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Comparative and demographic analysis of orang-utan genomes

Author

Listed:
  • Devin P. Locke

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • LaDeana W. Hillier

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Wesley C. Warren

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Kim C. Worley

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Lynne V. Nazareth

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Donna M. Muzny

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Shiaw-Pyng Yang

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Zhengyuan Wang

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Asif T. Chinwalla

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Pat Minx

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Makedonka Mitreva

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Lisa Cook

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Kim D. Delehaunty

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Catrina Fronick

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Heather Schmidt

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Lucinda A. Fulton

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Robert S. Fulton

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Joanne O. Nelson

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Vincent Magrini

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Craig Pohl

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Tina A. Graves

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Chris Markovic

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Andy Cree

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Huyen H. Dinh

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Jennifer Hume

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Christie L. Kovar

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Gerald R. Fowler

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Gerton Lunter

    (Anatomy and Genetics, University of Oxford, Le Gros Clark Building, South Parks Road, Oxford OX1 3QX, UK
    Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK)

  • Stephen Meader

    (Anatomy and Genetics, University of Oxford, Le Gros Clark Building, South Parks Road, Oxford OX1 3QX, UK)

  • Andreas Heger

    (Anatomy and Genetics, University of Oxford, Le Gros Clark Building, South Parks Road, Oxford OX1 3QX, UK)

  • Chris P. Ponting

    (Anatomy and Genetics, University of Oxford, Le Gros Clark Building, South Parks Road, Oxford OX1 3QX, UK)

  • Tomas Marques-Bonet

    (University of Washington School of Medicine
    IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain)

  • Can Alkan

    (University of Washington School of Medicine)

  • Lin Chen

    (University of Washington School of Medicine)

  • Ze Cheng

    (University of Washington School of Medicine)

  • Jeffrey M. Kidd

    (University of Washington School of Medicine)

  • Evan E. Eichler

    (University of Washington School of Medicine
    Howard Hughes Medical Institute, 1705 NE Pacific Street)

  • Simon White

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Stephen Searle

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Albert J. Vilella

    (European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK)

  • Yuan Chen

    (European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK)

  • Paul Flicek

    (European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK)

  • Jian Ma

    (Center for Biomolecular Science and Engineering, University of California
    Present address: Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.)

  • Brian Raney

    (Center for Biomolecular Science and Engineering, University of California)

  • Bernard Suh

    (Center for Biomolecular Science and Engineering, University of California)

  • Richard Burhans

    (Center for Comparative Genomics and Bioinformatics, Penn State University, University Park)

  • Javier Herrero

    (European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK)

  • David Haussler

    (Center for Biomolecular Science and Engineering, University of California)

  • Rui Faria

    (IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain
    CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão)

  • Olga Fernando

    (IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain
    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal)

  • Fleur Darré

    (IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain)

  • Domènec Farré

    (IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain)

  • Elodie Gazave

    (IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain)

  • Meritxell Oliva

    (IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain)

  • Arcadi Navarro

    (IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain
    ICREA (Institució Catalana de Recerca i Estudis Avançats) and INB (Instituto Nacional de Bioinformática) PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain)

  • Roberta Roberto

    (University of Bari, Via Orabona 4, 70125, Bari, Italy)

  • Oronzo Capozzi

    (University of Bari, Via Orabona 4, 70125, Bari, Italy)

  • Nicoletta Archidiacono

    (University of Bari, Via Orabona 4, 70125, Bari, Italy)

  • Giuliano Della Valle

    (University of Bologna, Via Selmi 3, 40126, Bologna, Italy)

  • Stefania Purgato

    (University of Bologna, Via Selmi 3, 40126, Bologna, Italy)

  • Mariano Rocchi

    (University of Bari, Via Orabona 4, 70125, Bari, Italy)

  • Miriam K. Konkel

    (Louisiana State University)

  • Jerilyn A. Walker

    (Louisiana State University)

  • Brygg Ullmer

    (Center for Computation and Technology, Louisiana State University)

