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 Darre; Domenec Farre; 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. Ordonez; Carlos Lopez-Otin; Tomas Vinar; Brona Brejova; Aakrosh Ratan; Robert S. Harris; Webb Miller; Carolin Kosiol; Heather A. Lawson; Vikas Taliwal; Andre 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; Richard K. Wilson

doi:10.1038/nature09687

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Comparative and demographic analysis of orang-utan genomes

Article de revue

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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, …

Nature (London), Vol.469(7331), pp.529-533

27/01/2011

DOI: https://doi.org/10.1038/nature09687

PMID: 21270892

Résumé

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

'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 mammal(1), 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.

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Titre: Comparative and demographic analysis of orang-utan genomes
Créateurs - sans rôle: Devin P. Locke - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
LaDeana W. Hillier - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Wesley C. Warren - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Kim C. Worley - Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA
Lynne V. Nazareth - Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA
Donna M. Muzny - Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA
Shiaw-Pyng Yang - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Zhengyuan Wang - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Asif T. Chinwalla - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Pat Minx - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Makedonka Mitreva - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Lisa Cook - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Kim D. Delehaunty - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Catrina Fronick - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Heather Schmidt - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Lucinda A. Fulton - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Robert S. Fulton - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Joanne O. Nelson - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Vincent Magrini - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Craig Pohl - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Tina A. Graves - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Chris Markovic - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Andy Cree - Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA
Huyen H. Dinh - Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA
Jennifer Hume - Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA
Christie L. Kovar - Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA
Gerald R. Fowler - Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA
Gerton Lunter - Univ Oxford, MRC, Funct Genom Unit, Oxford OX1 3QX, England
Stephen Meader - Univ Oxford, MRC, Funct Genom Unit, Oxford OX1 3QX, England
Andreas Heger - Univ Oxford, MRC, Funct Genom Unit, Oxford OX1 3QX, England
Chris P. Ponting - Univ Oxford, MRC, Funct Genom Unit, Oxford OX1 3QX, England
Tomas Marques-Bonet - Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA
Can Alkan - Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA
Lin Chen - Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA
Ze Cheng - Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA
Jeffrey M. Kidd - Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA
Evan E. Eichler - Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA
Simon White - Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England
Stephen Searle - Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England
Albert J. Vilella - European Bioinformat Inst, Cambridge CB10 1SD, England
Yuan Chen - European Bioinformat Inst, Cambridge CB10 1SD, England
Paul Flicek - European Bioinformat Inst, Cambridge CB10 1SD, England
Jian Ma - Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA
Brian Raney - Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA
Bernard Suh - Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA
Richard Burhans - Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Javier Herrero - European Bioinformat Inst, Cambridge CB10 1SD, England
David Haussler - Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA
Rui Faria - Univ Pompeu Fabra, PRBB, CSIC, IBE, Barcelona 08003, Spain
Olga Fernando - Univ Pompeu Fabra, PRBB, CSIC, IBE, Barcelona 08003, Spain
