ArticleNature genetics2016
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
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Article in Nature genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 348 papers.
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348citing papers in PubMed
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348 citing papers in PubMed, 666 citations in OpenAlex.
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288 more citing papers are in PubMed but not listed here.
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Authors and funding
61 authors at 20 institutions in 16 countries.
Ingo BraaschInstitute of Neuroscience, University of Oregon, Eugene, Oregon, USA.
Andrew R GehrkeDepartment of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA.
Jeramiah J SmithDepartment of Biology, University of Kentucky, Lexington, Kentucky, USA.ORCID http://orcid.org/0000-0001-5333-5531
Kazuhiko KawasakiDepartment of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA.
Tereza ManousakiInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece.
Jeremy PasquierInstitut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France.
Angel AmoresInstitute of Neuroscience, University of Oregon, Eugene, Oregon, USA.
Thomas DesvignesInstitute of Neuroscience, University of Oregon, Eugene, Oregon, USA.
Peter BatzelInstitute of Neuroscience, University of Oregon, Eugene, Oregon, USA.
Julian CatchenDepartment of Animal Biology, University of Illinois, Urbana-Champaign, Illinois, USA.
Aaron M BerlinBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Michael S CampbellEccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA.
Daniel BarrellWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
Kyle J MartinDepartment of Zoology, University of Oxford, Oxford, UK.
John F MulleySchool of Biological Sciences, Bangor University, Bangor, UK.ORCID http://orcid.org/0000-0002-1537-7316
Vydianathan RaviComparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.ORCID http://orcid.org/0000-0003-0807-7697
Alison P LeeComparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.
Tetsuya NakamuraDepartment of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA.
Domitille ChalopinInstitut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France.
Shaohua FanDepartment of Biology, University of Konstanz, Konstanz, Germany.
Dustin WciselDepartment of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA.
Cristian CañestroDepartament de Genètica, Universitat de Barcelona, Barcelona, Spain.ORCID http://orcid.org/0000-0003-4623-8105
Jason SydesInstitute of Neuroscience, University of Oregon, Eugene, Oregon, USA.ORCID http://orcid.org/0000-0003-4187-2828
Felix E G BeaudryDepartment of Biology, University of Victoria, Victoria, British Columbia, Canada.
Yi SunCenter for Circadian Clocks, Soochow University, Suzhou, China.
Jana HertelBioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany.
Michael J BeamInstitute of Neuroscience, University of Oregon, Eugene, Oregon, USA.
Mario FasoldBioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany.
Mikio IshiyamaDepartment of Dental Hygiene, Nippon Dental University College at Niigata, Niigata, Japan.
Jeremy JohnsonBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Steffi KehrBioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany.
Marcia LaraBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
John H LetawInstitute of Neuroscience, University of Oregon, Eugene, Oregon, USA.ORCID http://orcid.org/0000-0003-0030-0831
Gary W LitmanDepartment of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA.
Ronda T LitmanDepartment of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA.
Masato MikamiDepartment of Microbiology, Nippon Dental University School of Life Dentistry at Niigata, Niigata, Japan.
Tatsuya OtaDepartment of Evolutionary Studies of Biosystems, SOKENDAI (Graduate University for Advanced Studies), Hayama, Japan.
Nil Ratan SahaMolecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA.
Louise WilliamsBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Peter F StadlerBioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany.
Han WangCenter for Circadian Clocks, Soochow University, Suzhou, China.ORCID http://orcid.org/0000-0003-2420-3147
John S TaylorDepartment of Biology, University of Victoria, Victoria, British Columbia, Canada.
Quenton FontenotDepartment of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA.
Allyse FerraraDepartment of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA.
Stephen M J SearleWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
Bronwen AkenWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.ORCID http://orcid.org/0000-0002-3032-4095
Mark YandellEccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA.
Igor SchneiderInstituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Brazil.
