Comparative and demographic analysis of orang-utan genomes.
Comparative and demographic analysis of orang-utan genomes.
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DOI：
10.1038/nature09687
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发表时间：
2011-01-27
期刊：
影响因子：
64.8
通讯作者：
Wilson, Richard K.
中科院分区：
文献类型：
--
作者：
Locke, Devin P.;Hillier, LaDeana W.;Warren, Wesley C.;Worley, Kim C.;Nazareth, Lynne V.;Muzny, Donna M.;Yang, Shiaw-Pyng;Wang, Zhengyuan;Chinwalla, Asif T.;Minx, Pat;Mitreva, Makedonka;Cook, Lisa;Delehaunty, Kim D.;Fronick, Catrina;Schmidt, Heather;Fulton, Lucinda A.;Fulton, Robert S.;Nelson, Joanne O.;Magrini, Vincent;Pohl, Craig;Graves, Tina A.;Markovic, Chris;Cree, Andy;Dinh, Huyen H.;Hume, Jennifer;Kovar, Christie L.;Fowler, Gerald R.;Lunter, Gerton;Meader, Stephen;Heger, Andreas;Ponting, Chris P.;Marques-Bonet, Tomas;Alkan, Can;Chen, Lin;Cheng, Ze;Kidd, Jeffrey M.;Eichler, Evan E.;White, Simon;Searle, Stephen;Vilella, Albert J.;Chen, Yuan;Flicek, Paul;Ma, Jian;Raney, Brian;Suh, Bernard;Burhans, Richard;Herrero, Javier;Haussler, David;Faria, Rui;Fernando, Olga;Darre, Fleur;Farre, Domenec;Gazave, Elodie;Oliva, Meritxell;Navarro, Arcadi;Roberto, Roberta;Capozzi, Oronzo;Archidiacono, Nicoletta;Della Valle, Giuliano;Purgato, Stefania;Rocchi, Mariano;Konkel, Miriam K.;Walker, Jerilyn A.;Ullmer, Brygg;Batzer, Mark A.;Smit, Arian F. A.;Hubley, Robert;Casola, Claudio;Schrider, Daniel R.;Hahn, Matthew W.;Quesada, Victor;Puente, Xose S.;Ordonez, Gonzalo R.;Lopez-Otin, Carlos;Vinar, Tomas;Brejova, Brona;Ratan, Aakrosh;Harris, Robert S.;Miller, Webb;Kosiol, Carolin;Lawson, Heather A.;Taliwal, Vikas;Martins, Andre L.;Siepel, Adam;RoyChoudhury, Arindam;Ma, Xin;Degenhardt, Jeremiah;Bustamante, Carlos D.;Gutenkunst, Ryan N.;Mailund, Thomas;Dutheil, Julien Y.;Hobolth, Asger;Schierup, Mikkel H.;Ryder, Oliver A.;Yoshinaga, Yuko;de Jong, Pieter J.;Weinstock, George M.;Rogers, Jeffrey;Mardis, Elaine R.;Gibbs, Richard A.;Wilson, Richard K.
东南亚巨猿或猩猩的基因组已经被测序-特别是一个苏门答腊雌性个体的组装草图和来自另外五个苏门答腊猩猩和五个婆罗洲猩猩，Pongo abelii和Pongo pygmaeus的短读序列数据。红毛猩猩物种似乎在大约40万年前分裂，比大多数以前的估计都要晚，导致婆罗洲-苏门答腊的平均核苷酸同一性为99.68%。红毛猩猩基因组的结构进化似乎比其他类人猿（包括黑猩猩和人类）慢得多。由于这两种猩猩都在濒危名单上，作者希望基因组序列及其在种群之间的变异的知识将为自然资源保护者提供宝贵的资源。本文的在线版本（doi：10.1038/nature 09687）包含补充材料，可供授权用户使用。东南亚红毛猩猩的基因组已经被测序。一个苏门答腊人旁边的序列数据从五个苏门答腊和五个婆罗洲猩猩基因组的草案大会。所描述的资源和分析为进化基因组学提供了新的机会，深入了解原始人类生物学，并为保护工作提供了广泛的变异数据库。本文的在线版本（doi：10.1038/nature 09687）包含补充材料，可供授权用户使用。“猩猩”一词来源于马来语，意思是“森林中的人”，恰如其分地描述了原产于苏门答腊和婆罗洲的东南亚类人猿。红毛猩猩的物种，Pongo abelii（苏门答腊）和Pongo pygmaeus（婆罗洲），是与人类在遗传学上最遥远的类人猿，从而提供了一个关于原始人类进化的信息视角。在这里，我们提出了一个苏门答腊猩猩基因组组装草案和短读序列数据从五个苏门答腊和五个婆罗洲猩猩基因组。我们的分析显示，与其他灵长类动物相比，红毛猩猩的基因组具有许多独特的特征。红毛猩猩基因组的结构进化比其他类人猿慢得多，这表现在更少的重排、更少的片段复制、更低的基因家族更替率和令人惊讶的静止Alu重复序列，这些重复序列在其他灵长类动物基因组的重组中发挥了重要作用。我们还描述了灵长类动物的多态性neocentromere，发现在这两个Pongo物种，强调猩猩基因组结构的逐步演变。作为真兽目哺乳动物，红毛猩猩的能量消耗非常低，远远低于它们的原始亲戚。将它们的基因组添加到测序的灵长类动物库中，阐明了包括糖脂代谢在内的几种途径中正选择的新信号。从种群的角度来看，这两个庞戈物种都非常多样化;然而，苏门答腊个体比婆罗洲个体具有更大的多样性，并且具有更多的物种特异性变异。我们对婆罗洲/苏门答腊物种形成时间的估计是40万年前，比以前的大多数研究都要近，并强调了猩猩物种形成过程的复杂性。尽管现代人口普查的人口规模较小，但苏美尔人的有效人口规模（Ne）在分裂后相对于祖先Ne呈指数增长，而婆罗洲人的Ne在同一时期下降。总的来说，这里提出的资源和分析提供了新的机会，在进化基因组学，深入了解人科生物学，并为保护工作的变化广泛的数据库。本文的在线版本（doi：10.1038/nature 09687）包含补充材料，可供授权用户使用。
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. The online version of this article (doi:10.1038/nature09687) contains supplementary material, which is available to authorized users. The genome of the southeast Asian orang-utan has been sequenced. The draft assembly of a Sumatran individual alongside sequence data from five Sumatran and five Bornean orang-utan genomes is presented. The resources and analyses described offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts. The online version of this article (doi:10.1038/nature09687) contains supplementary material, which is available to authorized users. ‘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, 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. The online version of this article (doi:10.1038/nature09687) contains supplementary material, which is available to authorized users.
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影响因子：
4.5
作者：
Hobolth A;Christensen OF;Mailund T;Schierup MH
通讯作者：
Schierup MH
影响因子：
56.9
作者：
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通讯作者：
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影响因子：
3.3
作者：
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DOI：
10.1159/000130684
发表时间：
1976-01-01
期刊：
CYTOGENETICS AND CELL GENETICS
影响因子：
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作者：
SEUANEZ, H;FLETCHER, J;MARTIN, DE
通讯作者：
MARTIN, DE
影响因子：
10.7
作者：
Yi, SJ;Ellsworth, DL;Li, WH
通讯作者：
Li, WH