Gibbon genome and the fast karyotype evolution of small apes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-09-10

AUTHORS

Lucia Carbone, R. Alan Harris, Sante Gnerre, Krishna R. Veeramah, Belen Lorente-Galdos, John Huddleston, Thomas J. Meyer, Javier Herrero, Christian Roos, Bronwen Aken, Fabio Anaclerio, Nicoletta Archidiacono, Carl Baker, Daniel Barrell, Mark A. Batzer, Kathryn Beal, Antoine Blancher, Craig L. Bohrson, Markus Brameier, Michael S. Campbell, Oronzo Capozzi, Claudio Casola, Giorgia Chiatante, Andrew Cree, Annette Damert, Pieter J. de Jong, Laura Dumas, Marcos Fernandez-Callejo, Paul Flicek, Nina V. Fuchs, Ivo Gut, Marta Gut, Matthew W. Hahn, Jessica Hernandez-Rodriguez, LaDeana W. Hillier, Robert Hubley, Bianca Ianc, Zsuzsanna Izsvák, Nina G. Jablonski, Laurel M. Johnstone, Anis Karimpour-Fard, Miriam K. Konkel, Dennis Kostka, Nathan H. Lazar, Sandra L. Lee, Lora R. Lewis, Yue Liu, Devin P. Locke, Swapan Mallick, Fernando L. Mendez, Matthieu Muffato, Lynne V. Nazareth, Kimberly A. Nevonen, Majesta O’Bleness, Cornelia Ochis, Duncan T. Odom, Katherine S. Pollard, Javier Quilez, David Reich, Mariano Rocchi, Gerald G. Schumann, Stephen Searle, James M. Sikela, Gabriella Skollar, Arian Smit, Kemal Sonmez, Boudewijn ten Hallers, Elizabeth Terhune, Gregg W. C. Thomas, Brygg Ullmer, Mario Ventura, Jerilyn A. Walker, Jeffrey D. Wall, Lutz Walter, Michelle C. Ward, Sarah J. Wheelan, Christopher W. Whelan, Simon White, Larry J. Wilhelm, August E. Woerner, Mark Yandell, Baoli Zhu, Michael F. Hammer, Tomas Marques-Bonet, Evan E. Eichler, Lucinda Fulton, Catrina Fronick, Donna M. Muzny, Wesley C. Warren, Kim C. Worley, Jeffrey Rogers, Richard K. Wilson, Richard A. Gibbs

ABSTRACT

Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation ∼5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat. More... »

PAGES

195-201

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  • Journal

    TITLE

    Nature

    ISSUE

    7517

    VOLUME

    513

    Author Affiliations

  • Bioinformatics and Computational Biology Division, Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.,
  • Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,
  • Nabsys, 60 Clifford Street, Providence, Rhode Island 02903, USA.,
  • Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11790, USA.,
  • IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain.,
  • Howard Hughes Medical Institute, 1705 NE Pacific Street, Seattle, Washington 98195, USA.,
  • Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road Portland, Oregon 97239, USA.,
  • Present Address: Present addresses: Bill Lyons Informatics Center, UCL Cancer Institute, University College London, London WC1E 6DD, UK (J.He); Seven Bridges Genomics, Cambridge, Massachusetts 02138, USA (D.P.L.); Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA (F.L.M.); BioNano Genomics, San Diego, California 92121, USA (B.t.H.); University of Chicago, Department of Human Genetics, Chicago, Illinois 60637, USA (M.C.W.); Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, USA (C.W.W.); The CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (B.Z.).,
  • Leibniz Institute for Primate Research, Gene Bank of Primates, German Primate Center, Göttingen 37077, Germany.,
  • European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,
  • Department of Biology, University of Bari, Via Orabona 4, 70125, Bari, Italy.,
  • Department of Genome Sciences, University of Washington School of Medicine, Seattle, 98195 Washington USA
  • Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803 Louisiana USA
  • European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,
  • University of Paul Sabatier, Toulouse 31062, France.,
  • Department of Oncology, Division of Biostatistics and Bioinformatics, The Johns Hopkins University School of Medicine, Baltimore, 21205 Maryland USA
  • University of Utah, Salt Lake City, Utah 84112, USA.,
  • Department of Ecosystem Science and Management, Texas A&M University, College Station, 77843 Texas USA
  • Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,
  • Babes-Bolyai-University, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Cluj-Napoca 400084, Romania.,
  • Children’s Hospital Oakland Research Institute, BACPAC Resources, Oakland, 94609 California USA
  • Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, 80045 Colorado USA
  • Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany.,
  • Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona 08028, Spain.,
  • Indiana University, School of Informatics and Computing, Bloomington, 47408 Indiana USA
  • The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.,
  • Institute for Systems Biology, Seattle, 98109-5234 Washington USA
  • Department of Anthropology, The Pennsylvania State University, University Park, 16802 Pennsylvania USA
  • ARL Division of Biotechnology, University of Arizona, Tucson, 85721 Arizona USA
  • Department of Developmental Biology, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburg, 15261 Pennsylvania USA
  • Department of Genetics, Harvard Medical School, Boston, 02115 Massachusetts USA
  • Division of Neuroscience, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, Oregon 97006, USA.,
  • University of Cambridge, Cancer Research UK-Cambridge Institute, Cambridge CB2 0RE, UK.,
  • Division of Biostatistics, University of California, San Francisco, 94143-0794 California USA
  • Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany.,
  • Gibbon Conservation Center, 19100 Esguerra Rd, Santa Clarita, California 91350, USA.,
  • Oregon Health & Science University, Center for Spoken Language Understanding, Institute on Development and Disability, Portland, 97239 Oregon USA
  • Louisiana State University, School of Electrical Engineering and Computer Science, Baton Rouge, 70803 Louisiana USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature13679

    DOI

    http://dx.doi.org/10.1038/nature13679

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1010503391

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25209798


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    60 expansion
    61 fast karyotype evolution
    62 forelimb development
    63 genes
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    65 genome plasticity
    66 genus
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    68 gibbon genera
    69 gibbon genome
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    77 key nodes
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    80 mechanism
    81 molecular mechanisms
    82 monkeys
    83 near-instantaneous radiation
    84 nodes
    85 northern white-cheeked gibbon (Nomascus leucogenys) genome
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    87 plasticity
    88 positive selection
    89 possible molecular mechanisms
    90 premature termination site
    91 primate phylogeny
    92 propensity
    93 radiation
    94 rate
    95 rearrangement
    96 retrotransposons
    97 segregation genes
    98 selection
    99 signatures
    100 sites
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    102 small arboreal apes
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    104 tissue
    105 transcription
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