A high-quality bonobo genome refines the analysis of hominid evolution.
A high-quality bonobo genome refines the analysis of hominid evolution.
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高质量的BONOBO基因组完善了对人类进化的分析。
DOI：
10.1038/s41586-021-03519-x
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发表时间：
2021-06
期刊：
影响因子：
64.8
通讯作者：
Eichler EE
中科院分区：
文献类型：
--
作者：
Mao Y;Catacchio CR;Hillier LW;Porubsky D;Li R;Sulovari A;Fernandes JD;Montinaro F;Gordon DS;Storer JM;Haukness M;Fiddes IT;Murali SC;Dishuck PC;Hsieh P;Harvey WT;Audano PA;Mercuri L;Piccolo I;Antonacci F;Munson KM;Lewis AP;Baker C;Underwood JG;Hoekzema K;Huang TH;Sorensen M;Walker JA;Hoffman J;Thibaud-Nissen F;Salama SR;Pang AWC;Lee J;Hastie AR;Paten B;Batzer MA;Diekhans M;Ventura M;Eichler EE
黑猩猩和倭黑猩猩的分化提供了近代人科物种形成的少数例子之一。在这里，我们描述了一个完整的注释，高质量的倭黑猩猩基因组组装，这是构建没有参考基因组的指导下，通过应用多平台基因组学方法。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%的缺口被关闭，包括约一半的片段重复和几乎所有全长移动的元件的分辨率。我们将倭黑猩猩的基因组与其他类人猿的基因组进行了比较，并确定了超过5，569个固定的结构变异，这些变异特别区分了倭黑猩猩和黑猩猩的谱系。我们关注的是在倭黑猩猩进化的最后几百万年里丢失、结构改变或扩展的基因。我们制作了一个高分辨率的不完整谱系排序图，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，如果我们考虑到包括大猩猩和猩猩在内的更深的进化史，超过36.5%的基因组显示不完整的谱系排序。我们还表明，人类和黑猩猩或人类和倭黑猩猩之间的不完整谱系排序的片段中有26%是非随机分布的，并且与基因组的其余部分相比，这些簇集片段中的基因显示出显著过量的氨基酸替换。一个高质量的倭黑猩猩基因组组装提供了对原始人类不完整谱系排序及其与基因进化和现存原始人类之间遗传关系的相关性的见解。
The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation. 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 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. A high-quality bonobo genome assembly provides insights into incomplete lineage sorting in hominids and its relevance to gene evolution and the genetic relationship among living hominids.
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BONOBO基因组与黑猩猩和人类基因组相比。
影响因子：
64.8
作者：
Pruefer, Kay;Munch, Kasper;Hellmann, Ines;Akagi, Keiko;Miller, Jason R.;Walenz, Brian;Koren, Sergey;Sutton, Granger;Kodira, Chinnappa;Winer, Roger;Knight, James R.;Mullikin, James C.;Meader, Stephen J.;Ponting, Chris P.;Lunter, Gerton;Higashino, Saneyuki;Hobolth, Asger;Dutheil, Julien;Karakoc, Emre;Alkan, Can;Sajjadian, Saba;Catacchio, Claudia Rita;Ventura, Mario;Marques-Bonet, Tomas;Eichler, Evan E.;Andre, Claudine;Atencia, Rebeca;Mugisha, Lawrence;Junhold, Joerg;Patterson, Nick;Siebauer, Michael;Good, Jeffrey M.;Fischer, Anne;Ptak, Susan E.;Lachmann, Michael;Symer, David E.;Mailund, Thomas;Schierup, Mikkel H.;Andres, Aida M.;Kelso, Janet;Paeaebo, Svante
通讯作者：
Paeaebo, Svante
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
7
作者：
Sanders AD;Hills M;Porubský D;Guryev V;Falconer E;Lansdorp PM
通讯作者：
Lansdorp PM
DOI：
10.1126/science.aae0344
发表时间：
2016-04-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gordon D;Huddleston J;Chaisson MJ;Hill CM;Kronenberg ZN;Munson KM;Malig M;Raja A;Fiddes I;Hillier LW;Dunn C;Baker C;Armstrong J;Diekhans M;Paten B;Shendure J;Wilson RK;Haussler D;Chin CS;Eichler EE
通讯作者：
Eichler EE
影响因子：
48
作者：
Sedlazeck FJ;Rescheneder P;Smolka M;Fang H;Nattestad M;von Haeseler A;Schatz MC
通讯作者：
Schatz MC