes that mate choice preferences arise in a non-mating context, as a by-product of natural selection acting on a female’s perceptual system. Recent research has shown that many species of fishes, from across a large clade including poeciliids, goodeids, and medaka, have a bias for long wavelength (LW) colors (yellow, orange, red) in a non-mating context. Even species that do not have LW-colored ornaments, apparently because they have been lost secondarily, retain this latent bias for LW colors. Here, we predicted that female Oryzias latipes (Japanese medaka), a drab species with a latent preference for LW colors, would show a mate choice preference for males with an artificial secondary sexual trait—a colored stripe added to their flank. We confirmed that females were more responsive to red and orange objects in a non-mating context than to other colors. We also showed that females were less resistant towards males with an LW-colored stripe than to those enhanced with a non-LW stripe and that, for many females, responses towards specific LW colors were consistent across these non-mating and mating contexts. Therefore, our results provide support for the sensory bias model by providing a link between a sensory bias in a non-mating context and a mate choice preference in a drab species like medaka.
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Affiliation(s)
| | - F Helen Rodd
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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7
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Horie Y, Takahashi C. Development of an in vivo acute bioassay using the marine medaka Oryzias melastigma. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:725. [PMID: 34651255 DOI: 10.1007/s10661-021-09527-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
To determine whether the marine medaka Oryzias melastigma is a suitable model organism for in vivo acute toxicity bioassay in seawater, we first determined whether there were differences in the concentrations of chemicals that were toxic to marine medaka (O. melastigma) and freshwater medaka (O. latipes). We performed in vivo acute toxicity bioassay with 3-chloroaniline, triclosan, 3,4-dichloroaniline, fenitrothion, and pyriproxyfen on larvae of both species. Although the concentrations of 3-chloroaniline and fenitrothion that were lethal to the larvae were identical for both species, the toxic concentrations of triclosan, 3,4-dichloroaniline, and pyriproxyfen were lower for O. melastigma than for O. latipes. We then used an in vivo acute toxicity bioassay to monitor the quality of coastal seawater in Akita, Japan. No lethal effects were observed in the harbor and canal in 2019. O. melastigma could be used to monitor the quality of seawater with salinities in the range 2-25. Our findings suggest that O. melastigma can be used as the test fish for in vivo acute toxicity bioassay intended for water quality monitoring.
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Affiliation(s)
- Yoshifumi Horie
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan.
- Research Center for Inland Sea (KURCIS), Kobe University, Fukae Minami Kobe, Hyogo, 658-0022, Higashinada, Japan.
| | - Chiho Takahashi
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan
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8
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Yamahira K, Ansai S, Kakioka R, Yaguchi H, Kon T, Montenegro J, Kobayashi H, Fujimoto S, Kimura R, Takehana Y, Setiamarga DHE, Takami Y, Tanaka R, Maeda K, Tran HD, Koizumi N, Morioka S, Bounsong V, Watanabe K, Musikasinthorn P, Tun S, Yun LKC, Masengi KWA, Anoop VK, Raghavan R, Kitano J. Mesozoic origin and 'out-of-India' radiation of ricefishes (Adrianichthyidae). Biol Lett 2021; 17:20210212. [PMID: 34343438 DOI: 10.1098/rsbl.2021.0212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast-East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward 'out-of-India' after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast-East Asia. A review of geographic distributions of 'out-of-India' taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.
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Affiliation(s)
- Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hajime Yaguchi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Takeshi Kon
- Center for Strategic Research Project, University of the Ryukyus, Okinawa, Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Shingo Fujimoto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Yusuke Takehana
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Japan
| | - Davin H E Setiamarga
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Wakayama, Japan
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Ken Maeda
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hau D Tran
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
| | - Noriyuki Koizumi
- Strategic Planning Headquarters, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Shinsuke Morioka
- Fisheries Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | | | - Katsutoshi Watanabe
- Division of Biological Sciences, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Sein Tun
- Inlay Lake Wildlife Sanctuary, Ministry of Natural Resources and Environmental Conservation, Nyaungshwe, Myanmar
| | - L K C Yun
- Inlay Lake Wildlife Sanctuary, Ministry of Natural Resources and Environmental Conservation, Nyaungshwe, Myanmar
| | | | - V K Anoop
- School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
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9
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Horie Y, Takahashi C. Influence of salinity on physiological development and zinc toxicity in the marine medaka Oryzias melastigma. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1138-1149. [PMID: 34106375 DOI: 10.1007/s10646-021-02429-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
To determine whether the marine medaka Oryzias melastigma is a suitable model organism for evaluating the effects of environmental chemicals on marine teleosts, we examined the effect of salinity on physiological development and zinc toxicity. Growth as measured by total body length was significantly lower in fresh water compared to brackish water. Reproductive success was also significantly reduced in fresh water, although we observed cells in the pituitary producing gonadotropins such as Gpa (common glycoprotein hormone α), Fshb (follicle stimulating hormone β), and Lhb (luteinizing hormone β) at all salinities. These results indicate that O. melastigma is adaptable to various salinities from fresh to seawater, and brackish water is best for physiological processes including growth performance and reproduction. When zinc was dissolved in saltwater, a white precipitate formed immediately, and the dissolved concentration decreased in the supernatant and increased at precipitate. We performed zinc toxicity tests on early life stage and adult stage in fresh water, brackish water, and seawater. Among adults, the lowest observed effect concentration for mortality in freshwater (15.3 mg/L) was lower than in brackish water (>48 mg/L) or seawater (>48 mg/L). Similarly, among embryos and larvae, the lowest observed effect concentration for mortality in freshwater (4.8 mg/L) was lower than in brackish water (48 mg/L) or seawater (48 mg/L). These results highlight the importance of using marine organisms to evaluate the ecological effects of marine pollutants.
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Affiliation(s)
- Yoshifumi Horie
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan.
- Research Center for Inland Sea (KURCIS), Kobe University, Fukaeminami, Higashinada, Kobe, 658-0022, Japan.
| | - Chiho Takahashi
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan
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10
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Matsumoto Y, Oda S, Mitani H, Kawamura S. Orthologous Divergence and Paralogous Anticonvergence in Molecular Evolution of Triplicated Green Opsin Genes in Medaka Fish, Genus Oryzias. Genome Biol Evol 2021; 12:911-923. [PMID: 32467976 PMCID: PMC7337190 DOI: 10.1093/gbe/evaa111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2020] [Indexed: 11/30/2022] Open
Abstract
Gene duplication of green (RH2) opsin genes and their spectral differentiation are well documented in many teleost fish. However, their evolutionary divergence or conservation patterns among phylogenetically close but ecologically diverse species is not well explored. Medaka fish (genus Oryzias) are broadly distributed in fresh and brackish waters of Asia, with many species being laboratory-housed and feasible for genetic studies. We previously showed that a Japan strain (HNI) of medaka (Oryzias latipes) possessed three RH2 opsin genes (RH2-A, RH2-B, and RH2-C) encoding spectrally divergent photopigments. Here, we examined the three RH2 opsin genes from six Oryzias species representing three species groups: the latipes, the celebensis, and the javanicus. Photopigment reconstitution revealed that the peak absorption spectra (λmax) of RH2-A were divergent among the species (447–469 nm), whereas those of RH2-B and RH2-C were conservative (516–519 and 486–493 nm, respectively). For the RH2-A opsins, the largest spectral shift was detected in the phylogenetic branch leading to the latipes group. A single amino acid replacement T94C explained most of the spectral shift. For RH2-B and -C opsins, we detected tracts of gene conversion between the two genes homogenizing them. Nevertheless, several amino acid differences were maintained. We showed that the spectral difference between the two opsins was attributed to largely the E/Q amino acid difference at the site 122 and to several sites with individually small spectral effects. These results depict dynamism of spectral divergence of orthologous and paralogous green opsin genes in phylogenetically close but ecologically diverse species exemplified by medaka.
