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Adachi U, Koita R, Seto A, Maeno A, Ishizu A, Oikawa S, Tani T, Ishizaka M, Yamada K, Satoh K, Nakazawa H, Furudate H, Kawakami K, Iwanami N, Matsuda M, Kawamura A. Teleost Hox code defines regional identities competent for the formation of dorsal and anal fins. Proc Natl Acad Sci U S A 2024; 121:e2403809121. [PMID: 38861596 DOI: 10.1073/pnas.2403809121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024] Open
Abstract
The dorsal and anal fins can vary widely in position and length along the anterior-posterior axis in teleost fishes. However, the molecular mechanisms underlying the diversification of these fins remain unknown. Here, we used genetic approaches in zebrafish and medaka, in which the relative positions of the dorsal and anal fins are opposite, to demonstrate the crucial role of hox genes in the patterning of the teleost posterior body, including the dorsal and anal fins. By the CRISPR-Cas9-induced frameshift mutations and positional cloning of spontaneous dorsalfinless medaka, we show that various hox mutants exhibit the absence of dorsal or anal fins, or a stepwise posterior extension of these fins, with vertebral abnormalities. Our results indicate that multiple hox genes, primarily from hoxc-related clusters, encompass the regions responsible for the dorsal and anal fin formation along the anterior-posterior axis. These results further suggest that shifts in the anterior boundaries of hox expression which vary among fish species, lead to diversification in the position and size of the dorsal and anal fins, similar to how modulations in Hox expression can alter the number of anatomically distinct vertebrae in tetrapods. Furthermore, we show that hox genes responsible for dorsal fin formation are different between zebrafish and medaka. Our results suggest that a novel mechanism has occurred during teleost evolution, in which the gene network responsible for fin formation might have switched to the regulation downstream of other hox genes, leading to the remarkable diversity in the dorsal fin position.
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Affiliation(s)
- Urara Adachi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Rina Koita
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Akira Seto
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya 321-8505, Japan
| | - Akiteru Maeno
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Atsuki Ishizu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Sae Oikawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Taisei Tani
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Mizuki Ishizaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Kazuya Yamada
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Koumi Satoh
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Hidemichi Nakazawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Hiroyuki Furudate
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, and Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
| | - Norimasa Iwanami
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya 321-8505, Japan
| | - Masaru Matsuda
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya 321-8505, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
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2
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Medina-Gomez C, Mullin BH, Chesi A, Prijatelj V, Kemp JP, Shochat-Carvalho C, Trajanoska K, Wang C, Joro R, Evans TE, Schraut KE, Li-Gao R, Ahluwalia TS, Zillikens MC, Zhu K, Mook-Kanamori DO, Evans DS, Nethander M, Knol MJ, Thorleifsson G, Prokic I, Zemel B, Broer L, McGuigan FE, van Schoor NM, Reppe S, Pawlak MA, Ralston SH, van der Velde N, Lorentzon M, Stefansson K, Adams HHH, Wilson SG, Ikram MA, Walsh JP, Lakka TA, Gautvik KM, Wilson JF, Orwoll ES, van Duijn CM, Bønnelykke K, Uitterlinden AG, Styrkársdóttir U, Akesson KE, Spector TD, Tobias JH, Ohlsson C, Felix JF, Bisgaard H, Grant SFA, Richards JB, Evans DM, van der Eerden B, van de Peppel J, Ackert-Bicknell C, Karasik D, Kague E, Rivadeneira F. Bone mineral density loci specific to the skull portray potential pleiotropic effects on craniosynostosis. Commun Biol 2023; 6:691. [PMID: 37402774 PMCID: PMC10319806 DOI: 10.1038/s42003-023-04869-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 04/25/2023] [Indexed: 07/06/2023] Open
Abstract
Skull bone mineral density (SK-BMD) provides a suitable trait for the discovery of key genes in bone biology, particularly to intramembranous ossification, not captured at other skeletal sites. We perform a genome-wide association meta-analysis (n ~ 43,800) of SK-BMD, identifying 59 loci, collectively explaining 12.5% of the trait variance. Association signals cluster within gene-sets involved in skeletal development and osteoporosis. Among the four novel loci (ZIC1, PRKAR1A, AZIN1/ATP6V1C1, GLRX3), there are factors implicated in intramembranous ossification and as we show, inherent to craniosynostosis processes. Functional follow-up in zebrafish confirms the importance of ZIC1 on cranial suture patterning. Likewise, we observe abnormal cranial bone initiation that culminates in ectopic sutures and reduced BMD in mosaic atp6v1c1 knockouts. Mosaic prkar1a knockouts present asymmetric bone growth and, conversely, elevated BMD. In light of this evidence linking SK-BMD loci to craniofacial abnormalities, our study provides new insight into the pathophysiology, diagnosis and treatment of skeletal diseases.
