The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.
Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.
'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 (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) 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”一词源自马来语，意思是“森林中的人”，恰当地描述了原产于苏门答腊和婆罗洲的东南亚大型类人猿。猩猩物种，Pongo abelii（苏门答腊）和 Pongo pygmaeus（婆罗洲），是与人类亲缘关系最远的大型类人猿，从而为人类进化提供了有价值的视角。在这里，我们展示了一个苏门答腊猩猩的基因组草图组装和来自五个苏门答腊和五个婆罗洲猩猩基因组的短读序列数据。我们的分析表明，与其他灵长类动物相比，猩猩基因组具有许多独特的特征。猩猩基因组的结构进化比其他大型类人猿慢得多，这表现在更少的重排、更少的片段重复、基因家族更替率较低以及令人惊讶的静止 Alu 重复，这些重复在重构其他灵长类动物基因组中发挥了重要作用。我们还描述了一个灵长类多态性新着丝粒，在两个 Pongo 物种中都有发现，强调了猩猩基因组结构的逐渐进化。猩猩是真兽类哺乳动物中能量消耗极低的物种，远低于其人类近亲。将其基因组添加到已测序灵长类动物的基因组库中，揭示了几个途径中包括糖脂代谢在内的正选择的新信号。从种群角度来看，两个 Pongo 物种都非常多样化；然而，苏门答腊个体比它们的婆罗洲同类拥有更大的多样性，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为 40 万年前，比大多数先前的研究更新，突显了猩猩物种形成过程的复杂性。尽管现代种群规模较小，但与祖先 N(e)相比，苏门答腊的有效种群数量 (N(e)) 在分裂后呈指数级扩张，而婆罗洲的 N(e)在此期间下降。总的来说，这里提供的资源和分析为进化基因组学、人类生物学的深入了解以及保护工作提供了广泛的变异数据库提供了新的机会。
