Comparative and demographic analysis of orang-utan genomes

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  • Devin P. Locke, The Genome Center at Washington University, Washington University School of Medicine, USA
  • LaDeana W. Hillier, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Wesley C. Warren, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Shiaw-Pyng Yang, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Zhengyuan Wang, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Asif T. Chinwalla, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Pat Minx, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Makedonka Mitreva, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Lisa Cook, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Kim D. Delehaunty, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Catrina Fronick, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Heather Schmidt, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Lucinda A. Fulton, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Robert S. Fulton, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Joanne O. Nelson, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Vincent Magrini, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Craig Pohl, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Tina A. Graves, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Chris Markovic, The Genome Center at Washington University, Washington University School of Medicine, USA
  • George M. Weinstock, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Elaine R. Mardis, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Richard K. Wilson, The Genome Center at Washington University, Washington University School of Medicine, USA
  • Kim C. Worley, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Lynne V. Nazareth, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Donna M. Muzny, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Andy Cree, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Huyen H. Dinh, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Jennifer Hume, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Christie L. Kovar, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Gerald R. Fowler, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Jeffrey Rogers, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Richard A. Gibbs, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
  • Gerton Lunter, University of Oxford, Storbritannien
  • Stephen Meader, University of Oxford, Storbritannien
  • Andreas Heger, University of Oxford, Storbritannien
  • Chris P. Ponting, University of Oxford, Storbritannien
  • Tomas Marques-Bonet, Department of Genome Sciences, University of Washington School of Medicine, USA
  • Can Alkan, Department of Genome Sciences, University of Washington School of Medicine, USA
  • Lin Cheng, Department of Genome Sciences, University of Washington School of Medicine, USA
  • Ze Cheng, Department of Genome Sciences, University of Washington School of Medicine, USA
  • Jeffrey M. Kidd, Department of Genome Sciences, University of Washington School of Medicine, USA
  • Evan E. Eichler, Department of Genome Sciences, University of Washington School of Medicine, USA
  • Rui Faria, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spanien
  • Olga Fernando, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spanien
  • Fleur Darré, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spanien
  • Domèmec Farré, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spanien
  • Elodie Gazave, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spanien
  • Meritxell Oliva, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spanien
  • Arcadi Navarro, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spanien
  • Simon White, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Storbritannien
  • Stephen Searle, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Storbritannien
  • Albert J. Vilella, European Bioinformatics Institute, Wellcome Trust Genome Campus, Storbritannien
  • Yuan Chen, European Bioinformatics Institute, Wellcome Trust Genome Campus, Storbritannien
  • Paul Flicek, European Bioinformatics Institute, Wellcome Trust Genome Campus, Storbritannien
  • Javier Herrero, European Bioinformatics Institute, Wellcome Trust Genome Campus, Storbritannien
  • Jian Ma, Center for Biomolecular Science and Engineering, University of California, USA
  • Brian Raney, Center for Biomolecular Science and Engineering, University of California, USA
  • Bernard Suh, Center for Biomolecular Science and Engineering, University of California, USA
  • David Haussler, Center for Biomolecular Science and Engineering, University of California, USA
  • Richard Burhans, Center for Comparative Genomics and Bioinformatics, Penn State University, USA
  • Aakrosh Ratan, Center for Comparative Genomics and Bioinformatics, Penn State University, USA
  • Robert S. Harris, Center for Comparative Genomics and Bioinformatics, Penn State University, USA
  • Webb Miller, Center for Comparative Genomics and Bioinformatics, Penn State University, USA
  • Roberta Roberto, Department of Biology, University of Bari, Italien
  • Oronzo Capozzi, Department of Biology, University of Bari, Italien
  • Nicoletta Archidiacono, Department of Biology, University of Bari, Italien
  • Mariano Rocchi, Department of Biology, University of Bari, Italien
  • Giuliano Della Valle, Department of Biology, University of Bologna, Italien
  • Stefania Purgato, Department of Biology, University of Bologna, Italien
  • Miriam K. Konkel, Department of Biological Sciences, Louisiana State University, USA
  • Jerilyn A. Walker, Department of Biological Sciences, Louisiana State University, USA
  • Mark A. Batzer, Department of Biological Sciences, Louisiana State University, USA
  • Brygg Ullmer, Center for Computation and Technology, Department of Computer Sciences, Louisiana State University, USA
  • Adrian F. A. Smit, Institute for Systems Biology, Seattle, USA
  • Robert Hubley, Institute for Systems Biology, Seattle, USA
  • Claudio Casola, Department of Biology and School of Informatics and Computing, Indiana University, USA
  • Daniel R. Schrider, Department of Biology and School of Informatics and Computing, Indiana University, USA
  • Matthew W. Hahn, Department of Biology and School of Informatics and Computing, Indiana University, USA
  • Victor Quesada, Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Spanien
  • Xose S. Puente, Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Spanien
  • Gonzalo R. Ordoñez, Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Spanien
  • Carlos López-Otín, Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Spanien
  • Tomas Vinar, Faculty of Mathematics, Physics and Informatics, Comenius University, Slovakiet
  • Brona Brejova, Faculty of Mathematics, Physics and Informatics, Comenius University, Slovakiet
  • Carolin Kosiol, Institut für Populations genetik, Vetmeduni Vienna, Østrig
  • Heather A. Lawson, Department of Anatomy and Neurobiology, Washington University School of Medicine, USA
  • Vikas Taliwal, Department of Biological Statistics and Computational Biology, Cornell University, USA
  • André L. Martins, Department of Biological Statistics and Computational Biology, Cornell University, USA
  • Adam Siepel, Department of Biological Statistics and Computational Biology, Cornell University, USA
  • Xin Ma, Department of Biological Statistics and Computational Biology, Cornell University, USA
  • Jeremiah Degenhardt, Department of Biological Statistics and Computational Biology, Cornell University, USA
  • Arindam RoyChoudhury, Department of Biostatistics, Columbia University, USA
  • Carlos D. Bustamante, Stanford University, USA
  • Ryan N. Gutenkunst, Department of Molecular and Cellular Biology, University of Arizona, USA
  • Thomas Mailund
  • Julien Dutheil, Danmark
  • Asger Hobolth
  • Mikkel Heide Schierup
  • Oliver A. Ryder, San Diego Zoo's Institute for Conservation Research, USA
  • Yuko Yoshinaga, Children’s Hospital Oakland Research Institute, USA
  • Pieter J. de Jong, Children’s Hospital Oakland Research Institute, USA
‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.
OriginalsprogEngelsk
TidsskriftNature
Vol/bind469
Sider (fra-til)529-533
Antal sider5
ISSN0028-0836
DOI
StatusUdgivet - 2011

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