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Grants
- UL1 TR000128 NCATS NIH HHS
- U01 AG042124 NIA NIH HHS
- U01 AG042145 NIA NIH HHS
- U01 AG042168 NIA NIH HHS
- U01 AG042140 NIA NIH HHS
- U24 AG051129 NIA NIH HHS
- R01 AR051124 NIAMS NIH HHS
- U01 AG027810 NIA NIH HHS
- U01 AR066160 NIAMS NIH HHS
- MC_UU_00007/10 Medical Research Council
- R01 HD058886 NICHD NIH HHS
- RC2 AR058973 NIAMS NIH HHS
- Wellcome Trust
- M01 RR000240 NCRR NIH HHS
- U01 AG042143 NIA NIH HHS
- UL1 RR026314 NCRR NIH HHS
- U01 AG042139 NIA NIH HHS
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- European Cooperation in Science and Technology (COST)
- Wellcome Trust (Wellcome)
- Department of Health | National Health and Medical Research Council (NHMRC)
- U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)
- ZonMw (Netherlands Organisation for Health Research and Development)
- EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- Vetenskapsrådet (Swedish Research Council)
- U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
- Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
- NCHA (Netherlands Consortium Healthy Ageing) Leiden/ Rotterdam; Dutch Ministry of Economic Affairs, Agriculture and Innovation (project KB-15-004-003); the Research Institute for Diseases in the Elderly [Netherlands] (014-93-015; RIDE2)
- Clinical and Translational Research Center (5-MO1-RR-000240 and UL1 RR-026314); U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) GrantRecipient="Au50"
- European Commission FP6 STRP grant number 018947 (LSHG-CT-2006-01947); Netherlands Organization for Scientific Research and the Russian Foundation for Basic Research (NWO-RFBR 047.017.043); Netherlands Brain Foundation (project number F2013(1)-28) GrantRecipient="Au40"
- Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710) GrantRecipient="Au28"
- Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710) GrantRecipient="Au38"
- The Pawsey Supercomputing Centre (with Funding from the Australian Government and the Government of Western Australia; PG 16/0162, PG 17/director2025) GrantRecipient="Au45”
- European Commission (EC)
- U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS);NIH Roadmap for Medical Research [USA]: U01 AG027810, U01 AG042124, U01 AG042139, U01 AG042140, U01 AG042143, U01 AG042145, U01 AG042168, U01 AR066160, and UL1 TR000128 GrantRecipient="Au39”
- Versus Arthritis [USA] 21937 GrantRecipient="Au57”
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Affiliation(s)
- Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
| | - Alessandra Chesi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Vid Prijatelj
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - John P Kemp
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, 4102, Australia
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | | | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Carol Wang
- School of Women's and Infants' Health, University of Western Australia, Crawley, WA, 6009, Australia
| | - Raimo Joro
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, 70211, Finland
| | - Tavia E Evans
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX, Scotland
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH8 9AG, Scotland
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
- Steno Diabetes Center Copenhagen, Herlev, 2820, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Kun Zhu
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Maria Nethander
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Maria J Knol
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - Ivana Prokic
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Babette Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of GI, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Fiona E McGuigan
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Malmö, Sweden
| | - Natasja M van Schoor
- Department of Epidemiology and Data Science, Amsterdam UMC, 1081 HV, Amsterdam, The Netherlands
| | - Sjur Reppe
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0372, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, 0372, Oslo, Norway
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, 0456, Oslo, Norway
| | - Mikolaj A Pawlak
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Neurology, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Stuart H Ralston
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Nathalie van der Velde
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Geriatric Medicine, Amsterdam Public Health Research Institute, Amsterdam UMC, 1105 AZ, Amsterdam, The Netherlands
| | - Mattias Lorentzon
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia
| | | | - Hieab H H Adams
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Latin American Brain Health (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
| | - Timo A Lakka
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, 70211, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, 70100, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Kaare M Gautvik
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, 0456, Oslo, Norway
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Eric S Orwoll
- Department of Public Health & Preventive Medicine, Oregon Health & Science University, Portland, OR, OR97239, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - Kristina E Akesson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Malmö, Sweden
- Department of Orthopedics Malmö, Skåne University Hospital, S-21428, Malmö, Sweden
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jonathan H Tobias
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Bristol, BS10 5NB, UK
| | - Claes Ohlsson
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Region Västra Götaland, SE-413 45, Gothenburg, Sweden
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - J Brent Richards
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
- Lady Davis Institute, Jewish General Hospital, Montreal, H3T 1E2, QC, Canada
| | - David M Evans
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, 4102, Australia
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
- Marcus Institute for Aging Research, Hebrew SeniorLife, Roslindale, MA, 02131, USA
| | - Erika Kague
- The School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Fernando Rivadeneira
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands.
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Inoue Y, Takeda H. Teratorn and its relatives - a cross-point of distinct mobile elements, transposons and viruses. Front Vet Sci 2023; 10:1158023. [PMID: 37187934 PMCID: PMC10175614 DOI: 10.3389/fvets.2023.1158023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Mobile genetic elements (e.g., transposable elements and plasmids) and viruses display significant diversity with various life cycles, but how this diversity emerges remains obscure. We previously reported a novel and giant (180 kb long) mobile element, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn is a composite DNA transposon created by a fusion of a piggyBac-like DNA transposon (piggyBac) and a novel herpesvirus of the Alloherpesviridae family. Genomic survey revealed that Teratorn-like herpesviruses are widely distributed among teleost genomes, the majority of which are also fused with piggyBac, suggesting that fusion with piggyBac is a trigger for the life-cycle shift of authentic herpesviruses to an intragenomic parasite. Thus, Teratorn-like herpesvirus provides a clear example of how novel mobile elements emerge, that is to say, the creation of diversity. In this review, we discuss the unique sequence and life-cycle characteristics of Teratorn, followed by the evolutionary process of piggyBac-herpesvirus fusion based on the distribution of Teratorn-like herpesviruses (relatives) among teleosts. Finally, we provide other examples of evolutionary associations between different classes of elements and propose that recombination could be a driving force generating novel mobile elements.
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Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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4
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Inoue Y, Takeda H. Teratorn and Its Related Elements – a Novel Group of Herpesviruses Widespread in Teleost Genomes. Zoolog Sci 2023; 40:83-90. [PMID: 37042688 DOI: 10.2108/zs220069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/12/2022] [Indexed: 03/08/2023]
Abstract
Herpesviruses are a large family of DNA viruses infecting vertebrates and invertebrates, and are important pathogens in the field of aquaculture. In general, herpesviruses do not have the ability to integrate into the host genomes since they do not have a chromosomal integration step in their life cycles. Recently, we identified a novel group of herpesviruses, "Teratorn" and its related elements, in the genomes of various teleost fish species. At least some of the Teratorn-like herpesviruses are fused with a piggyBac-like DNA transposon, suggesting that they have acquired the transposon-like intragenomic lifestyle by hijacking the transposon system. In this review, we describe the sequence characteristics of Teratorn-like herpesviruses and phylogenetic relationships with other herpesviruses. Then we discuss the process of transposon-herpesvirus fusion, their life cycle, and the generality of transposon-virus fusion. Teratorn-like herpesviruses provide a piece of concrete evidence that even non-retroviral elements can become intragenomic parasites retaining replication capacity, by acquiring transposition machinery from other sources.