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Affiliation(s)
- Yoshifumi Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.,Live Imaging Center, Central Institute for Experimental Animals (CIEA), Kawasaki, Kanagawa, Japan
| | - Shoji Oda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Mitani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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11
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Horoiwa M, Mandagi IF, Sutra N, Montenegro J, Tantu FY, Masengi KWA, Nagano AJ, Kusumi J, Yasuda N, Yamahira K. Mitochondrial introgression by ancient admixture between two distant lacustrine fishes in Sulawesi Island. PLoS One 2021; 16:e0245316. [PMID: 34111145 PMCID: PMC8192020 DOI: 10.1371/journal.pone.0245316] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Sulawesi, an island located in a biogeographical transition zone between Indomalaya and Australasia, is famous for its high levels of endemism. Ricefishes (family Adrianichthyidae) are an example of taxa that have uniquely diversified on this island. It was demonstrated that habitat fragmentation due to the Pliocene juxtaposition among tectonic subdivisions of this island was the primary factor that promoted their divergence; however, it is also equally probable that habitat fusions and resultant admixtures between phylogenetically distant species may have frequently occurred. Previous studies revealed that some individuals of Oryzias sarasinorum endemic to a tectonic lake in central Sulawesi have mitochondrial haplotypes that are similar to the haplotypes of O. eversi, which is a phylogenetically related but geologically distant (ca. 190 km apart) adrianichthyid endemic to a small fountain. In this study, we tested if this reflects ancient admixture of O. eversi and O. sarasinorum. Population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that O. eversi and O. sarasinorum are substantially reproductively isolated from each other. Comparison of demographic models revealed that the models assuming ancient admixture from O. eversi to O. sarasinorum was more supported than the models assuming no admixture; this supported the idea that the O. eversi-like mitochondrial haplotype in O. sarasinorum was introgressed from O. eversi. This study is the first to demonstrate ancient admixture of lacustrine or pond organisms in Sulawesi beyond 100 km. The complex geological history of this island enabled such island-wide admixture of lacustrine organisms, which usually experience limited migration.
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Affiliation(s)
- Mizuki Horoiwa
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ixchel F. Mandagi
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Nobu Sutra
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
- Graduate School of Hasanuddin University, Makassar, Indonesia
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Fadly Y. Tantu
- Faculty of Animal Husbandry and Fisheries, Tadulako University, Palu, Indonesia
| | | | | | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Nina Yasuda
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail:
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12
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Audira G, Siregar P, Chen KHC, Roldan MJM, Huang JC, Lai HT, Hsiao CD. Interspecies Behavioral Variability of Medaka Fish Assessed by Comparative Phenomics. Int J Mol Sci 2021; 22:ijms22115686. [PMID: 34073632 PMCID: PMC8197923 DOI: 10.3390/ijms22115686] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/23/2021] [Accepted: 05/23/2021] [Indexed: 12/12/2022] Open
Abstract
Recently, medaka has been used as a model organism in various research fields. However, even though it possesses several advantages over zebrafish, fewer studies were done in medaka compared to zebrafish, especially with regard to its behavior. Thus, to provide more information regarding its behavior and to demonstrate the behavioral differences between several species of medaka, we compared the behavioral performance and biomarker expression in the brain between four medaka fishes, Oryzias latipes, Oryzias dancena, Oryzias woworae, and Oryzias sinensis. We found that each medaka species explicitly exhibited different behaviors to each other, which might be related to the different basal levels of several biomarkers. Furthermore, by phenomics and genomic-based clustering, the differences between these medaka fishes were further investigated. Here, the phenomic-based clustering was based on the behavior results, while the genomic-based clustering was based on the sequence of the nd2 gene. As we expected, both clusterings showed some resemblances to each other in terms of the interspecies relationship between medaka and zebrafish. However, this similarity was not displayed by both clusterings in the medaka interspecies comparisons. Therefore, these results suggest a re-interpretation of several prior studies in comparative biology. We hope that these results contribute to the growing database of medaka fish phenotypes and provide one of the foundations for future phenomics studies of medaka fish.
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Affiliation(s)
- Gilbert Audira
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (G.A.); (P.S.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
| | - Petrus Siregar
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (G.A.); (P.S.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
| | - Kelvin H.-C. Chen
- Department of Applied Chemistry, National Pingtung University, Pingtung 900391, Taiwan;
| | - Marri Jmelou M. Roldan
- Faculty of Pharmacy and The Graduate School, University of Santo Tomas, Manila 1008, Philippines;
| | - Jong-Chin Huang
- Department of Applied Chemistry, National Pingtung University, Pingtung 900391, Taiwan;
- Correspondence: (J.-C.H.); (H.-T.L.); (C.-D.H.)
| | - Hong-Thih Lai
- Department of Aquatic Biosciences, National Chiayi University, 300 University Rd., Chiayi 600, Taiwan
- Correspondence: (J.-C.H.); (H.-T.L.); (C.-D.H.)
| | - Chung-Der Hsiao
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (G.A.); (P.S.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
- Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
- Research Center for Aquatic Toxicology and Pharmacology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
- Correspondence: (J.-C.H.); (H.-T.L.); (C.-D.H.)
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13
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Dong Z, Li X, Yao Z, Wang C, Guo Y, Wang Q, Shao C, Wang Z. Oryzias curvinotus in Sanya Does Not Contain the Male Sex-Determining Gene dmy. Animals (Basel) 2021; 11:ani11051327. [PMID: 34066583 PMCID: PMC8148570 DOI: 10.3390/ani11051327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/24/2021] [Accepted: 05/03/2021] [Indexed: 01/18/2023] Open
Abstract
Hainan medaka (Oryzias curvinotus) is distributed in the coastal waters of the South China Sea and is able to adapt to a wide range of salinities. In this study, we characterized O. curvinotus in Sanya River (SY-medaka), which lacks dmy (a male sex-determining gene in O. latipes and O. curvinotus). In a comparison of SY-medaka and Gaoqiao medaka (GQ-medaka), the morphological difference between the two populations does not reach the subspecies level and they can be considered two geographic populations of O. curvinotus. A mitochondrial cytochrome oxidase subunit I (CoI) sequence alignment showed that the sequence identities between SY-medaka and other geographic populations of O. curvinotus are as high as 95%. A phylogenetic analysis of the mitochondrial genome also indicated that SY-medaka belongs to O. curvinotus. Molecular marker-based genetic sex assays and whole genome re-sequencing showed that SY-medaka does not contain dmy. Further, in RNA-Seq analyses of the testis and ovaries of sexually mature SY-medaka, dmy expression was not detected. We speculate that high temperatures resulted in the loss of dmy in SY-medaka during evolution, or the lineage has another sex-determining gene. This study provides a valuable dataset for elucidating the mechanism underlying sex determination in Oryzias genus and advances research on functional genomics or reproduction biology in O. curvinotus.
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Affiliation(s)
- Zhongdian Dong
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; (X.L.); (Z.Y.); (C.W.); (Y.G.)
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Correspondence: (Z.D.); (Z.W.)
| | - Xueyou Li
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; (X.L.); (Z.Y.); (C.W.); (Y.G.)
| | - Zebin Yao
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; (X.L.); (Z.Y.); (C.W.); (Y.G.)
| | - Chun Wang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; (X.L.); (Z.Y.); (C.W.); (Y.G.)
| | - Yusong Guo
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; (X.L.); (Z.Y.); (C.W.); (Y.G.)
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
| | - Qian Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Qingdao 266071, China; (Q.W.); (C.S.)
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Qingdao 266071, China; (Q.W.); (C.S.)
| | - Zhongduo Wang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; (X.L.); (Z.Y.); (C.W.); (Y.G.)
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- State Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University School, Changsha 410081, China
- Correspondence: (Z.D.); (Z.W.)
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14
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Sumarto BKA, Nofrianto AB, Mokodongan DF, Lawelle SA, Masengi KWA, Fujimoto S, Yamahira K. Variation in Mating Behaviors Between a Tropical and a Temperate Species of Medaka Fishes. Zoolog Sci 2021; 38:45-50. [PMID: 33639717 DOI: 10.2108/zs200114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/27/2020] [Indexed: 11/17/2022]
Abstract
In medaka fishes, the family Adrianichthyidae, tropical species are known to be sexually more dimorphic than temperate species. If this reflects that tropical species are exposed to stronger sexual-selection pressures than temperate species, mating behaviors may also differ between tropical and temperate species. Our mating experiments revealed that males of Oryzias woworae, a tropical species of the family, perform "chasing" another male more frequently than males of O. sakaizumii, a temperate congener, and that male-male "combats" of O. woworae tended to be followed by chasing compared with combats of O. sakaizumii males, indicating that O. woworae males are more aggressive in male-male interactions than O. sakaizumii males. Males of O. woworae also performed "approaching" a female and "mating dance" more frequently than O. sakaizumii males, indicating that O. woworae males are also more active in courting females. Males of O. sakaizumii often omitted "mating dance" in their mating sequences, supporting this view. Moreover, O. woworae females tended to reject male "wrapping", an attempt for fertilization, more frequently than O. sakaizumii females, suggesting that O. woworae females are choosier in mating than O. sakaizumii females. These findings are concordant with the view that O. woworae is exposed to stronger sexual-selection pressures than O. sakaizumii.
