Comparative and demographic analysis of orang-utan genomes

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 Cook, Kim D. Delehaunty, Catrina Fronick, Heather Schmidt, Lucinda A. Fulton, Robert S. Fulton, Joanne O. Nelson, Vincent Magrini, Craig Pohl, Tina A. Graves, Chris Markovic, Andy Cree, Huyen H. Dinh, Jennifer Hume, Christie L. Kovar, Gerald R. Fowler, Gerton Lunter, Stephen Meader, Andreas Heger, Chris P. Ponting, Tomas Marques-Bonet, Can Alkan, Lin Chen, Ze Cheng, Jeffrey M. Kidd, Evan E. Eichler, Simon White, Stephen Searle, Albert J. Vilella, Yuan Chen, Paul Flicek, Jian Ma, Brian Raney, Bernard Suh, Richard Burhans, Javier Herrero, David Haussler, Rui Faria, Olga Fernando, Fleur Darré, Domènec Farré, Elodie Gazave, Meritxell Oliva, Arcadi Navarro, Roberta Roberto, Oronzo Capozzi, Nicoletta Archidiacono, Giuliano Della Valle, Stefania Purgato, Mariano Rocchi, Miriam K. Konkel, Jerilyn A. Walker, Brygg Ullmer, Mark A. Batzer, Arian F. A. Smit, Robert Hubley, Claudio Casola, Daniel R. Schrider, Matthew W. Hahn, Victor Quesada, Xose S. Puente, Gonzalo R. Ordoñez, Carlos López-Otín, Tomas Vinar, Brona Brejova, Aakrosh Ratan, Robert S. Harris, Webb Miller, Carolin Kosiol, Heather A. Lawson, Vikas Taliwal, André L. Martins, Adam Siepel, Arindam RoyChoudhury, Xin Ma, Jeremiah Degenhardt, Carlos D. Bustamante, Ryan N. Gutenkunst, Thomas Mailund, Julien Y. Dutheil, Asger Hobolth, Mikkel H. Schierup, Oliver A. Ryder, Yuko Yoshinaga, Pieter J. de Jong, George M. Weinstock, Jeffrey Rogers, Elaine R. Mardis, Richard A. Gibbs and Richard K. Wilson
Additional contact information
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
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
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
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
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
Olga Fernando: IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain
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
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

Nature, 2011, vol. 469, issue 7331, 529-533

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.

Date: 2011
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/nature09687 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:469:y:2011:i:7331:d:10.1038_nature09687

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/nature09687

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().