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Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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5
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Rees L, König D, Jaźwińska A. Platyfish bypass the constraint of the caudal fin ventral identity in teleosts. Dev Dyn 2022; 251:1862-1879. [PMID: 35803741 PMCID: PMC9796532 DOI: 10.1002/dvdy.518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The caudal fin of teleosts is characterized by dorsoventral symmetry. Despite this external morphology, the principal rays of this appendage connect to bones below the notochord, indicating the ventral (hypochordal) identity of this organ. RESULTS Here, we report that this typical architecture of the caudal fin is not fully conserved in the platyfish (Xiphophorus maculatus) and the guppy (Poecilia reticulata), representatives of the Poeciliidae family. We show that in these species, 3-4 principal rays connect to bones above the notochord, suggesting an epichordal contribution. Consistently, as examined in platyfish, dorsal identity genes zic1/4 were highly expressed in these rays, providing molecular evidence of their epichordal origin. Developmental analysis revealed that the earliest rays above the notochord emerge at the 10-ray stage of fin morphogenesis. In contrast to zebrafish and medaka, platyfish and guppies display a mirrored shape of dorsal and ventral processes of the caudal endoskeleton. Our study suggests that an ancestral bauplan expanded in poeciliids by advancing its symmetrical pattern. CONCLUSION The platyfish evolved a fin architecture with the epichordal origin of its upper principal rays and a high level of symmetry in the caudal endoskeleton. This innovative architecture highlights the adaptation of the teleost skeleton.
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Affiliation(s)
- Lana Rees
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Désirée König
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Anna Jaźwińska
- Department of BiologyUniversity of FribourgFribourgSwitzerland
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Heilig AK, Nakamura R, Shimada A, Hashimoto Y, Nakamura Y, Wittbrodt J, Takeda H, Kawanishi T. Wnt11 acts on dermomyotome cells to guide epaxial myotome morphogenesis. eLife 2022; 11:71845. [PMID: 35522214 PMCID: PMC9075960 DOI: 10.7554/elife.71845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/19/2022] [Indexed: 12/30/2022] Open
Abstract
The dorsal axial muscles, or epaxial muscles, are a fundamental structure covering the spinal cord and vertebrae, as well as mobilizing the vertebrate trunk. To date, mechanisms underlying the morphogenetic process shaping the epaxial myotome are largely unknown. To address this, we used the medaka zic1/zic4-enhancer mutant Double anal fin (Da), which exhibits ventralized dorsal trunk structures resulting in impaired epaxial myotome morphology and incomplete coverage over the neural tube. In wild type, dorsal dermomyotome (DM) cells reduce their proliferative activity after somitogenesis. Subsequently, a subset of DM cells, which does not differentiate into the myotome population, begins to form unique large protrusions extending dorsally to guide the epaxial myotome dorsally. In Da, by contrast, DM cells maintain the high proliferative activity and mainly form small protrusions. By combining RNA- and ChIP-sequencing analyses, we revealed direct targets of Zic1, which are specifically expressed in dorsal somites and involved in various aspects of development, such as cell migration, extracellular matrix organization, and cell-cell communication. Among these, we identified wnt11 as a crucial factor regulating both cell proliferation and protrusive activity of DM cells. We propose that dorsal extension of the epaxial myotome is guided by a non-myogenic subpopulation of DM cells and that wnt11 empowers the DM cells to drive the coverage of the neural tube by the epaxial myotome.
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Affiliation(s)
- Ann Kathrin Heilig
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan.,Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Atsuko Shimada
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yuka Hashimoto
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yuta Nakamura
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Toru Kawanishi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
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7
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Ikeda T, Inamori K, Kawanishi T, Takeda H. Reemployment of Kupffer's vesicle cells into axial and paraxial mesoderm via transdifferentiation. Dev Growth Differ 2022; 64:163-177. [PMID: 35129208 DOI: 10.1111/dgd.12774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 01/25/2023]
Abstract
Kupffer's vesicle (KV) in the teleost embryo is a fluid-filled vesicle surrounded by a layer of epithelial cells with rotating primary cilia. KV transiently acts as the left-right organizer and degenerates after the establishment of left-right asymmetric gene expression. Previous labelling experiments in zebrafish embryos indicated that descendants of KV-epithelial cells are incorporated into mesodermal tissues after the collapse of KV. However, the overall picture of their differentiation potency had been unclear due to the lack of suitable genetic tools and molecular analyses. In the present study, we established a novel zebrafish transgenic line with a promoter of dand5, in which all KV-epithelial cells and their descendants are specifically labelled until the larval stage. We found that KV-epithelial cells undergo epithelial-mesenchymal transition upon KV collapse and infiltrate into adjacent mesodermal progenitors, the presomitic mesoderm and chordoneural hinge. Once incorporated, the descendants of KV-epithelial cells expressed distinct mesodermal differentiation markers and contributed to the mature populations such as the axial muscles and notochordal sheath through normal developmental process. These results indicate that differentiated KV-epithelial cells possess unique plasticity in that they are reemployed into mesodermal lineages through transdifferentiation after they complete their initial role in KV.