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Affiliation(s)
- Bayu K A Sumarto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Andy B Nofrianto
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia
| | - Daniel F Mokodongan
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia
| | - Sjamsu A Lawelle
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia
| | - Kawilarang W A Masengi
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado 95115, Indonesia
| | - Shingo Fujimoto
- Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0125, Japan,
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan,
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15
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Ansai S, Mochida K, Fujimoto S, Mokodongan DF, Sumarto BKA, Masengi KWA, Hadiaty RK, Nagano AJ, Toyoda A, Naruse K, Yamahira K, Kitano J. Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes. Nat Commun 2021; 12:1350. [PMID: 33649298 PMCID: PMC7921647 DOI: 10.1038/s41467-021-21697-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Sexual selection drives rapid phenotypic diversification of mating traits. However, we know little about the causative genes underlying divergence in sexually selected traits. Here, we investigate the genetic basis of male mating trait diversification in the medaka fishes (genus Oryzias) from Sulawesi, Indonesia. Using linkage mapping, transcriptome analysis, and genome editing, we identify csf1 as a causative gene for red pectoral fins that are unique to male Oryzias woworae. A cis-regulatory mutation enables androgen-induced expression of csf1 in male fins. csf1-knockout males have reduced red coloration and require longer for mating, suggesting that coloration can contribute to male reproductive success. Contrary to expectations, non-red males are more attractive to a predatory fish than are red males. Our results demonstrate that integrating genomics with genome editing enables us to identify causative genes underlying sexually selected traits and provides a new avenue for testing theories of sexual selection.
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Affiliation(s)
- Satoshi Ansai
- grid.288127.60000 0004 0466 9350Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan ,grid.419396.00000 0004 0618 8593Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan ,grid.69566.3a0000 0001 2248 6943Present Address: Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi Japan
| | - Koji Mochida
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan ,grid.26091.3c0000 0004 1936 9959Department of Biology, Keio University, Yokohama, Kanagawa, Japan
| | - Shingo Fujimoto
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan ,grid.267625.20000 0001 0685 5104Present Address: Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa Japan
| | - Daniel F. Mokodongan
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan ,grid.249566.a0000 0004 0644 6054Present Address: Museum Zoologicum Bogoriense (MZB), Zoology Division of Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia
| | - Bayu Kreshna Adhitya Sumarto
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Kawilarang W. A. Masengi
- grid.412381.d0000 0001 0702 3254Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Renny K. Hadiaty
- grid.249566.a0000 0004 0644 6054Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia
| | - Atsushi J. Nagano
- grid.440926.d0000 0001 0744 5780Faculty of Agriculture, Ryukoku University, Ohtsu, Shiga, Japan
| | - Atsushi Toyoda
- grid.288127.60000 0004 0466 9350Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kiyoshi Naruse
- grid.419396.00000 0004 0618 8593Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kazunori Yamahira
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Jun Kitano
- grid.288127.60000 0004 0466 9350Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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16
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Abstract
Oryzias dancena (Beloniformes; Teleostei), is a euryhaline teleost that mainly inhabits the brackish or freshwater of river mouths and estuaries around the Bay of Bengal and the Malay Peninsula. It also has a short interval between generations, with spawning possibilities just 60 days after hatching. The aim of this paper is to provide a review for the study of O. dancena based on the studies collected so far, and could form the basis for a wide category of researches including zootoxy, cytogenetics, anesthesia, tagging, salinity tolerance, reproduction, fish disease, chromosome engineering, and trnasgenesis in order to highlight the recent progress in different fields of study using this species.
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Affiliation(s)
- In-Seok Park
- Division of Marine Bioscience, College of Ocean Science and Technology, Korea Maritime & Ocean University, Busan, 49112, Republic of Korea.
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17
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Sumarto BKA, Kobayashi H, Kakioka R, Tanaka R, Maeda K, Tran HD, Koizumi N, Morioka S, Bounsong V, Watanabe K, Musikasinthorn P, Tun S, Yun LKC, Anoop VK, Raghavan R, Masengi KWA, Fujimoto S, Yamahira K. Latitudinal variation in sexual dimorphism in a freshwater fish group. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
Tropical animals are characterized by showy ornaments and conspicuous body colours as compared with their temperate relatives. Some recent studies have hypothesized that sexual selection pressures are stronger in the tropics than in the temperate zone. Although negative correlations between latitude and the degree of sexual dimorphism would support this hypothesis, phylogeny should be taken into account in such comparative studies. Comparisons of the degree of sexual dimorphism in body size and fin lengths among species of the Adrianichthyidae, a freshwater fish family having a wide geographical range throughout Southeast and East Asia, revealed that lower latitude species are sexually more dimorphic in all characters than higher latitude species. Phylogenetic generalized least squares analyses using a mitochondrial DNA phylogeny demonstrated that the negative correlations between latitude and the degree of sexual dimorphism become non-significant when phylogeny is considered, but that the variance in the degree of sexual dimorphism is explained not only by phylogeny but also almost equally by latitude. Ancestral state reconstruction indicated that sexual dimorphisms have evolved independently even within major clades. These findings are consistent with the view that tropical species are exposed to stronger sexual selection pressures than temperate species. We discuss possible causes of the latitudinal variation in sexual selection pressure.
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Affiliation(s)
- Bayu K A Sumarto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Ken Maeda
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hau D Tran
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
| | - Noriyuki Koizumi
- Institute for Rural Engineering, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Shinsuke Morioka
- Fisheries Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | | | | | | | - Sein Tun
- Inlay Lake Wildlife Sanctuary, Nature and Wildlife Conservation Division, Forest Department, Ministry of Natural Resources and Environmental Conservation, Myanmar
| | - L K C Yun
- Inlay Lake Wildlife Sanctuary, Nature and Wildlife Conservation Division, Forest Department, Ministry of Natural Resources and Environmental Conservation, Myanmar
| | - V K Anoop
- School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | | | - Shingo Fujimoto
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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18
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Lee BY, Park JC, Kim MS, Choi BS, Kim DH, Lim JS, Yum S, Hwang UK, Nah GJ, Lee JS. The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology. MARINE POLLUTION BULLETIN 2020; 154:111118. [PMID: 32319931 DOI: 10.1016/j.marpolbul.2020.111118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
The Java medaka (Oryzias javanicus) is distributed in tropical brackish water and is considered as an ecotoxicological experimental organism for assessing diverse pollutions and global climate change effects in the ocean. In this study, we sequenced and assembled the genome of O. javanicus using the Oxford Nanopore technique and anchored the scaffolds to the 24 genetic linkage map of a sister species Oryzias melastigma. The assembled genome consisted of 773 scaffolds including 24 LG-based scaffolds, and the estimated genome length was 846.3 Mb (N50 = 19.3 Mb), containing 24,498 genes. As detoxification processes are crucial in aquatic organisms, antioxidant-related genes including glutathione S-transferases, superoxide dismutase, catalase, and glutathione peroxidase were identified in this study. In the genome of O. javanicus, a total of 21 GSTs, 4 SODs, 1 CAT, and 7 GPxs were identified and showed high similarities between sister species O. melastigma and Oryzias latipes. In addition, despite having 8 classes of cytosolic GSTs family, medaka showed no presence of GST pi and sigma classes, which are predominantly found in carp and salmon, but not in neoteleostei. This study adds another set to genome-library of Oryzias spp. and is a useful resource for better understanding of the molecular ecotoxicology.
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Affiliation(s)
- Bo-Young Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jong-Sung Lim
- NICEM, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Seungshic Yum
- Risk Assessment Research Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje 53201, South Korea
| | - Un-Ki Hwang
- Marine Ecological Risk Assessment Center, West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon 46083, South Korea
| | - Gyoung Ju Nah
- NICEM, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea.
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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19
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Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity. G3-GENES GENOMES GENETICS 2020; 10:907-915. [PMID: 31988161 PMCID: PMC7056978 DOI: 10.1534/g3.119.400725] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behavior, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies. Complementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6,3 Mbp and a L50 of 37 scaffolds. We identified 21454 predicted transcripts for a total transcriptome size of 57, 146, 583 bps. We provide here a high-quality chromosome scale draft genome assembly of the euryhaline Javafish medaka (321 scaffolds anchored on 24 chromosomes (representing 97.7% of the total bases)), and give emphasis on the evolutionary adaptation to salinity.
