The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation^1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes^1,3,4,5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome.

^{黑猩猩和倭黑猩猩的分歧提供了最近人类物种形成1,2}的少数例子之一。在这里，我们描述了一个完全注释的高质量倭黑猩猩基因组组装，它是在没有参考基因组指导的情况下通过应用多平台基因组学方法构建的。我们生成了一个倭黑猩猩基因组组装，其中超过 98% 的基因被完全注释，99% 的间隙被关闭，包括大约一半的节段重复和几乎所有全长移动元件的分辨率。我们将倭黑猩猩基因组与其他类人猿的基因组进行比较^1,3,4,5并识别出超过 5,569 个固定结构变体，专门区分倭黑猩猩和黑猩猩谱系。我们关注在过去几百万年倭黑猩猩进化中丢失、结构改变或扩展的基因。我们制作了不完整谱系分类的高分辨率地图，并估计大约 5.1% 的人类基因组在遗传上更接近黑猩猩或倭黑猩猩，如果我们考虑更深层次的系统发育，包括大猩猩和倭黑猩猩，超过 36.5% 的基因组显示不完整的谱系分类。猩猩。我们还表明，人类和黑猩猩或人类和倭黑猩猩之间不完全谱系分类的片段中有 26% 是非随机分布的，并且与基因组的其余部分相比，这些聚集片段中的基因显示出显着过量的氨基酸替代。