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Affiliation(s)
- Takafumi Ikeda
- Laboratory of Embryology, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kiichi Inamori
- Laboratory of Embryology, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Toru Kawanishi
- Laboratory of Embryology, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Takeda
- Laboratory of Embryology, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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8
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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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9
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Seleit A, Gross K, Onistschenko J, Hoang OP, Theelke J, Centanin L. Local tissue interactions govern pLL patterning in medaka. Dev Biol 2021; 481:1-13. [PMID: 34517003 DOI: 10.1016/j.ydbio.2021.09.002] [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: 05/26/2021] [Revised: 08/12/2021] [Accepted: 09/03/2021] [Indexed: 11/03/2022]
Abstract
Vertebrate organs are arranged in a stereotypic, species-specific position along the animal body plan. Substantial morphological variation exists between related species, especially so in the vastly diversified teleost clade. It is still unclear how tissues, organs and systems can accommodate such diverse scaffolds. Here, we use the distinctive arrangement of neuromasts in the posterior lateral line (pLL) system of medaka fish to address the tissue-interactions defining a pattern. We show that patterning in this peripheral nervous system is established by autonomous organ precursors independent of neuronal wiring. In addition, we target the keratin 15 gene to generate stuck-in-the-midline (siml) mutants, which display epithelial lesions and a disrupted pLL patterning. By using siml/wt chimeras, we determine that the aberrant siml pLL pattern depends on the mutant epithelium, since a wild type epithelium can rescue the siml phenotype. Inducing epithelial lesions by 2-photon laser ablation during pLL morphogenesis phenocopies siml genetic mutants and reveals that epithelial integrity defines the final position of the embryonic pLL neuromasts. Our results using the medaka pLL disentangle intrinsic from extrinsic properties during the establishment of a sensory system. We speculate that intrinsic programs guarantee proper organ morphogenesis, while instructive interactions from surrounding tissues facilitates the accommodation of sensory organs to the diverse body plans found among teleosts.
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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, Universität Heidelberg, 69120, Heidelberg, Germany; Heidelberg Biosciences International Graduate School (HBIGS), Universität Heidelberg, Heidelberg, Germany
| | - Karen Gross
- Laboratory of Clonal Analysis of Post-Embryonic Stem Cells, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Universität Heidelberg, 69120, Heidelberg, Germany; Heidelberg Biosciences International Graduate School (HBIGS), Universität Heidelberg, Heidelberg, Germany
| | - Jasmin Onistschenko
- Laboratory of Clonal Analysis of Post-Embryonic Stem Cells, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Universität Heidelberg, 69120, Heidelberg, Germany; Heidelberg Biosciences International Graduate School (HBIGS), Universität Heidelberg, Heidelberg, Germany
| | - Oi Pui Hoang
- Laboratory of Clonal Analysis of Post-Embryonic Stem Cells, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Universität Heidelberg, 69120, Heidelberg, Germany
| | - Jonas Theelke
- Laboratory of Clonal Analysis of Post-Embryonic Stem Cells, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Universität Heidelberg, 69120, Heidelberg, Germany
| | - Lázaro Centanin
- Laboratory of Clonal Analysis of Post-Embryonic Stem Cells, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Universität Heidelberg, 69120, Heidelberg, Germany.
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10
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Wang L, Sun F, Wan ZY, Ye B, Wen Y, Liu H, Yang Z, Pang H, Meng Z, Fan B, Alfiko Y, Shen Y, Bai B, Lee MSQ, Piferrer F, Schartl M, Meyer A, Yue GH. Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish. Mol Biol Evol 2021; 38:3383-3396. [PMID: 33871625 PMCID: PMC8321530 DOI: 10.1093/molbev/msab110] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long-fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole-genome sequencing, quantitative trait loci mapping, genome-wide association studies, and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino, and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double-tail mutant was suggested to be caused by a deletion in a zic1/zic4 coenhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Fei Sun
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Baoqing Ye
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Yanfei Wen
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Huiming Liu
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zituo Yang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Hongyan Pang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zining Meng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Fan
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, China
| | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Jakarta, Indonesia
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Bin Bai
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - May Shu Qing Lee
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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11
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Schartl M, Kneitz S, Ormanns J, Schmidt C, Anderson JL, Amores A, Catchen J, Wilson C, Geiger D, Du K, Garcia-Olazábal M, Sudaram S, Winkler C, Hedrich R, Warren WC, Walter R, Meyer A, Postlethwait JH. The Developmental and Genetic Architecture of the Sexually Selected Male Ornament of Swordtails. Curr Biol 2021; 31:911-922.e4. [PMID: 33275891 PMCID: PMC8580132 DOI: 10.1016/j.cub.2020.11.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/12/2020] [Accepted: 11/11/2020] [Indexed: 12/21/2022]
Abstract
Sexual selection results in sex-specific characters like the conspicuously pigmented extension of the ventral tip of the caudal fin-the "sword"-in males of several species of Xiphophorus fishes. To uncover the genetic architecture underlying sword formation and to identify genes that are associated with its development, we characterized the sword transcriptional profile and combined it with genetic mapping approaches. Results showed that the male ornament of swordtails develops from a sexually non-dimorphic prepattern of transcription factors in the caudal fin. Among genes that constitute the exclusive sword transcriptome and are located in the genomic region associated with this trait we identify the potassium channel, Kcnh8, as a sword development gene. In addition to its neural function kcnh8 performs a known role in fin growth. These findings indicate that during evolution of swordtails a brain gene has been co-opted for an additional novel function in establishing a male ornament.