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20
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Ngamniyom A, Sriyapai T, Sriyapai P. Molecular analysis of population and De Novo transcriptome sequencing of Thai medaka, Oryzias minutillus (Teleostei: Adrianichthyidae). Heliyon 2020; 6:e03079. [PMID: 31909257 PMCID: PMC6938829 DOI: 10.1016/j.heliyon.2019.e03079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/13/2019] [Accepted: 12/16/2019] [Indexed: 12/27/2022] Open
Abstract
Thai medaka (Oryzias minutillus) are alternatively known as Thai rice-fish or dwarf medaka, and they widely inhabit natural freshwater environments in all regions of Thailand. In this study, we aimed to investigate the molecular genetics of the Thai medaka population in Thailand inferred from the mitochondrial control region (D-loop) and the cytochrome c oxidase subunit 1 (coxI) sequences. Furthermore, we examined RNA sequencing (RNA-seq) of adult males and females was performed with next-generation sequencing. Together, the combination of the D-loop and coxI sequences clearly distinguished the Thai medaka populations into 2 groups, such as group 1, which generally included samples from the central, northern, western, and eastern regions of the northeastern region. In this group, the fish populations seem to be a little monophyly in which the first subpopulation comprised the main samples from the northern and central regions. The second subpopulation commonly contained fish from the eastern region and specimens from the southern part of the central region near the Gulf of Thailand. Although these subgroups related to geographical distribution, bootstrap values were low in branch considered significant for both subgroups. Group 2 consisted of almost all samples from the southern population and those from the central and southern part of the northeastern region. Group 2 was found that it was made of samples from the northeastern region and samples from the southern population. A total of 73551 unigenes were identified after gene annotation. Signal transduction was the predominant protein classification among the Thai medaka orthologous groups. A differentially expressed gene (DEG) analysis identified 6 subclusters between both sexes that were composed of 257, 131, 364, 386, 114 and 108 genes. Phototransduction was the most enriched pathway and was highly expressed in males, while viral carcinogenesis, oocyte genesis, and the complement and coagulation cascades were highly expressed in females. Further details of these DEGs are discussed below. These results suggest that Thai medaka may genetically exhibit independent populations in the geographic habitats of Thailand. Moreover, these fish also reveal the genes that are conserved in other organisms and those that may be specific to this species.
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Affiliation(s)
- Arin Ngamniyom
- Major in Environment, Faculty of Environmental Culture and Eco-tourism, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thayat Sriyapai
- Major in Environment, Faculty of Environmental Culture and Eco-tourism, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Pichapack Sriyapai
- Department of Microbiology, Faculty of Sciences, Srinakharinwirot University, Bangkok, 10110, Thailand
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Ma J, Long S, Wang Z. Complete mitogenome and phylogenetic analysis of Oryzias celebensis (Teleostei: Beloniformes). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 5:27-28. [PMID: 33366406 PMCID: PMC7721023 DOI: 10.1080/23802359.2019.1695550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The complete Oryzias celebensis mitogenome was determined using next-generation sequencing (NGS) method and the resulting data analyzed in this article. The mitochondrial genome was 16,493 base pair (bp) length, and its content and structure were highly homologous to that of other teleostean fishes, including 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNA, and 1 control region. Among the PCGs, ATG was used as the initiation codon, except for GTG in the COI gene. There were 6 overlapping genes with overlap lengths ranging from 1 to 10 nucleotides (nt), while 10 intergenic regions with a total of 59 nt and a maximum interval of 38 nt between tRNA-Asn and tRNA-Cys were detected during the annotation of this complete mitochondrial DNA.
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Affiliation(s)
- Jiangru Ma
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Shuisheng Long
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
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Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma. G3-GENES GENOMES GENETICS 2019; 9:3537-3545. [PMID: 31530635 PMCID: PMC6829124 DOI: 10.1534/g3.119.400708] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Medaka (Oryzias sp.) is an important fish species in ecotoxicology and considered as a model species due to its biological features including small body size and short generation time. Since Japanese medaka Oryzias latipes is a freshwater species with access to an excellent genome resource, the marine medaka Oryzias melastigma is also applicable for the marine ecotoxicology. In genome era, a high-density genetic linkage map is a very useful resource in genomic research, providing a means for comparative genomic analysis and verification of de novo genome assembly. In this study, we developed a high-density genetic linkage map for O. melastigma using restriction-site associated DNA sequencing (RAD-seq). The genetic map consisted of 24 linkage groups with 2,481 single nucleotide polymorphism (SNP) markers. The total map length was 1,784 cM with an average marker space of 0.72 cM. The genetic map was integrated with the reference-assisted chromosome assembly (RACA) of O. melastigma, which anchored 90.7% of the assembled sequence onto the linkage map. The values of complete Benchmarking Universal Single-Copy Orthologs were similar to RACA assembly but N50 (23.74 Mb; total genome length 779.4 Mb; gap 5.29%) increased to 29.99 Mb (total genome length 778.7 Mb; gap 5.2%). Using MapQTL analysis with SNP markers, we identified a major quantitative trait locus for sex traits on the Om10. The integration of the genetic map with the reference genome of marine medaka will serve as a good resource for studies in molecular toxicology, genomics, CRISPR/Cas9, and epigenetics.
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Horie Y, Kanazawa N, Suzuki A, Yonekura K, Chiba T. Influences of Salinity and Organic Compounds on Embryo Development in Three Medaka Oryzias Congeners with Habitats Ranging from Freshwater to Marine. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2019; 103:411-415. [PMID: 31203410 DOI: 10.1007/s00128-019-02649-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/08/2019] [Indexed: 06/09/2023]
Abstract
To clarify whether Oryzias congeners, including freshwater, brackish water, and marine medaka, would be useful models for evaluating environmental chemical effects in various aquatic ecosystems, we examined the influence of salinity on their embryo development. We also compared the toxicity values of the organotin compounds triphenyltin and tributyltin, which remain pollutants of marine and freshwater ecosystems, between Oryzias latipes (freshwater), Oryzias melastigma (brackish water), and Oryzias javanicus (saltwater). Hatching and survival rates of O. latipes were significantly decreased at a salinity of 34, whereas O. melastigma and O. javanicus were adaptable to various salinities from freshwater to seawater. The lowest observed effect concentrations of organotin compounds for survival and embryo development were the similar in the three species. The similarity of the species' responses to organotin compounds indicated that Oryzias congeners are useful for ecological risk assessment of chemicals in a range of aquatic ecosystems, from freshwater to marine.
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Affiliation(s)
- Yoshifumi Horie
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan.
| | - Nobuhiro Kanazawa
- Faculty of Systems Science and Technology, Akita Prefectural University, 84-4 Ebinokuchi, Tsuchiya, Yurihonjo, Akita, 015-0055, Japan
| | - Ayaka Suzuki
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan
| | - Kei Yonekura
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan
| | - Takashi Chiba
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan
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Sutra N, Kusumi J, Montenegro J, Kobayashi H, Fujimoto S, Masengi KWA, Nagano AJ, Toyoda A, Matsunami M, Kimura R, Yamahira K. Evidence for sympatric speciation in a Wallacean ancient lake. Evolution 2019; 73:1898-1915. [DOI: 10.1111/evo.13821] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Nobu Sutra
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Junko Kusumi
- Faculty of Social and Cultural StudiesKyushu University Fukuoka 819‐0395 Japan
| | - Javier Montenegro
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Shingo Fujimoto
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | | | | | - Atsushi Toyoda
- Comparative Genomics LaboratoryNational Institute of Genetics Mishima 411‐8540 Japan
| | | | - Ryosuke Kimura
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
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Hilgers L, Schwarzer J. The untapped potential of medaka and its wild relatives. eLife 2019; 8:46994. [PMID: 31287418 PMCID: PMC6615862 DOI: 10.7554/elife.46994] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/12/2019] [Indexed: 01/04/2023] Open
Abstract
The medaka is a fish that has served as a model organism for over a century, yet there is still much to learn about its life in the wild. Here we summarize the current knowledge, highlight recent progress and outline remaining gaps in our understanding of the natural history of medaka. It has also become clear over time that rather than being a single species, medaka comprises an entire species complex, so disentangling the species boundaries is an important goal for future research. Moreover, medaka and other ricefishes exhibit striking functional diversity, little of which has been investigated to date. As such, there are opportunities to use the resources developed for medaka to study other ricefishes, and to learn more about medaka itself in an evolutionary context.
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Affiliation(s)
- Leon Hilgers
- Zoological Research Museum Alexander Koenig, Bonn, Germany
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26
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Hosoishi S, Ogata K. Cryptic Diversity in the Widespread Asian Ant Crematogaster rothneyi (Hymenoptera: Formicidae) Inferred from Morphological and Genetic Evidence. Zool Stud 2019; 58:e11. [PMID: 31966312 PMCID: PMC6778772 DOI: 10.6620/zs.2019.58-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/07/2019] [Indexed: 11/18/2022]
Abstract
The myrmicine species Crematogaster rothneyi is one of the most widely distributed ants in Asia, but it has rarely been collected in the field. Its distribution range covers South and Southeast Asia, extending approximately 5,000 km from India in the west to Sulawesi in the east. Despite this wide distribution range, C. rothneyi has been treated as a single taxonomic species, and no combined morphological or molecular analysis has been conducted to assess whether any intraspecific variation exists. The sequence divergences of C. rothneyi populations, mainly obtained from Southeast Asia, were investigated by analyzing 387 bp and 175 bp sequences of the 12S ribosomal RNA and cytochrome c oxidase subunit (COI) genes, respectively. Phylogenetic analysis indicated that the C. rothneyi populations were separated into three groups: group I from Thailand and Cambodia, group II from Bangladesh and Myanmar, and group III from Krakatau and Sulawesi. Groups II and III were recovered as a single clade, sister to group I. The interspecific divergences were 7.3% to 8.5% for 12S and 14.5% to 23.3% for COI between most C. rothneyi specimens and Cambodian specimens, while divergence for 12S was 3.5% between Thai and Cambodian specimens. The Thai specimens are not morphologically differentiated, and are considered conspecific to C. rothneyi. We describe the Cambodian series as a new species, Crematogaster yaharai sp. nov., based on unique antennal morphology and mesosomal sculpture patterns with molecular evidence. Crematogaster rothneyi civa Forel, 1902 is synonymized under C. rothneyi. Crematogaster rothneyi is widespread and has sister species, suggesting recent diversification within the Indochinese Peninsula.
