Comparative and demographic analysis of orang-utan genomes

被引：368

作者：

Locke, Devin P. ^{[1
]}

Hillier, LaDeana W. ^{[1
]}

Warren, Wesley C. ^{[1
]}

Worley, Kim C. ^{[2
]}

Nazareth, Lynne V. ^{[2
]}

Muzny, Donna M. ^{[2
]}

Yang, Shiaw-Pyng ^{[1
]}

Wang, Zhengyuan ^{[1
]}

Chinwalla, Asif T. ^{[1
]}

Minx, Pat ^{[1
]}

Mitreva, Makedonka ^{[1
]}

Cook, Lisa ^{[1
]}

Delehaunty, Kim D. ^{[1
]}

Fronick, Catrina ^{[1
]}

Schmidt, Heather ^{[1
]}

Fulton, Lucinda A. ^{[1
]}

Fulton, Robert S. ^{[1
]}

Nelson, Joanne O. ^{[1
]}

Magrini, Vincent ^{[1
]}

Pohl, Craig ^{[1
]}

Graves, Tina A. ^{[1
]}

Markovic, Chris ^{[1
]}

Cree, Andy ^{[2
]}

Dinh, Huyen H. ^{[2
]}

Hume, Jennifer ^{[2
]}

Kovar, Christie L. ^{[2
]}

Fowler, Gerald R. ^{[2
]}

Lunter, Gerton ^{[3
,4
,5
]}

Meader, Stephen ^{[3
,4
]}

Heger, Andreas ^{[3
,4
]}

Ponting, Chris P. ^{[3
,4
]}

Marques-Bonet, Tomas ^{[6
,7
]}

Alkan, Can ^{[6
]}

Chen, Lin ^{[6
]}

Cheng, Ze ^{[6
]}

Kidd, Jeffrey M. ^{[6
]}

Eichler, Evan E. ^{[6
,8
]}

White, Simon ^{[9
]}

Searle, Stephen ^{[9
]}

Vilella, Albert J. ^{[10
]}

Chen, Yuan ^{[10
]}

Flicek, Paul ^{[10
]}

Ma, Jian ^{[11
]}

Raney, Brian ^{[11
]}

Suh, Bernard ^{[11
]}

Burhans, Richard ^{[12
]}

Herrero, Javier ^{[10
]}

Haussler, David ^{[11
]}

Faria, Rui ^{[7
,13
]}

Fernando, Olga ^{[7
,14
]}

机构：

[1] Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA

[2] Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA

[3] Univ Oxford, MRC, Funct Genom Unit, Oxford OX1 3QX, England

[4] Univ Oxford, Dept Physiol Anat & Genet, Oxford OX1 3QX, England

[5] Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England

[6] Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA

[7] Univ Pompeu Fabra, PRBB, CSIC, IBE, Barcelona 08003, Spain

[8] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA

[9] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[10] European Bioinformat Inst, Cambridge CB10 1SD, England

[11] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

[12] Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA

[13] Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, P-4485661 Vairao, Portugal

[14] Univ Nova Lisboa, Inst Tecnol Quim & Biol, P-2780157 Oeiras, Portugal

[15] ICREA, Barcelona 08003, Spain

[16] PRBB, INB, Barcelona 08003, Spain

[17] Univ Bari, Dept Biol, I-70125 Bari, Italy

[18] Univ Bologna, Dept Biol, I-40126 Bologna, Italy

[19] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA

[20] Louisiana State Univ, Dept Comp Sci, Ctr Computat & Technol, Baton Rouge, LA 70803 USA

[21] Inst Syst Biol, Seattle, WA 98103 USA

[22] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA

[23] Indiana Univ, Sch Informat & Comp, Bloomington, IN 47405 USA

[24] Univ Oviedo, Dept Bioquim & Biol Mol, Inst Univ Oncol, E-33006 Oviedo, Spain

[25] Comenius Univ, Fac Math Phys & Informat, Bratislava 84248, Slovakia

[26] Vetmeduni Vienna, Inst Populat Genet, A-1210 Vienna, Austria

[27] Washington Univ, Sch Med, Dept Anat & Neurobiol, St Louis, MO 63110 USA

[28] Cornell Univ, Dept Biol Stat & Computat Biol, Ithaca, NY 14853 USA

[29] Columbia Univ, Dept Biostat, New York, NY 10032 USA

[30] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[31] Univ Arizona, Dept Mol & Cellular Biol, Tucson, AZ 85721 USA

[32] Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus C, Denmark

[33] San Diego Zoos Inst Conservat Res, Escondido, CA 92027 USA

[34] Childrens Hosp Oakland, Res Inst, Oakland, CA 94609 USA

来源：

NATURE | 2011年 / 469卷 / 7331期

基金：

英国医学研究理事会; 美国国家科学基金会; 美国国家卫生研究院;

关键词：

LOW NUCLEOTIDE DIVERSITY; RETROTRANSPOSONS; CHIMPANZEES; EVOLUTION; HUMANS; ANCESTOR; SEQUENCE;

D O I：

10.1038/nature09687

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

'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.

引用

页码：529 / 533

页数：5

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