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Affiliation(s)
- Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Jenny Ormanns
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Cornelia Schmidt
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Jennifer L Anderson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA
| | - Julian Catchen
- Department of Animal Biology, University of Illinois, Urbana, IL 6812, USA
| | - Catherine Wilson
- Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA
| | - Dietmar Geiger
- Julius-von-Sachs-Institute for Biosciences, Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | | | - Sudha Sudaram
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Christoph Winkler
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Rainer Hedrich
- Julius-von-Sachs-Institute for Biosciences, Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Wesley C Warren
- 440G Bond Life Sciences Center, 1201 Rollins Street, University of Missouri, Columbia, MO 65211, USA
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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12
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Abe K, Shimada A, Tayama S, Nishikawa H, Kaneko T, Tsuda S, Karaiwa A, Matsui T, Ishitani T, Takeda H. Horizontal Boundary Cells, a Special Group of Somitic Cells, Play Crucial Roles in the Formation of Dorsoventral Compartments in Teleost Somite. Cell Rep 2020; 27:928-939.e4. [PMID: 30995487 DOI: 10.1016/j.celrep.2019.03.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/27/2019] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Establishment of robust gene expression boundary is crucial for creating elaborate morphology during development. However, mechanisms underlying boundary formation have been extensively studied only in a few model systems. We examined the establishment of zic1/zic4-expression boundary demarcating dorsoventral boundary of the entire trunk of medaka fish (Oryzias latipes) and identified a subgroup of dermomyotomal cells called horizontal boundary cells (HBCs) as crucial players for the boundary formation. Embryological and genetic analyses demonstrated that HBCs play crucial roles in the two major events of the process, i.e., refinement and maintenance. In the refinement, HBCs could serve as a chemical barrier against Wnts from the neural tube by expressing Hhip. At later stages, HBCs participate in the maintenance of the boundary by differentiating into the horizontal myoseptum physically inhibiting cell mixing across the boundary. These findings reveal the mechanisms underlying the dorsoventral boundary in the teleost trunk by specialized boundary cells.
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Affiliation(s)
- Kota Abe
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Molecular Medicine, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan
| | - Atsuko Shimada
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sayaka Tayama
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hotaka Nishikawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takuya Kaneko
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sachiko Tsuda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Saitama University Brain Science Institute, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Research and Development Bureau, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Akari Karaiwa
- Gene Regulation Research, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Takaaki Matsui
- Gene Regulation Research, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tohru Ishitani
- Department of Molecular Medicine, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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13
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Ahi EP, Richter F, Lecaudey LA, Sefc KM. Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species. Sci Rep 2019; 9:9052. [PMID: 31227799 PMCID: PMC6588699 DOI: 10.1038/s41598-019-45599-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/11/2019] [Indexed: 01/09/2023] Open
Abstract
Comparative analyses of gene regulation inform about the molecular basis of phenotypic trait evolution. Here, we address a fin shape phenotype that evolved multiple times independently across teleost fish, including several species within the family Cichlidae. In a previous study, we proposed a gene regulatory network (GRN) involved in the formation and regeneration of conspicuous filamentous elongations adorning the unpaired fins of the Neolamprologus brichardi. Here, we tested the members of this network in the blockhead cichlid, Steatocranus casuarius, which displays conspicuously elongated dorsal and moderately elongated anal fins. Our study provided evidence for differences in the anatomy of fin elongation and suggested gene regulatory divergence between the two cichlid species. Only a subset of the 20 genes tested in S. casuarius showed the qPCR expression patterns predicted from the GRN identified in N. brichardi, and several of the gene-by-gene expression correlations differed between the two cichlid species. In comparison to N. brichardi, gene expression patterns in S. casuarius were in better (but not full) agreement with gene regulatory interactions inferred in zebrafish. Within S. casuarius, the dorsoventral asymmetry in ornament expression was accompanied by differences in gene expression patterns, including potential regulatory differentiation, between the anal and dorsal fin.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria. .,Department of Comparative Physiology, Uppsala University, Norbyvägen 18A, SE-75 236, Uppsala, Sweden.
| | - Florian Richter
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | | | - Kristina M Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
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14
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Onimaru K, Kuraku S. Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications. Brief Funct Genomics 2019; 17:352-361. [PMID: 29566222 PMCID: PMC6158797 DOI: 10.1093/bfgp/ely008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as ‘chronological reconstruction of ohnolog functions (CHROF)’. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.
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Affiliation(s)
- Koh Onimaru
- RIKEN Center for Life Science Technologies, Kobe, Hyogo Japan.,Department of biological science, Tokyo Institute of Technology, Tokyo, Japan
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15
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An Evolutionarily Conserved Mesodermal Enhancer in Vertebrate Zic3. Sci Rep 2018; 8:14954. [PMID: 30297839 PMCID: PMC6175831 DOI: 10.1038/s41598-018-33235-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/25/2018] [Indexed: 11/08/2022] Open
Abstract
Zic3 encodes a zinc finger protein essential for the development of meso-ectodermal tissues. In mammals, Zic3 has important roles in the development of neural tube, axial skeletons, left-right body axis, and in maintaining pluripotency of ES cells. Here we characterized cis-regulatory elements required for Zic3 expression. Enhancer activities of human-chicken-conserved noncoding sequences around Zic1 and Zic3 were screened using chick whole-embryo electroporation. We identified enhancers for meso-ectodermal tissues. Among them, a mesodermal enhancer (Zic3-ME) in distant 3' flanking showed robust enhancement of reporter gene expression in the mesodermal tissue of chicken and mouse embryos, and was required for mesodermal Zic3 expression in mice. Zic3-ME minimal core region is included in the DNase hypersensitive region of ES cells, mesoderm, and neural progenitors, and was bound by T (Brachyury), Eomes, Lef1, Nanog, Oct4, and Zic2. Zic3-ME is derived from an ancestral sequence shared with a sequence encoding a mitochondrial enzyme. These results indicate that Zic3-ME is an integrated cis-regulatory element essential for the proper expression of Zic3 in vertebrates, serving as a hub for a gene regulatory network including Zic3.