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Affiliation(s)
- Shingo Hosoishi
- Institute of Tropical Agriculture, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395 Japan.
| | - Kazuo Ogata
- Institute of Tropical Agriculture, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395 Japan.
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27
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Gammerdinger WJ, Kocher TD. Unusual Diversity of Sex Chromosomes in African Cichlid Fishes. Genes (Basel) 2018; 9:E480. [PMID: 30287777 PMCID: PMC6210639 DOI: 10.3390/genes9100480] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.
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Affiliation(s)
- William J Gammerdinger
- Institute of Science and Technology (IST) Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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Horie Y, Kanazawa N, Yamagishi T, Yonekura K, Tatarazako N. Ecotoxicological Test Assay Using OECD TG 212 in Marine Java Medaka (Oryzias javanicus) and Freshwater Japanese Medaka (Oryzias latipes). BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2018; 101:344-348. [PMID: 30022344 DOI: 10.1007/s00128-018-2398-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
The lethal effects of chemicals is a serious concern to the protection of ecosystems, and the OECD TG 212 was established to estimate the lethal and sublethal effects on embryo and sac-fry stages of fish. It is still unclear, however, whether this test can effectively estimate the impacts of chemicals using marine fish. Therefore, this study aimed to use a recognized testing method on the marine fish Oryzias javanicus, and to assess differences in response to organotin compounds between a freshwater congener (Oryzias latipes) and O. javanicus. The lowest observed effect concentration (LOEC) of triphenyltin for lethal effect was the same in both species. The LOEC of tributyltin for lethal and sublethal effects were the same in both species. Our results provide the first evidence that O. javanicus and O. latipes are similarly affected by organotin compounds, suggesting that O. javanicus is a good model marine fish for the ecotoxicological assessment of chemicals.
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Affiliation(s)
- Yoshifumi Horie
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan.
| | - Nobuhiro Kanazawa
- Faculty of System Science and Technology, Akita Prefectural University, 84-4 Ebinokuchi, Tsuchiya, Yurihonjo, Akita, 015-0055, Japan
| | - Takahiro Yamagishi
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Kei Yonekura
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan
| | - Norihisa Tatarazako
- Graduate School of Agriculture, Ehime University, Tarumi 3-5-7, Matsuyama, 790-8566, Japan
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Mandagi IF, Mokodongan DF, Tanaka R, Yamahira K. A New Riverine Ricefish of the GenusOryzias(Beloniformes, Adrianichthyidae) from Malili, Central Sulawesi, Indonesia. COPEIA 2018. [DOI: 10.1643/ci-17-704] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Myosho T, Takahashi H, Yoshida K, Sato T, Hamaguchi S, Sakamoto T, Sakaizumi M. Hyperosmotic tolerance of adult fish and early embryos are determined by discrete, single loci in the genus Oryzias. Sci Rep 2018; 8:6897. [PMID: 29720646 PMCID: PMC5932013 DOI: 10.1038/s41598-018-24621-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 03/29/2018] [Indexed: 11/09/2022] Open
Abstract
The acquisition of environmental osmolality tolerance traits in individuals and gametes is an important event in the evolution and diversification of organisms. Although teleost fish exhibit considerable intra- and interspecific variation in salinity tolerance, the genetic mechanisms underlying this trait remain unclear. Oryzias celebensis survives in sea and fresh water during both the embryonic and adult stages, whereas its close relative Oryzias woworae cannot survive in sea water at either stage. A linkage analysis using backcross progeny identified a single locus responsible for adult hyperosmotic tolerance on a fused chromosome that corresponds to O. latipes linkage groups (LGs) 6 and 23. Conversely, O. woworae eggs fertilised with O. celebensis sperm died in sea water at the cleavage stages, whereas O. celebensis eggs fertilised with O. woworae sperm developed normally, demonstrating that maternal factor(s) from O. celebensis are responsible for hyperosmotic tolerance during early development. A further linkage analysis using backcrossed females revealed a discrete single locus relating to the maternal hyperosmotic tolerance factor in a fused chromosomal region homologous to O. latipes LGs 17 and 19. These results indicate that a maternal factor governs embryonic hyperosmotic tolerance and maps to a locus distinct from that associated with adult hyperosmotic tolerance.
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Affiliation(s)
- Taijun Myosho
- Laboratory of Molecular Reproductive Biology, Institute for Environmental Science, University of Shizuoka, Shizuoka, 422-8526, Japan. .,Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan.
| | - Hideya Takahashi
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan.,Ushimado Marine Institute, Faculty of Science, Okayama University, Setouchi, Okayama, 701-4303, Japan
| | - Kento Yoshida
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan
| | - Tadashi Sato
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan
| | - Satoshi Hamaguchi
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Faculty of Science, Okayama University, Setouchi, Okayama, 701-4303, Japan
| | - Mitsuru Sakaizumi
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan
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Complete fusion of a transposon and herpesvirus created the Teratorn mobile element in medaka fish. Nat Commun 2017; 8:551. [PMID: 28916771 PMCID: PMC5601938 DOI: 10.1038/s41467-017-00527-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 07/05/2017] [Indexed: 01/02/2023] Open
Abstract
Mobile genetic elements (e.g., transposable elements and viruses) display significant diversity with various life cycles, but how novel elements emerge remains obscure. Here, we report a giant (180-kb long) transposon, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn belongs to the piggyBac superfamily and retains the transposition activity. Remarkably, Teratorn is largely derived from a herpesvirus of the Alloherpesviridae family that could infect fish and amphibians. Genomic survey of Teratorn-like elements reveals that some of them exist as a fused form between piggyBac transposon and herpesvirus genome in teleosts, implying the generality of transposon-herpesvirus fusion. We propose that Teratorn was created by a unique fusion of DNA transposon and herpesvirus, leading to life cycle shift. Our study supports the idea that recombination is the key event in generation of novel mobile genetic elements. Teratorn is a large mobile genetic element originally identified in the small teleost fish medaka. Here, the authors show that Teratorn is derived from the fusion of a piggyBac superfamily DNA transposon and an alloherpesvirus and that it is widely found across teleost fish.
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Wang Z, Long S, Liao J, Huang C, Zhang H, Huang S, Zhang Y, Liu L, Guo Y. Complete mitogenome of Hainan medaka Oryzias curvinotus (Teleostei: Beloniformes) and transcriptional differences between male and female liver. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:157-158. [PMID: 33490443 PMCID: PMC7800997 DOI: 10.1080/23802359.2017.1303340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this study, combining the liver transcripts from both sexes by RNA-Seq with DNA sequences by conventional PCRs, we have determined the complete mitogenome of Hainan medaka Oryzias curvinotus collected from the mangrove seawater of the Leizhou Peninsula in tropical South China (Accession no.: KY364884). The mitochondrial genome is 16,676 bp, and its content and structure are highly homologous to those of other teleostean fishes, including 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNA and 1 control region. Among the PCGs, ATG is used as the initiation codon, except for GTG in COI gene. There are 7 overlapping genes with overlap lengths ranging from 1 to 10 nucleotides (nt), while ten intergenic regions with a total of 66 nt and a maximum interval of 37 nt between tRNAAsn and tRNACys. Moreover, the data from RNA-Seq shows that the significant differences exist in the expression patterns of mitogenomes between male and female.
