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

ABSTRACT: 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^1,3-5 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.

SUBMITTER: Mao Y

PROVIDER: S-EPMC8172381 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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

Mao Yafei Y Catacchio Claudia R CR Hillier LaDeana W LW Porubsky David D Li Ruiyang R Sulovari Arvis A Fernandes Jason D JD Montinaro Francesco F Gordon David S DS Storer Jessica M JM Haukness Marina M Fiddes Ian T IT Murali Shwetha Canchi SC Dishuck Philip C PC Hsieh PingHsun P Harvey William T WT Audano Peter A PA Mercuri Ludovica L Piccolo Ilaria I Antonacci Francesca F Munson Katherine M KM Lewis Alexandra P AP Baker Carl C Underwood Jason G JG Hoekzema Kendra K Huang Tzu-Hsueh TH Sorensen Melanie M Walker Jerilyn A JA Hoffman Jinna J Thibaud-Nissen Françoise F Salama Sofie R SR Pang Andy W C AWC Lee Joyce J Hastie Alex R AR Paten Benedict B Batzer Mark A MA Diekhans Mark M Ventura Mario M Eichler Evan E EE

Nature 20210505 7861

The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation<sup>1,2</sup>. 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 al ...[more]

PMID: 33953399

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

Publications

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

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