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16
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Tohmonda T, Kamiya A, Ishiguro A, Iwaki T, Fujimi TJ, Hatayama M, Aruga J. Identification and Characterization of Novel Conserved Domains in Metazoan Zic Proteins. Mol Biol Evol 2018; 35:2205-2229. [DOI: 10.1093/molbev/msy122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Takahide Tohmonda
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akiko Kamiya
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akira Ishiguro
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Takashi Iwaki
- Meguro Parasitological Museum, Meguro-Ku, Tokyo, Japan
| | - Takahiko J Fujimi
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Minoru Hatayama
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
| | - Jun Aruga
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
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17
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Abstract
Zic family genes encode five C2H2-type zinc finger domain-containing proteins that have many roles in animal development and maintenance. Recent phylogenetic analyses showed that Zic family genes are distributed in metazoans (multicellular animals), except Porifera (sponges) and Ctenophora (comb jellies). The sequence comparisons revealed that the zinc finger domains were absolutely conserved among the Zic family genes. Zic zinc finger domains are similar to, but distinct from those of the Gli, Glis, and Nkl gene family, and these zinc finger protein families are proposed to have been derived from a common ancestor gene. The Gli-Glis-Nkl-Zic superfamily and some other eukaryotic zinc finger proteins share a tandem CWCH2 (tCWCH2) motif, a hallmark for inter-zinc finger interaction between two adjacent C2H2 zinc fingers. In Zic family proteins, there exist additional evolutionally conserved domains known as ZOC and ZFNC, both of which may have appeared before cnidarian-bilaterian divergence. Comparison of the exon-intron boundaries in the Zic zinc finger domains revealed an intron (A-intron) that was absolutely conserved in bilaterians (metazoans with bilateral symmetry) and a placozoan (a simple nonparasitic metazoan). In vertebrates, there are five to seven Zic paralogs among which Zic1, Zic2, and Zic3 are generated through a tandem gene duplication and carboxy-terminal truncation in a vertebrate common ancestor, sharing a conserved carboxy-terminal sequence. Several hypotheses have been proposed to explain the Zic family phylogeny, including their origin, unique features in the first and second zinc finger motif, evolution of the nuclear localization signal, significance of the animal taxa-selective degeneration, gene multiplication in the vertebrate lineage, and involvement in the evolutionary alteration of the animal body plan.
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Abe K, Kawanishi T, Takeda H. Zic Genes in Teleosts: Their Roles in Dorsoventral Patterning in the Somite. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:141-156. [DOI: 10.1007/978-981-10-7311-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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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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Seki S, Kusano K, Lee S, Iwasaki Y, Yagisawa M, Ishida M, Hiratsuka T, Sasado T, Naruse K, Yoshizaki G. Production of the medaka derived from vitrified whole testes by germ cell transplantation. Sci Rep 2017; 7:43185. [PMID: 28256523 PMCID: PMC5335710 DOI: 10.1038/srep43185] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/19/2017] [Indexed: 11/14/2022] Open
Abstract
The medaka (Oryzias latipes) is a teleost model distinguished from other model organisms by the presence of inbred strains, wild stocks, and related species. Cryopreservation guarantees preservation of these unique biological resources. However, because of their large size, cryopreservation techniques for their eggs and embryos have not been established. In the present study, we established a methodology to produce functional gametes from cryopreserved testicular cells (TCs). Whole testes taken from medaka were cryopreserved by vitrification. After thawing, the cells dissociated from cryopreserved testicular tissues were intraperitoneally transplanted into sterile triploid hatchlings. Some cells, presumably spermatogonial stem cells, migrated into the genital ridges of recipients and resulted in the production of eggs or sperm, based on sex of the recipient. Mating of recipients resulted in successful production of cryopreserved TC-derived offspring. We successfully produced individuals from the Kaga inbred line, an endangered wild population in Tokyo, and a sub-fertile mutant (wnt4b−/−) from cryopreserved their TCs. This methodology facilitates semi-permanent preservation of various medaka strains.
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Affiliation(s)
- Shinsuke Seki
- Bioscience Education and Research Support Center, Akita University, 1-1-1 Hondo, Akita, Akita 010-8543, Japan.,Department of Marine Bioscience, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Kazunari Kusano
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Seungki Lee
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Yoshiko Iwasaki
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Masaru Yagisawa
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Mariko Ishida
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Tadashi Hiratsuka
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Takao Sasado
- Laboratory of Bioresources, National Institute for Basic Biology, 38 Saigo-naka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, 38 Saigo-naka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| | - Goro Yoshizaki
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
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21
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Ota KG, Abe G. Goldfish morphology as a model for evolutionary developmental biology. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2016; 5:272-95. [PMID: 26952007 PMCID: PMC6680352 DOI: 10.1002/wdev.224] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 12/06/2015] [Accepted: 12/07/2015] [Indexed: 12/11/2022]
Abstract
Morphological variation of the goldfish is known to have been established by artificial selection for ornamental purposes during the domestication process. Chinese texts that date to the Song dynasty contain descriptions of goldfish breeding for ornamental purposes, indicating that the practice originated over one thousand years ago. Such a well-documented goldfish breeding process, combined with the phylogenetic and embryological proximities of this species with zebrafish, would appear to make the morphologically diverse goldfish strains suitable models for evolutionary developmental (evodevo) studies. However, few modern evodevo studies of goldfish have been conducted. In this review, we provide an overview of the historical background of goldfish breeding, and the differences between this teleost and zebrafish from an evolutionary perspective. We also summarize recent progress in the field of molecular developmental genetics, with a particular focus on the twin-tail goldfish morphology. Furthermore, we discuss unanswered questions relating to the evolution of the genome, developmental robustness, and morphologies in the goldfish lineage, with the goal of blazing a path toward an evodevo study paradigm using this teleost species as a new model species. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Kinya G Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Gembu Abe
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
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22
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23
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Otsuka T, Tsukahara T, Takeda H. Development of the pancreas in medaka, Oryzias latipes, from embryo to adult. Dev Growth Differ 2015; 57:557-69. [PMID: 26435359 DOI: 10.1111/dgd.12237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 07/17/2015] [Accepted: 07/19/2015] [Indexed: 12/17/2022]
Abstract
To address conserved and unique features of fish pancreas development, we performed extensive analyses of pancreatic development in medaka embryos and adults using pdx1- and ptf1a-transgenic medaka, in situ hybridization and immunohistochemistry. The markers used in these analyses included pdx1, nkx6.1, nkx6.2, nkx2.2, Islet1, insulin, Somatostatin, glucagon, ptf1a, ela3l, trypsin, and amylase. The double transgenic (Tg) fish produced in the present study visualizes the development of endocrine (pdx1+) and exocrine (ptf1a+) parts simultaneously in living fishes. Like other vertebrates, the medaka pancreas develops as two (dorsal and ventral) buds in the anterior gut tube, which soon fuse into a single anlagen. The double Tg fish demonstrates that the differential property between the two buds is already established at the initial phase of bud development as indicated by strong pdx1 expression in the dorsal one. This Tg fish also allowed us to examine the gross morphology and the structure of adult pancreas and revealed unique characters of medaka pancreas such as broad and multiple connections with the gut tube along the anterior-posterior axis.