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Affiliation(s)
- Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Shuisheng Long
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jian Liao
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Chengqin Huang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Hairui Zhang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Shunkai Huang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yanping Zhang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Li Liu
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yusong Guo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
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Sasado T, Kondoh H, Furutani-Seiki M, Naruse K. Mutation in cpsf6/CFIm68 (Cleavage and Polyadenylation Specificity Factor Subunit 6) causes short 3'UTRs and disturbs gene expression in developing embryos, as revealed by an analysis of primordial germ cell migration using the medaka mutant naruto. PLoS One 2017; 12:e0172467. [PMID: 28253363 PMCID: PMC5333813 DOI: 10.1371/journal.pone.0172467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/06/2017] [Indexed: 02/02/2023] Open
Abstract
Our previous studies analyzing medaka mutants defective in primordial germ cell (PGC) migration identified cxcr4b and cxcr7, which are both receptors of the chemokine sdf1/cxcl12, as key regulators of PGC migration. Among PGC migration mutants, naruto (nar) is unique in that the mutant phenotype includes gross morphological abnormalities of embryos, suggesting that the mutation affects a broader range of processes. A fine genetic linkage mapping and genome sequencing showed the nar gene encodes Cleavage and Polyadenylation Specificity Factor subunit 6 (CPSF6/CFIm68). CPSF6 is a component of the Cleavage Factor Im complex (CFIm) which plays a key role in pre-mRNA 3'-cleavage and polyadenylation. 3'RACE of sdf1a/b and cxcr7 transcripts in the mutant embryos indicated shorter 3'UTRs with poly A additions occurring at more upstream positions than wild-type embryos, suggesting CPSF6 functions to prevent premature 3'UTR cleavage. In addition, expression of the coding region sequences of sdf1a/b in nar mutants was more anteriorly extended in somites than wild-type embryos, accounting for the abnormally extended distribution of PGCs in nar mutants. An expected consequence of shortening 3'UTR is the escape from the degradation mechanism mediated by microRNAs interacting with distal 3'UTR sequence. The abnormal expression pattern of sdf1a coding sequence may be at least partially accounted for by this mechanism. Given the pleiotropic effects of nar mutation, further analysis using the nar mutant will reveal processes in which CPSF6 plays essential regulatory roles in poly A site selection and involvement of 3'UTRs in posttranscriptional gene regulation in various genes in vivo.
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Affiliation(s)
- Takao Sasado
- Laboratory of Bioresources, National Institute for Basic Biology, Aichi, Japan
| | - Hisato Kondoh
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | | | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Aichi, Japan
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Juo JJ, Kang CK, Yang WK, Yang SY, Lee TH. A Stenohaline Medaka, Oryzias woworae, Increases Expression of Gill Na(+), K(+)-ATPase and Na(+), K(+), 2Cl(-) Cotransporter 1 to Tolerate Osmotic Stress. Zoolog Sci 2017; 33:414-25. [PMID: 27498801 DOI: 10.2108/zs150157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present study aimed to evaluate the osmoregulatory mechanism of Daisy's medaka, O. woworae,as well as demonstrate the major factors affecting the hypo-osmoregulatory characteristics of euryhaline and stenohaline medaka. The medaka phylogenetic tree indicates that Daisy's medaka belongs to the celebensis species group. The salinity tolerance of Daisy's medaka was assessed. Our findings revealed that 20‰ (hypertonic) saltwater (SW) was lethal to Daisy's medaka. However, 62.5% of individuals survived 10‰ (isotonic) SW with pre-acclimation to 5‰ SW for one week. This transfer regime, "Experimental (Exp.) 10‰ SW", was used in the following experiments. After 10‰ SW-transfer, the plasma osmolality of Daisy's medaka significantly increased. The protein abundance and distribution of branchial Na(+), K(+)-ATPase (NKA) and Na(+), K(+), 2Cl(-) cotransporter 1 (NKCC1) were also examined after transfer to 10‰ SW for one week. Gill NKA activity increased significantly after transfer to 10‰ SW. Meanwhile, elevation of gill NKA αα-subunit protein-abundance was found in the 10‰ SW-acclimated fish. In gill cross-sections, more and larger NKA-immunoreactive (NKA-IR) cells were observed in the Exp. 10‰ SW medaka. The relative abundance of branchial NKCC1 protein increased significantly after transfer to 10‰ SW. NKCC1 was distributed in the basolateral membrane of NKA-IR cells of the Exp. 10‰ SW group. Furthermore, a higher abundance of NKCC1 protein was found in the gill homogenates of the euryhaline medaka, O. dancena, than in that of the stenohaline medaka, O. woworae.
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Affiliation(s)
- Jiun-Jang Juo
- 1 Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.,† JJJ, CKK, and WKY contributed equally to this paper
| | - Chao-Kai Kang
- 2 Tainan Hydraulics Laboratory, National Cheng Kung University, Tainan 709, Taiwan.,† JJJ, CKK, and WKY contributed equally to this paper
| | - Wen-Kai Yang
- 1 Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.,† JJJ, CKK, and WKY contributed equally to this paper
| | - Shu-Yuan Yang
- 1 Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
| | - Tsung-Han Lee
- 1 Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.,3 Department of Biological Science and Technology, China Medical University,Taichung 404, Taiwan
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Matsuda M, Sakaizumi M. Evolution of the sex-determining gene in the teleostean genus Oryzias. Gen Comp Endocrinol 2016; 239:80-88. [PMID: 26449160 DOI: 10.1016/j.ygcen.2015.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 08/05/2015] [Accepted: 10/03/2015] [Indexed: 01/10/2023]
Abstract
In the genetic sex determination of vertebrates, the gonadal sex depends on the combination of sex chromosomes that a zygote possesses. Despite the discovery of the sex-determining gene (SRY/Sry) in mammals in 1990s, the sex-determining gene in non-mammalian vertebrates remained an enigma for over a decade. In most mammals, the male-inducing master sex-determining gene is located on the Y chromosome and is therefore absent from XX females. A second sex-determining gene, Dmy, was described in the Oryzias latipes in 2002 and has a DNA-binding motif that is different from the motif in the mammalian sex-determining gene SRY or Sry. Dmy is also located on the Y chromosome and is therefore absent in XX females. Seven other sex-determining genes, including candidate genes, are now known in birds, a frog species, and 5 fish species. These findings over the past twenty years have increased our knowledge of sex-determining genes and sex chromosomes among vertebrates. Here, we review recent advances in our understanding of sex-determining genes and genetic sex determination systems in fish, especially those of the Oryzias species, which are described in detail. The facts suggest some patterns of how new sex-determining genes emerged and evolved. We believe that these facts are common not only in Oryzias but also in other fish species. This knowledge will help to elucidate the conserved mechanisms from which various sex-determining mechanisms have evolved.
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Affiliation(s)
- Masaru Matsuda
- Center for Bioscience Research & Education, Utsunomiya University, Utsunomiya 321-8505, Japan.
| | - Mitsuru Sakaizumi
- Department of Environmental Sciences, Faculty of Science, Niigata University, Niigata 950-2181, Japan.
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Zhou W, Song N, Wang J, Gao T. Effects of geological changes and climatic fluctuations on the demographic histories and low genetic diversity of Squaliobarbus curriculus in Yellow River. Gene 2016; 590:149-58. [PMID: 27317893 DOI: 10.1016/j.gene.2016.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 05/20/2016] [Accepted: 06/03/2016] [Indexed: 11/16/2022]
Abstract
The 104 samples of Squaliobarbus curriculus were collected from four localities in Yellow River and one region in Yangtze River. Analyses of the first hypervariable region of mitochondrial DNA control region of 555bp revealed only 15 polymorphism sites and defined 19 haplotypes. Low-to-moderate levels of haplotype diversity and low nucleotide diversity were observed in Yellow River populations (h=0.2529-0.7510, π=0.0712%-0.2197%). In contrast, Poyang Lake population showed high haplotype diversity and lower-middle nucleotide diversity (h=0.9636, π=0.5317%). Low genetic differentiation was estimated among Yellow River populations and significant level of genetic structure was detected between two rivers. Population genetic structure between two rivers was believed to be connected with geographical barriers and paleoclimatic events. The demographic history of S. curriculus in Yellow River examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden and spatial population expansion dating to the Holocene. Climatic warming and changes of Yellow River course may have important effects on demographic facet of S. curriculus history. The same signal was also obtained on Poyang Lake population in late Pleistocene during the last interglacial period. During the period, the pronounced climatic change and the water system variation of PYL may have an important influence on the population.
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Affiliation(s)
- Wei Zhou
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Na Song
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Jun Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Tianxiang Gao
- Fisheries College, Zhejaing Ocean University, Zhoushan 316022, China.