Fleur Darre - Univ Pompeu Fabra, PRBB, CSIC, IBE, Barcelona 08003, Spain
Domenec Farre - Univ Pompeu Fabra, PRBB, CSIC, IBE, Barcelona 08003, Spain
Elodie Gazave - Univ Pompeu Fabra, PRBB, CSIC, IBE, Barcelona 08003, Spain
Meritxell Oliva - Univ Pompeu Fabra, PRBB, CSIC, IBE, Barcelona 08003, Spain
Arcadi Navarro - Univ Pompeu Fabra, PRBB, CSIC, IBE, Barcelona 08003, Spain
Roberta Roberto - Univ Bari, Dept Biol, I-70125 Bari, Italy
Oronzo Capozzi - Univ Bari, Dept Biol, I-70125 Bari, Italy
Nicoletta Archidiacono - Univ Bari, Dept Biol, I-70125 Bari, Italy
Giuliano Della Valle - Univ Bologna, Dept Biol, I-40126 Bologna, Italy
Stefania Purgato - Univ Bologna, Dept Biol, I-40126 Bologna, Italy
Mariano Rocchi - Univ Bari, Dept Biol, I-70125 Bari, Italy
Miriam K. Konkel - Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA
Jerilyn A. Walker - Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA
Brygg Ullmer - Louisiana State Univ, Dept Comp Sci, Ctr Computat & Technol, Baton Rouge, LA 70803 USA
Mark A. Batzer - Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA
Arian F. A. Smit - Inst Syst Biol, Seattle, WA 98103 USA
Robert Hubley - Inst Syst Biol, Seattle, WA 98103 USA
Claudio Casola - Indiana Univ, Dept Biol, Bloomington, IN 47405 USA
Daniel R. Schrider - Indiana Univ, Dept Biol, Bloomington, IN 47405 USA
Matthew W. Hahn - Indiana University Bloomington
Victor Quesada - Univ Oviedo, Dept Bioquim & Biol Mol, Inst Univ Oncol, E-33006 Oviedo, Spain
Xose S. Puente - Univ Oviedo, Dept Bioquim & Biol Mol, Inst Univ Oncol, E-33006 Oviedo, Spain
Gonzalo R. Ordonez - Univ Oviedo, Dept Bioquim & Biol Mol, Inst Univ Oncol, E-33006 Oviedo, Spain
Carlos Lopez-Otin - Univ Oviedo, Dept Bioquim & Biol Mol, Inst Univ Oncol, E-33006 Oviedo, Spain
Tomas Vinar - Comenius Univ, Fac Math Phys & Informat, Bratislava 84248, Slovakia
Brona Brejova - Comenius Univ, Fac Math Phys & Informat, Bratislava 84248, Slovakia
Aakrosh Ratan - Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Robert S. Harris - Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Webb Miller - Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Carolin Kosiol - Vetmeduni Vienna, Inst Populat Genet, A-1210 Vienna, Austria
Heather A. Lawson - Washington Univ, Sch Med, Dept Anat & Neurobiol, St Louis, MO 63110 USA
Vikas Taliwal - Cornell Univ, Dept Biol Stat & Computat Biol, Ithaca, NY 14853 USA
Andre L. Martins - Cornell Univ, Dept Biol Stat & Computat Biol, Ithaca, NY 14853 USA
Adam Siepel - Cornell Univ, Dept Biol Stat & Computat Biol, Ithaca, NY 14853 USA
Arindam RoyChoudhury - Columbia Univ, Dept Biostat, New York, NY 10032 USA
Xin Ma - Cornell Univ, Dept Biol Stat & Computat Biol, Ithaca, NY 14853 USA
Jeremiah Degenhardt - Cornell Univ, Dept Biol Stat & Computat Biol, Ithaca, NY 14853 USA
Carlos D. Bustamante - Stanford Univ, Dept Genet, Stanford, CA 94305 USA
Ryan N. Gutenkunst - Univ Arizona, Dept Mol & Cellular Biol, Tucson, AZ 85721 USA
Thomas Mailund - Aarhus University
Julien Y. Dutheil - Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus C, Denmark
Asger Hobolth - Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus C, Denmark
Mikkel H. Schierup - Aarhus University
Oliver A. Ryder - San Diego Zoos Inst Conservat Res, Escondido, CA 92027 USA
Yuko Yoshinaga - Childrens Hosp Oakland, Res Inst, Oakland, CA 94609 USA
Pieter J. de Jong - Childrens Hosp Oakland, Res Inst, Oakland, CA 94609 USA
George M. Weinstock - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Jeffrey Rogers - College Station Medical Center
Elaine R. Mardis - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Richard A. Gibbs - College Station Medical Center
Richard K. Wilson - Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA
Détails de publication: Nature (London), Vol.469(7331), pp.529-533
Éditeur: Springer Nature
Nombre de pages: 5
Note de subvention: IRG-224885; IRG-231025 / Commission of the European Communities; European Union (EU) MC_U137761446; G0501331 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) ICREA U54 HG003079; U54 HG003273 / National Human Genome Research Institute (NHGRI); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI) PRIN; Ministry of Education, Universities and Research (MIUR); Research Projects of National Relevance (PRIN) Cornell University David and Lucile Packard Foundation; The David & Lucile Packard Foundation BFU2006-15413-C02-01; BFU2009-13409-C02-02 / MCI-Spain CEGBA Fundacion M. Botin
Identifiants: 99159454709311
Unité académique: Institut des Sciences de l'Evolution - Montpellier - ISEM
Langue: English
Type de ressource: Journal article