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Affiliation(s)
- Takayoshi Otsuka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tatsuya Tsukahara
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,JST, CREST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
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24
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Fleming A, Kishida MG, Kimmel CB, Keynes RJ. Building the backbone: the development and evolution of vertebral patterning. Development 2015; 142:1733-44. [PMID: 25968309 DOI: 10.1242/dev.118950] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The segmented vertebral column comprises a repeat series of vertebrae, each consisting of two key components: the vertebral body (or centrum) and the vertebral arches. Despite being a defining feature of the vertebrates, much remains to be understood about vertebral development and evolution. Particular controversy surrounds whether vertebral component structures are homologous across vertebrates, how somite and vertebral patterning are connected, and the developmental origin of vertebral bone-mineralizing cells. Here, we assemble evidence from ichthyologists, palaeontologists and developmental biologists to consider these issues. Vertebral arch elements were present in early stem vertebrates, whereas centra arose later. We argue that centra are homologous among jawed vertebrates, and review evidence in teleosts that the notochord plays an instructive role in segmental patterning, alongside the somites, and contributes to mineralization. By clarifying the evolutionary relationship between centra and arches, and their varying modes of skeletal mineralization, we can better appreciate the detailed mechanisms that regulate and diversify vertebral patterning.
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Affiliation(s)
- Angeleen Fleming
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Marcia G Kishida
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Charles B Kimmel
- Institute of Neuroscience, 1254 University of Oregon, Eugene OR 97403-1254, USA
| | - Roger J Keynes
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
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25
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Harris MP, Henke K, Hawkins MB, Witten PE. Fish is Fish: the use of experimental model species to reveal causes of skeletal diversity in evolution and disease. ZEITSCHRIFT FUR ANGEWANDTE ICHTHYOLOGIE = JOURNAL OF APPLIED ICHTHYOLOGY 2014; 30:616-629. [PMID: 25221374 PMCID: PMC4159207 DOI: 10.1111/jai.12533] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fishes are wonderfully diverse. This variety is a result of the ability of ray-finned fishes to adapt to a wide range of environments, and has made them more specious than the rest of vertebrates combined. With such diversity it is easy to dismiss comparisons between distantly related fishes in efforts to understand the biology of a particular fish species. However, shared ancestry and the conservation of developmental mechanisms, morphological features and physiology provide the ability to use comparative analyses between different organisms to understand mechanisms of development and physiology. The use of species that are amenable to experimental investigation provides tools to approach questions that would not be feasible in other 'non-model' organisms. For example, the use of small teleost fishes such as zebrafish and medaka has been powerful for analysis of gene function and mechanisms of disease in humans, including skeletal diseases. However, use of these fish to aid in understanding variation and disease in other fishes has been largely unexplored. This is especially evident in aquaculture research. Here we highlight the utility of these small laboratory fishes to study genetic and developmental factors that underlie skeletal malformations that occur under farming conditions. We highlight several areas in which model species can serve as a resource for identifying the causes of variation in economically important fish species as well as to assess strategies to alleviate the expression of the variant phenotypes in farmed fish. We focus on genetic causes of skeletal deformities in the zebrafish and medaka that closely resemble phenotypes observed both in farmed as well as natural populations of fishes.
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Affiliation(s)
- M P Harris
- Department of Genetics, Harvard Medical School, Boston, MA, USA ; Department of Orthopaedic Research, Boston Children's Hospital, Boston, MA, USA
| | - K Henke
- Department of Genetics, Harvard Medical School, Boston, MA, USA ; Department of Orthopaedic Research, Boston Children's Hospital, Boston, MA, USA
| | - M B Hawkins
- Department of Genetics, Harvard Medical School, Boston, MA, USA ; Department of Orthopaedic Research, Boston Children's Hospital, Boston, MA, USA ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - P E Witten
- Department of Biology, Ghent University, Ghent, Belgium
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26
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Nakamura R, Tsukahara T, Qu W, Ichikawa K, Otsuka T, Ogoshi K, Saito TL, Matsushima K, Sugano S, Hashimoto S, Suzuki Y, Morishita S, Takeda H. Large hypomethylated domains serve as strong repressive machinery for key developmental genes in vertebrates. Development 2014; 141:2568-80. [PMID: 24924192 DOI: 10.1242/dev.108548] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA methylation is a fundamental epigenetic modification in vertebrate genomes and a small fraction of genomic regions is hypomethylated. Previous studies have implicated hypomethylated regions in gene regulation, but their functions in vertebrate development remain elusive. To address this issue, we generated epigenomic profiles that include base-resolution DNA methylomes and histone modification maps from both pluripotent cells and mature organs of medaka fish and compared the profiles with those of human ES cells. We found that a subset of hypomethylated domains harbor H3K27me3 (K27HMDs) and their size positively correlates with the accumulation of H3K27me3. Large K27HMDs are conserved between medaka and human pluripotent cells and predominantly contain promoters of developmental transcription factor genes. These key genes were found to be under strong transcriptional repression, when compared with other developmental genes with smaller K27HMDs. Furthermore, human-specific K27HMDs show an enrichment of neuronal activity-related genes, which suggests a distinct regulation of these genes in medaka and human. In mature organs, some of the large HMDs become shortened by elevated DNA methylation and associate with sustained gene expression. This study highlights the significance of domain size in epigenetic gene regulation. We propose that large K27HMDs play a crucial role in pluripotent cells by strictly repressing key developmental genes, whereas their shortening consolidates long-term gene expression in adult differentiated cells.