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Yang WK, Kang CK, Hsu AD, Lin CH, Lee TH. Different Modulatory Mechanisms of Renal FXYD12 for Na(+)-K(+)-ATPase between Two Closely Related Medakas upon Salinity Challenge. Int J Biol Sci 2016; 12:730-45. [PMID: 27194950 PMCID: PMC4870716 DOI: 10.7150/ijbs.15066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 03/21/2016] [Indexed: 12/02/2022] Open
Abstract
Upon salinity challenge, the Na+-K+-ATPase (NKA) of fish kidney plays a crucial role in maintaining ion and water balance. Moreover, the FXYD protein family was found to be a regulator of NKA. Our preliminary results revealed that fxyd12 was highly expressed in the kidneys of the two closely related euryhaline medaka species (Oryzias dancena and O. latipes) from different natural habitats (brackish water and fresh water). In this study, we investigated the expression and association of renal FXYD12 and NKA α-subunit as well as potential functions of FXYD12 in the two medakas. These findings illustrated and compared the regulatory roles of FXYD12 for NKA in kidneys of the two medakas in response to salinity changes. In this study, at the mRNA and/or protein level, the expression patterns were similar for renal FXYD12 and NKA in the two medakas. However, different patterns of NKA activities and different interaction levels between FXYD12 and NKA were found in the kidneys of these two medakas. The results revealed that different strategies were used in the kidneys of the two medaka species upon salinity challenge. On the other hand, gene knockdown experiments demonstrated that the function of O. dancena FXYD12 allowed maintenance of a high level of NKA activity. The results of the present study indicated that the kidneys of the examined euryhaline medakas originating from brackish water and fresh water exhibited different modulatory mechanisms through which renal FXYD12 enhanced NKA activity to maintain internal homeostasis. Our findings broadened the knowledge of expression and functions of FXYD proteins, the modulators of NKA, in vertebrates.
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Affiliation(s)
- Wen-Kai Yang
- 1. Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
| | - Chao-Kai Kang
- 2. Tainan Hydraulics Laboratory, National Cheng Kung University, Tainan 709, Taiwan
| | - An-Di Hsu
- 1. Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
| | - Chia-Hao Lin
- 3. National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Tsung-Han Lee
- 1. Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.; 4. Department of Biological Science and Technology, China Medical University, Taichung 404, Taiwan
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Kim BM, Kim J, Choi IY, Raisuddin S, Au DWT, Leung KMY, Wu RSS, Rhee JS, Lee JS. Omics of the marine medaka (Oryzias melastigma) and its relevance to marine environmental research. MARINE ENVIRONMENTAL RESEARCH 2016; 113:141-152. [PMID: 26716363 DOI: 10.1016/j.marenvres.2015.12.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/11/2015] [Accepted: 12/12/2015] [Indexed: 06/05/2023]
Abstract
In recent years, the marine medaka (Oryzias melastigma), also known as the Indian medaka or brackish medaka, has been recognized as a model fish species for ecotoxicology and environmental research in the Asian region. O. melastigma has several promising features for research, which include a short generation period (3-4 months), daily spawning, small size (3-4 cm), transparent embryos, sexual dimorphism, and ease of mass culture in the laboratory. There have been extensive transcriptome and genome studies on the marine medaka in the past decade. Such omics data can be useful in understanding the signal transduction pathways of small teleosts in response to environmental stressors. An omics-integrated approach in the study of the marine medaka is important for strengthening its role as a small fish model for marine environmental studies. In this review, we present current omics information about the marine medaka and discuss its potential applications in the study of various molecular pathways that can be targets of marine environmental stressors, such as chemical pollutants. We believe that this review will encourage the use of this small fish as a model species in marine environmental research.
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Affiliation(s)
- Bo-Mi Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jaebum Kim
- Department of Animal Biotechnology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029, South Korea
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sheikh Raisuddin
- Department of Medical Elementology & Toxicology, Hamdard University, 110062, New Delhi, India
| | - Doris W T Au
- State Key Laboratory on Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Kenneth M Y Leung
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Rudolf S S Wu
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, 22012, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
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Mokodongan DF, Yamahira K. Origin and intra-island diversification of Sulawesi endemic Adrianichthyidae. Mol Phylogenet Evol 2015; 93:150-60. [DOI: 10.1016/j.ympev.2015.07.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 07/26/2015] [Accepted: 07/27/2015] [Indexed: 11/17/2022]
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Abstract
Sex chromosomes and the sex-determining (SD) gene are variable in vertebrates. In particular, medaka fishes in the genus Oryzias show an extremely large diversity in sex chromosomes and the SD gene, providing a good model to study the evolutionary process by which they turnover. Here, we investigated the sex determination system and sex chromosomes in six celebensis group species. Our sex-linkage analysis demonstrated that all species had an XX-XY sex determination system, and that the Oryzias marmoratus and O. profundicola sex chromosomes were homologous to O. latipes linkage group (LG) 10, while those of the other four species, O. celebensis, O. matanensis, O. wolasi, and O. woworae, were homologous to O. latipes LG 24. The phylogenetic relationship suggested a turnover of the sex chromosomes from O. latipes LG 24 to LG 10 within this group. Six sex-linkage maps showed that the former two and the latter four species shared a common SD locus, respectively, suggesting that the LG 24 acquired the SD function in a common ancestor of the celebensis group, and that the LG 10 SD function appeared in a common ancestor of O. marmoratus and O. profundicola after the divergence of O. matanensis. Additionally, fine mapping and association analysis in the former two species revealed that Sox3 on the Y chromosome is a prime candidate for the SD gene, and that the Y-specific 430-bp insertion might be involved in its SD function.
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Lai KP, Li JW, Wang SY, Chiu JMY, Tse A, Lau K, Lok S, Au DWT, Tse WKF, Wong CKC, Chan TF, Kong RYC, Wu RSS. Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes. BMC Genomics 2015; 16:135. [PMID: 25765076 PMCID: PMC4352242 DOI: 10.1186/s12864-015-1325-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 02/06/2015] [Indexed: 11/12/2022] Open
Abstract
Background The marine medaka Oryzias melastigma has been demonstrated as a novel model for marine ecotoxicological studies. However, the lack of genome and transcriptome reference has largely restricted the use of O. melastigma in the assessment of in vivo molecular responses to environmental stresses and the analysis of biological toxicity in the marine environment. Although O. melastigma is believed to be phylogenetically closely related to Oryzias latipes, the divergence between these two species is still largely unknown. Using Illumina high-throughput RNA sequencing followed by de novo assembly and comprehensive gene annotation, we provided transcriptomic resources for the brain, liver, ovary and testis of O. melastigma. We also investigated the possible extent of divergence between O. melastigma and O. latipes at the transcriptome level. Results More than 14,000 transcripts across brain, liver, ovary and testis in marine medaka were annotated, of which 5880 transcripts were orthologous between O. melastigma and O. latipes. Tissue-enriched genes were identified in O. melastigma, and Gene Ontology analysis demonstrated the functional specificity of the annotated genes in respective tissue. Lastly, the identification of marine medaka-enriched transcripts suggested the necessity of generating transcriptome dataset of O. melastigma. Conclusions Orthologous transcripts between O. melastigma and O. latipes, tissue-enriched genes and O. melastigma-enriched transcripts were identified. Genome-wide expression studies of marine medaka require an assembled transcriptome, and this sequencing effort has generated a valuable resource of coding DNA for a non-model species. This transcriptome resource will aid future studies assessing in vivo molecular responses to environmental stresses and those analyzing biological toxicity in the marine environment. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1325-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keng Po Lai
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Jing-Woei Li
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, SAR, China.
| | - Simon Yuan Wang
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Jill Man-Ying Chiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Anna Tse
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Karen Lau
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Si Lok
- Genome Research Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, 5 Sassoon Road, Pokfulam, Hong Kong, SAR, China.
| | - Doris Wai-Ting Au
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - William Ka-Fai Tse
- Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China.
| | - Chris Kong-Chu Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Ting-Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, SAR, China.
| | - Richard Yuen-Chong Kong
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Rudolf Shiu-Sun Wu
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
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Hubert N, Kadarusman, Wibowo A, Busson F, Caruso D, Sulandari S, Nafiqoh N, Pouyaud L, Rüber L, Avarre JC, Herder F, Hanner R, Keith P, Hadiaty RK. DNA Barcoding Indonesian freshwater fishes: challenges and prospects. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractWith 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.
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Mokodongan DF, Tanaka R, Yamahira K. A New Ricefish of the GenusOryzias(Beloniformes, Adrianichthyidae) from Lake Tiu, Central Sulawesi, Indonesia. COPEIA 2014. [DOI: 10.1643/ci-13-081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kimura T, Nagao Y, Hashimoto H, Yamamoto-Shiraishi YI, Yamamoto S, Yabe T, Takada S, Kinoshita M, Kuroiwa A, Naruse K. Leucophores are similar to xanthophores in their specification and differentiation processes in medaka. Proc Natl Acad Sci U S A 2014; 111:7343-8. [PMID: 24803434 PMCID: PMC4034200 DOI: 10.1073/pnas.1311254111] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Animal body color is generated primarily by neural crest-derived pigment cells in the skin. Mammals and birds have only melanocytes on the surface of their bodies; however, fish have a variety of pigment cell types or chromatophores, including melanophores, xanthophores, and iridophores. The medaka has a unique chromatophore type called the leucophore. The genetic basis of chromatophore diversity remains poorly understood. Here, we report that three loci in medaka, namely, leucophore free (lf), lf-2, and white leucophore (wl), which affect leucophore and xanthophore differentiation, encode solute carrier family 2, member 15b (slc2a15b), paired box gene 7a (pax7a), and solute carrier family 2 facilitated glucose transporter, member 11b (slc2a11b), respectively. Because lf-2, a loss-of-function mutant for pax7a, causes defects in the formation of xanthophore and leucophore precursor cells, pax7a is critical for the development of the chromatophores. This genetic evidence implies that leucophores are similar to xanthophores, although it was previously thought that leucophores were related to iridophores, as these chromatophores have purine-dependent light reflection. Our identification of slc2a15b and slc2a11b as genes critical for the differentiation of leucophores and xanthophores in medaka led to a further finding that the existence of these two genes in the genome coincides with the presence of xanthophores in nonmammalian vertebrates: birds have yellow-pigmented irises with xanthophore-like intracellular organelles. Our findings provide clues for revealing diverse evolutionary mechanisms of pigment cell formation in animals.
