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Gibbon genome and the fast karyotype evolution of small apes.
Carbone, Lucia; Harris, R Alan; Gnerre, Sante; Veeramah, Krishna R; Lorente-Galdos, Belen; Huddleston, John; Meyer, Thomas J; Herrero, Javier; Roos, Christian; Aken, Bronwen; Anaclerio, Fabio; Archidiacono, Nicoletta; Baker, Carl; Barrell, Daniel; Batzer, Mark A; Beal, Kathryn; Blancher, Antoine; Bohrson, Craig L; Brameier, Markus; Campbell, Michael S; Capozzi, Oronzo; Casola, Claudio; Chiatante, Giorgia; Cree, Andrew; Damert, Annette; de Jong, Pieter J; Dumas, Laura; Fernandez-Callejo, Marcos; Flicek, Paul; Fuchs, Nina V; Gut, Ivo; Gut, Marta; Hahn, Matthew W; Hernandez-Rodriguez, Jessica; Hillier, LaDeana W; Hubley, Robert; Ianc, Bianca; Izsvák, Zsuzsanna; Jablonski, Nina G; Johnstone, Laurel M; Karimpour-Fard, Anis; Konkel, Miriam K; Kostka, Dennis; Lazar, Nathan H; Lee, Sandra L; Lewis, Lora R; Liu, Yue; Locke, Devin P; Mallick, Swapan; Mendez, Fernando L.
Affiliation
  • Carbone L; 1] Oregon Health &Science University, Department of Behavioral Neuroscience, 3181 SW Sam Jackson Park Road Portland, Oregon 97239, USA. [2] Oregon National Primate Research Center, Division of Neuroscience, 505 NW 185th Avenue, Beaverton, Oregon 97006, USA. [3] Oregon Health &Science Univers
  • Harris RA; Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, Texas 77030, USA.
  • Gnerre S; Nabsys, 60 Clifford Street, Providence, Rhode Island 02903, USA.
  • Veeramah KR; 1] University of Arizona, ARL Division of Biotechnology, Tucson, Arizona 85721, USA. [2] Stony Brook University, Department of Ecology and Evolution, Stony Brook, New York 11790, USA.
  • Lorente-Galdos B; IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain.
  • Huddleston J; 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA. [2] Howard Hughes Medical Institute, 1705 NE Pacific Street, Seattle, Washington 98195, USA.
  • Meyer TJ; Oregon Health &Science University, Department of Behavioral Neuroscience, 3181 SW Sam Jackson Park Road Portland, Oregon 97239, USA.
  • Herrero J; 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK. [3] Bill Lyons Informatics Center, UCL Cancer Institute, University College London,
  • Roos C; Leibniz Institute for Primate Research, Gene Bank of Primates, German Primate Center, Göttingen 37077, Germany.
  • Aken B; 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Anaclerio F; University of Bari, Department of Biology, Via Orabona 4, 70125, Bari, Italy.
  • Archidiacono N; University of Bari, Department of Biology, Via Orabona 4, 70125, Bari, Italy.
  • Baker C; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.
  • Barrell D; 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Batzer MA; Louisiana State University, Department of Biological Sciences, Baton Rouge, Louisiana 70803, USA.
  • Beal K; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Blancher A; University of Paul Sabatier, Toulouse 31062, France.
  • Bohrson CL; The Johns Hopkins University School of Medicine, Department of Oncology, Division of Biostatistics and Bioinformatics, Baltimore, Maryland 21205, USA.
  • Brameier M; Leibniz Institute for Primate Research, Gene Bank of Primates, German Primate Center, Göttingen 37077, Germany.
  • Campbell MS; University of Utah, Salt Lake City, Utah 84112, USA.
  • Capozzi O; University of Bari, Department of Biology, Via Orabona 4, 70125, Bari, Italy.
  • Casola C; Texas A&M University, Department of Ecosystem Science and Management, College Station, Texas 77843, USA.
  • Chiatante G; University of Bari, Department of Biology, Via Orabona 4, 70125, Bari, Italy.
  • Cree A; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
  • Damert A; Babes-Bolyai-University, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Cluj-Napoca 400084, Romania.
  • de Jong PJ; Children's Hospital Oakland Research Institute, BACPAC Resources, Oakland, California 94609, USA.
  • Dumas L; University of Colorado School of Medicine, Department of Biochemistry and Molecular Genetics, Aurora, Colorado 80045, USA.
  • Fernandez-Callejo M; IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain.
  • Flicek P; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Fuchs NV; Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany.
  • Gut I; Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona 08028, Spain.
  • Gut M; Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona 08028, Spain.
  • Hahn MW; Indiana University, School of Informatics and Computing, Bloomington, Indiana 47408, USA.
  • Hernandez-Rodriguez J; IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain.
  • Hillier LW; The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.
  • Hubley R; Institute for Systems Biology, Seattle, Washington 98109-5234, USA.
  • Ianc B; Babes-Bolyai-University, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Cluj-Napoca 400084, Romania.
  • Izsvák Z; Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany.
  • Jablonski NG; The Pennsylvania State University, Department of Anthropology, University Park, Pennsylvania 16802, USA.
  • Johnstone LM; University of Arizona, ARL Division of Biotechnology, Tucson, Arizona 85721, USA.
  • Karimpour-Fard A; University of Colorado School of Medicine, Department of Biochemistry and Molecular Genetics, Aurora, Colorado 80045, USA.
  • Konkel MK; Louisiana State University, Department of Biological Sciences, Baton Rouge, Louisiana 70803, USA.
  • Kostka D; University of Pittsburgh School of Medicine, Department of Developmental Biology, Department of Computational and Systems Biology, Pittsburg, Pennsylvania 15261, USA.
  • Lazar NH; Oregon Health &Science University, Bioinformatics and Computational Biology Division, Department of Medical Informatics &Clinical Epidemiology, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.
  • Lee SL; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
  • Lewis LR; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
  • Liu Y; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
  • Locke DP; 1] The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA. [2] Bill Lyons Informatics Center, UCL Cancer Institute, University College London, London WC1E 6DD, UK (J.He); Seven Bridges Genomics, Cambridge, Massa
  • Mallick S; Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, USA.
  • Mendez FL; 1] University of Arizona, ARL Division of Biotechnology, Tucson, Arizona 85721, USA. [2] 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
Nature ; 513(7517): 195-201, 2014 Sep 11.
Article in En | MEDLINE | ID: mdl-25209798
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.
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Full text: 1 Database: MEDLINE Main subject: Phylogeny / Genome / Karyotype / Hylobates Limits: Animals / Humans Language: En Journal: Nature Year: 2014 Type: Article
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Full text: 1 Database: MEDLINE Main subject: Phylogeny / Genome / Karyotype / Hylobates Limits: Animals / Humans Language: En Journal: Nature Year: 2014 Type: Article