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Affiliation(s)
- Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tatsuya Tsukahara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Wei Qu
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
| | - Takayoshi Otsuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Katsumi Ogoshi
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Taro L Saito
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
| | - Kouji Matsushima
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Sumio Sugano
- Department of Medical Genome, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Shinichi Hashimoto
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan Department of Laboratory Medicine, Kanazawa University, Kanazawa 920-8641, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
| | - Shinichi Morishita
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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27
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Doosey MH, Domke ND. Early Development of the Caudal Fin Skeleton of Capelin,Mallotus villosus(Osmeridae). COPEIA 2014. [DOI: 10.1643/cg-13-098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Moriyama Y, Takeda H. Evolution and development of the homocercal caudal fin in teleosts. Dev Growth Differ 2013; 55:687-98. [PMID: 24102138 DOI: 10.1111/dgd.12088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/19/2013] [Accepted: 08/19/2013] [Indexed: 12/18/2022]
Abstract
The vertebrate caudal skeleton is one of the most innovative structures in vertebrate evolution and has been regarded as an excellent model for functional morphology, a discipline that relates a structure to its function. Teleosts have an internally-asymmetrical caudal fin, called the homocercal caudal fin, formed by the upward bending of the caudal-most portion of the body axis, the ural region. This homocercal type of the caudal fin ensures powerful and complex locomotion and is thought to be one of the most important evolutionary innovations for teleosts during adaptive radiation in an aquatic environment. In this review, we summarize the past and present research of fish caudal skeletons, especially focusing on the homocercal caudal fin seen in teleosts. A series of studies with a medaka spontaneous mutant have provided important insight into the evolution and development of the homocercal caudal skeleton. By comparing developmental processes in various vertebrates, we propose a scenario for acquisition and morphogenesis of the homocercal caudal skeleton during vertebrate evolution.
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Affiliation(s)
- Yuuta Moriyama
- Cardiovascular Regeneration, Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan
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29
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Kawanishi T, Kaneko T, Moriyama Y, Kinoshita M, Yokoi H, Suzuki T, Shimada A, Takeda H. Modular development of the teleost trunk along the dorsoventral axis and zic1/zic4 as selector genes in the dorsal module. Development 2013; 140:1486-96. [PMID: 23462471 DOI: 10.1242/dev.088567] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Teleost fish exhibit remarkable diversity in morphology, such as fins and coloration, particularly on the dorsal side. These structures are evolutionary adaptive because their back is highly visible to other individuals. However, owing to the late phenotypic appearance (from larva to adult) and lack of appropriate mutants, the genetic mechanisms that regulate these dorsoventrally asymmetric external patterns are largely unknown. To address this, we have analyzed the spontaneous medaka mutant Double anal fin (Da), which exhibits a mirror-image duplication of the ventral half across the lateral midline from larva to adult. Da is an enhancer mutant for zic1 and zic4 in which their expression in dorsal somites is lost. We show that the dorsoventral polarity in Da somites is lost and then demonstrate using transplantation techniques that somites and their derived tissues globally determine the multiple dorsal-specific characteristics of the body (fin morphology and pigmentation) from embryo to adult. Intriguingly, the zic1/zic4 expression in the wild type persists throughout life in the dorsal parts of somite derivatives, i.e. the myotome, dermis and vertebrae, forming a broad dorsal domain in the trunk. Comparative analysis further implies a central role for zic1/zic4 in morphological diversification of the teleost body. Taken together, we propose that the teleost trunk consists of dorsal/ventral developmental modules and that zic1/zic4 in somites function as selector genes in the dorsal module to regulate multiple dorsal morphologies.
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Affiliation(s)
- Toru Kawanishi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo, Japan
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30
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Washio Y, Aritaki M, Fujinami Y, Shimizu D, Yokoi H, Suzuki T. Ocular-Side Lateralization of Adult-Type Chromatophore Precursors: Development of Pigment Asymmetry in Metamorphosing Flounder Larvae. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:151-65. [DOI: 10.1002/jez.b.22491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/09/2013] [Accepted: 01/22/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Youhei Washio
- Laboratory of Marine Life Science and Genetics; Graduate School of Agricultural Science, Tohoku University; Sendai; Japan
| | - Masato Aritaki
- Seikai National Fisheries Research Institute; Fisheries Research Agency; Nagasaki; Japan
| | - Yuichiro Fujinami
- Miyako Station; Tohoku National Fisheries Research Institute, Fisheries Research Agency; Iwate; Japan
| | - Daisuke Shimizu
- Miyako Station; Tohoku National Fisheries Research Institute, Fisheries Research Agency; Iwate; Japan
| | - Hayato Yokoi
- Laboratory of Marine Life Science and Genetics; Graduate School of Agricultural Science, Tohoku University; Sendai; Japan
| | - Tohru Suzuki
- Laboratory of Marine Life Science and Genetics; Graduate School of Agricultural Science, Tohoku University; Sendai; Japan
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