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Affiliation(s)
- Tetsuaki Kimura
- Interuniversity Bio-Backup Project Center, National Institute for Basic Biology, Okazaki 444-8787, Aichi, Japan;Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan;
| | - Yusuke Nagao
- Bioscience and Biotechnology Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hisashi Hashimoto
- Bioscience and Biotechnology Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yo-ichi Yamamoto-Shiraishi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shiori Yamamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Taijiro Yabe
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan;Okazaki Institute for Integrative Bioscience and National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Shinji Takada
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan;Okazaki Institute for Integrative Bioscience and National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masato Kinoshita
- Division of Applied Bioscience, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; and
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kiyoshi Naruse
- Interuniversity Bio-Backup Project Center, National Institute for Basic Biology, Okazaki 444-8787, Aichi, Japan;Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan;Laboratory of Bioresources, National Institute for Basic Biology, Okazaki 444-8585, Aichi, Japan
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Kawaguchi M, Inoue K, Iuchi I, Nishida M, Yasumasu S. Molecular co-evolution of a protease and its substrate elucidated by analysis of the activity of predicted ancestral hatching enzyme. BMC Evol Biol 2013; 13:231. [PMID: 24161109 PMCID: PMC3819744 DOI: 10.1186/1471-2148-13-231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 10/23/2013] [Indexed: 02/08/2023] Open
Abstract
Background Hatching enzyme is a protease that digests the egg envelope, enabling hatching of the embryo. We have comprehensively studied the molecular mechanisms of the enzyme action to its substrate egg envelope, and determined the gene/protein structure and phylogenetic relationships. Because the hatching enzyme must have evolved while maintaining its ability to digest the egg envelope, the hatching enzyme-egg envelope protein pair is a good model for studying molecular co-evolution of a protease and its substrate. Results Hatching enzymes from medaka (Oryzias latipes) and killifish (Fundulus heteroclitus) showed species-specific egg envelope digestion. We found that by introducing four medaka-type residue amino acid substitutions into recombinant killifish hatching enzyme, the mutant killifish hatching enzyme could digest medaka egg envelope. Further, we studied the participation of the cleavage site of the substrate in the species-specificity of hatching enzyme. A P2-site single amino acid substitution was responsible for the species-specificity. Estimation of the activity of the predicted ancestral enzymes towards various types of cleavage sites along with prediction of the evolutionary timing of substitutions allowed prediction of a possible evolutionary pathway, as follows: ancestral hatching enzyme, which had relatively strict substrate specificity, developed broader specificity as a result of four amino acid substitutions in the active site cleft of the enzyme. Subsequently, a single substitution occurred within the cleavage site of the substrate, and the recent feature of species-specificity was established in the hatching enzyme-egg envelope system. Conclusions The present study clearly provides an ideal model for protease-substrate co-evolution. The evolutionary process giving rise to species-specific egg envelope digestion of hatching enzyme was initiated by amino acid substitutions in the enzyme, resulting in altered substrate specificity, which later allowed an amino acid substitution in the substrate.
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Affiliation(s)
| | | | | | | | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan.
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Uno Y, Asada Y, Nishida C, Takehana Y, Sakaizumi M, Matsuda Y. Divergence of Repetitive DNA Sequences in the Heterochromatin of Medaka Fishes: Molecular Cytogenetic Characterization of Constitutive Heterochromatin in Two Medaka Species: Oryzias hubbsi and O. celebensis (Adrianichthyidae, Beloniformes). Cytogenet Genome Res 2013; 141:212-26. [DOI: 10.1159/000354668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Kikuchi K, Hamaguchi S. Novel sex-determining genes in fish and sex chromosome evolution. Dev Dyn 2013; 242:339-53. [PMID: 23335327 DOI: 10.1002/dvdy.23927] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 12/25/2012] [Accepted: 12/26/2012] [Indexed: 12/13/2022] Open
Abstract
Although the molecular mechanisms underlying many developmental events are conserved across vertebrate taxa, the lability at the top of the sex-determining (SD) cascade has been evident from the fact that four master SD genes have been identified: mammalian Sry; chicken DMRT1; medaka Dmy; and Xenopus laevis DM-W. This diversity is thought to be associated with the turnover of sex chromosomes, which is likely to be more frequent in fishes and other poikilotherms than in therian mammals and birds. Recently, four novel candidates for vertebrate SD genes were reported, all of them in fishes. These include amhy in the Patagonian pejerrey, Gsdf in Oryzias luzonensis, Amhr2 in fugu and sdY in rainbow trout. These studies provide a good opportunity to infer patterns from the seemingly chaotic picture of sex determination systems. Here, we review recent advances in our understanding of the master SD genes in fishes.
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Affiliation(s)
- Kiyoshi Kikuchi
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan.
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Imoto JM, Saitoh K, Sasaki T, Yonezawa T, Adachi J, Kartavtsev YP, Miya M, Nishida M, Hanzawa N. Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene 2013; 514:112-24. [DOI: 10.1016/j.gene.2012.10.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 09/10/2012] [Accepted: 10/19/2012] [Indexed: 10/27/2022]
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Expression profiles of branchial FXYD proteins in the brackish medaka Oryzias dancena: a potential saltwater fish model for studies of osmoregulation. PLoS One 2013; 8:e55470. [PMID: 23383199 PMCID: PMC3561181 DOI: 10.1371/journal.pone.0055470] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/23/2012] [Indexed: 12/03/2022] Open
Abstract
FXYD proteins are novel regulators of Na+-K+-ATPase (NKA). In fish subjected to salinity challenges, NKA activity in osmoregulatory organs (e.g., gills) is a primary driving force for the many ion transport systems that act in concert to maintain a stable internal environment. Although teleostean FXYD proteins have been identified and investigated, previous studies focused on only a limited group of species. The purposes of the present study were to establish the brackish medaka (Oryzias dancena) as a potential saltwater fish model for osmoregulatory studies and to investigate the diversity of teleostean FXYD expression profiles by comparing two closely related euryhaline model teleosts, brackish medaka and Japanese medaka (O. latipes), upon exposure to salinity changes. Seven members of the FXYD protein family were identified in each medaka species, and the expression of most branchial fxyd genes was salinity-dependent. Among the cloned genes, fxyd11 was expressed specifically in the gills and at a significantly higher level than the other fxyd genes. In the brackish medaka, branchial fxyd11 expression was localized to the NKA-immunoreactive cells in gill epithelia. Furthermore, the FXYD11 protein interacted with the NKA α-subunit and was expressed at a higher level in freshwater-acclimated individuals relative to fish in other salinity groups. The protein sequences and tissue distributions of the FXYD proteins were very similar between the two medaka species, but different expression profiles were observed upon salinity challenge for most branchial fxyd genes. Salinity changes produced different effects on the FXYD11 and NKA α-subunit expression patterns in the gills of the brackish medaka. To our knowledge, this report is the first to focus on FXYD expression in the gills of closely related euryhaline teleosts. Given the advantages conferred by the well-developed Japanese medaka system, we propose the brackish medaka as a saltwater fish model for osmoregulatory studies.
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Hwang DS, Kim BM, Au DWT, Lee JS. Complete mitochondrial genome of the marine medaka Oryzias melastigma (Beloniformes, Adrianichthyidae). ACTA ACUST UNITED AC 2012; 23:308-9. [PMID: 22708854 DOI: 10.3109/19401736.2012.683181] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome was obtained from the assembled genome data sequenced by next-generation sequencer from the marine medaka Oryzias melastigma. The mitochondrial genome sequence was 16,864 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 4 genes (CO3, ND3, ND4, and Cytb) had incomplete stop codons. The base composition of O. melastigma mitogenome showed high A+T (59.65%) and anti-G bias (8.73%) on the 3rd position of PCGs.
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Affiliation(s)
- Dae-Sik Hwang
- Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul 133-791, South Korea
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