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A high-quality bonobo genome refines the analysis of hominid evolution

Nature 2021
Mao Y. et al

The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. 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 apes1,3-5 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.


Yafei Mao # 1Claudia R Catacchio # 2LaDeana W Hillier 1David Porubsky 1Ruiyang Li 1Arvis Sulovari 1Jason D Fernandes 3Francesco Montinaro 2 4David S Gordon 1 5Jessica M Storer 6Marina Haukness 3Ian T Fiddes 3Shwetha Canchi Murali 1 5Philip C Dishuck 1PingHsun Hsieh 1William T Harvey 1Peter A Audano 1Ludovica Mercuri 2Ilaria Piccolo 2Francesca Antonacci 2Katherine M Munson 1Alexandra P Lewis 1Carl Baker 1Jason G Underwood 7Kendra Hoekzema 1Tzu-Hsueh Huang 1Melanie Sorensen 1Jerilyn A Walker 8Jinna Hoffman 9Françoise Thibaud-Nissen 9Sofie R Salama 3 10Andy W C Pang 11Joyce Lee 11Alex R Hastie 11Benedict Paten 3Mark A Batzer 8Mark Diekhans 3Mario Ventura 12Evan E Eichler 1


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