Jeffrey A YoderDepartment of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA.ORCID http://orcid.org/0000-0002-6083-1311
Jean-Nicolas VolffInstitut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France.
Axel MeyerDepartment of Biology, University of Konstanz, Konstanz, Germany.ORCID http://orcid.org/0000-0002-0888-8193
Chris T AmemiyaMolecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA.
Byrappa VenkateshComparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.
Peter W H HollandDepartment of Zoology, University of Oxford, Oxford, UK.
Yann GuiguenInstitut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France.
Julien BobeInstitut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France.ORCID http://orcid.org/0000-0002-9355-8227
Neil H ShubinDepartment of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA.
Federica Di PalmaBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Jessica AlföldiBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID http://orcid.org/0000-0001-9713-6200
Kerstin Lindblad-TohBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
John H PostlethwaitInstitute of Neuroscience, University of Oregon, Eugene, Oregon, USA.
University of Oregon · USBroad Institute · USLeipzig University · DEAgency for Science, Technology and Research · SGLaboratoire de Physiologie et Génomique des Poissons · FRUniversity of Chicago · USBenaroya Research InstituteCollege of Medical Sciences · NPÉcole Normale Supérieure de Lyon · FREuropean Bioinformatics Institute · GBNicholls State University · USNippon Dental University · JPNorth Carolina State University · USUniversity of Konstanz · DEUniversity of Oxford · GBUniversity of South Florida St. Petersburg · USUniversity of Utah · USUniversity of Victoria · CABangor University · GBHellenic Centre for Marine Research · GR
Funding
Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6MResources for Teleost Gene Duplicates and Human DiseaseR01OD011116 · OD · UNIVERSITY OF OREGON · PI POSTLETHWAIT, JOHN H. · 2012 to 2020
$5.4MRESOURCES FOR TELEOST GENE DUPLICATES AND HUMAN DISEASER01RR020833 · NCRR · UNIVERSITY OF OREGON · PI POSTLETHWAIT, JOHN H. · 2005 to 2011
$3.6MTraining Program in Developmental BiologyT32HD055164 · NICHD · UNIVERSITY OF CHICAGO · PI Sally Horne-Badovinac, Paschalis Kratsios · 2008 to 2026
$3.6MNovel Innate Immune Receptors in ZebrafishR01AI057559 · NIAID · UNIVERSITY OF SOUTH FLORIDA · PI LITMAN, GARY WILLIAM · 2005 to 2013
$3.4MAdvancing the Scientific Potential of Transcriptomics in Aquatic ModelsR24OD011199 · OD · UNIVERSITY OF OREGON · PI CRESKO, WILLIAM A, POSTLETHWAIT, JOHN H. · 2012 to 2014
$1.8MDevelopmental and genomic studies on the agnatha VLR systemR21GM079492 · NIGMS · BENAROYA RESEARCH INST AT VIRGINIA MASON · PI AMEMIYA, CHRIS T. · 2007 to 2008
$503kGenomics Resources and Infrastucture for the ZebrafishR24OD010922 · OD · BENAROYA RESEARCH INST AT VIRGINIA MASON · PI AMEMIYA, CHRIS T. · 2012 to 2012
$448kEuropean Research Council 268513NCRR NIH HHS R01 RR020833NHGRI NIH HHS U54 HG003067NHGRI NIH HHS U54 HG03067NIAID NIH HHS R01 AI057559NICHD NIH HHS T32 HD055164NIGMS NIH HHS R01 GM079492NIGMS NIH HHS R21 GM079492NIH HHS R01 OD011116NIH HHS R24 OD010922NIH HHS R24 OD01119004Wellcome TrustWellcome Trust WT095908Wellcome Trust WT098051
Abstract
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
Indexed as
AnimalsEvolution, MolecularFemaleFishesGenomeHumansKaryotypeModels, GeneticOrgan SpecificitySequence Analysis, DNATranscriptome
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