  • Mark A. Batzer

    (Louisiana State University)

  • Arian F. A. Smit

    (Institute for Systems Biology)

  • Robert Hubley

    (Institute for Systems Biology)

  • Claudio Casola

    (Indiana University)

  • Daniel R. Schrider

    (Indiana University)

  • Matthew W. Hahn

    (Indiana University)

  • Victor Quesada

    (Instituto Universitario de Oncologia, Universidad de Oviedo, Oviedo 33006, Spain)

  • Xose S. Puente

    (Instituto Universitario de Oncologia, Universidad de Oviedo, Oviedo 33006, Spain)

  • Gonzalo R. Ordoñez

    (Instituto Universitario de Oncologia, Universidad de Oviedo, Oviedo 33006, Spain)

  • Carlos López-Otín

    (Instituto Universitario de Oncologia, Universidad de Oviedo, Oviedo 33006, Spain)

  • Tomas Vinar

    (Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska Dolina, Bratislava 84248, Slovakia)

  • Brona Brejova

    (Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska Dolina, Bratislava 84248, Slovakia)

  • Aakrosh Ratan

    (Center for Comparative Genomics and Bioinformatics, Penn State University, University Park)

  • Robert S. Harris

    (Center for Comparative Genomics and Bioinformatics, Penn State University, University Park)

  • Webb Miller

    (Center for Comparative Genomics and Bioinformatics, Penn State University, University Park)

  • Carolin Kosiol

    (Institut für Populations genetik, Vetmeduni Vienna, Veterinärplatz 1)

  • Heather A. Lawson

    (Washington University School of Medicine)

  • Vikas Taliwal

    (Cornell University)

  • André L. Martins

    (Cornell University)

  • Adam Siepel

    (Cornell University)

  • Arindam RoyChoudhury

    (Columbia University)

  • Xin Ma

    (Cornell University)

  • Jeremiah Degenhardt

    (Cornell University)

  • Carlos D. Bustamante

    (Stanford University)

  • Ryan N. Gutenkunst

    (University of Arizona)

  • Thomas Mailund

    (Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark)

  • Julien Y. Dutheil

    (Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark)

  • Asger Hobolth

    (Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark)

  • Mikkel H. Schierup

    (Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark)

  • Oliver A. Ryder

    (San Diego Zoo's Institute for Conservation Research)

  • Yuko Yoshinaga

    (Children’s Hospital Oakland Research Institute)

  • Pieter J. de Jong

    (Children’s Hospital Oakland Research Institute)

  • George M. Weinstock

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Jeffrey Rogers

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Elaine R. Mardis

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

  • Richard A. Gibbs

    (Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA)

  • Richard K. Wilson

    (The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA)

Abstract

Sequence analyses of endangered orang-utan species The genome of the Southeast Asian great ape or orang-utan has been sequenced — specifically a draft assembly of a Sumatran female individual and short-read sequence data from five further Sumatran and five Bornean orang-utan, Pongo abelii and Pongo pygmaeus, respectively. Orang-utan species appear to have split around 400,000 years ago, more recent than most previous estimates suggested, resulting in an average Bornean–Sumatran nucleotide identity of 99.68%. Structural evolution of the orang-utan genome seems to have proceeded much more slowly than that of other great apes, including chimpanzees and humans. With both orang-utan species on the endangered list, the authors hope that knowledge of the genome sequence and its variation between populations will provide a valuable resource for conservationists.

Suggested Citation

  • Devin P. Locke & LaDeana W. Hillier & Wesley C. Warren & Kim C. Worley & Lynne V. Nazareth & Donna M. Muzny & Shiaw-Pyng Yang & Zhengyuan Wang & Asif T. Chinwalla & Pat Minx & Makedonka Mitreva & Lisa, 2011. "Comparative and demographic analysis of orang-utan genomes," Nature, Nature, vol. 469(7331), pages 529-533, January.
    • Handle: RePEc:nat:nature:v:469:y:2011:i:7331:d:10.1038_nature09687
    DOI: 10.1038/nature09687
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