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

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

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

Yafei Mao, Claudia R. Catacchio, LaDeana W. Hillier, David Porubsky, Ruiyang Li, Arvis Sulovari, Jason D. Fernandes, Francesco Montinaro, David S. Gordon, Jessica M. Storer, Marina Haukness, Ian T. Fiddes, Shwetha Canchi Murali, Philip C. Dishuck, PingHsun Hsieh, William T. Harvey, Peter A. Audano, Ludovica Mercuri, Ilaria Piccolo, Francesca Antonacci, Katherine M. Munson, Alexandra P. Lewis, Carl Baker, Jason G. Underwood, Kendra Hoekzema, Tzu-Hsueh Huang, Melanie Sorensen, Jerilyn A. Walker, Jinna Hoffman, Françoise Thibaud-Nissen, Sofie R. Salama, Andy W. C. Pang, Joyce Lee, Alex R. Hastie, Benedict Paten, Mark A. Batzer, Mark Diekhans, Mario Ventura () and Evan E. Eichler ()
Additional contact information
Yafei Mao: University of Washington School of Medicine
Claudia R. Catacchio: University of Bari
LaDeana W. Hillier: University of Washington School of Medicine
David Porubsky: University of Washington School of Medicine
Ruiyang Li: University of Washington School of Medicine
Arvis Sulovari: University of Washington School of Medicine
Jason D. Fernandes: University of California, Santa Cruz
Francesco Montinaro: University of Bari
David S. Gordon: University of Washington School of Medicine
Jessica M. Storer: Institute for Systems Biology
Marina Haukness: University of California, Santa Cruz
Ian T. Fiddes: University of California, Santa Cruz
Shwetha Canchi Murali: University of Washington School of Medicine
Philip C. Dishuck: University of Washington School of Medicine
PingHsun Hsieh: University of Washington School of Medicine
William T. Harvey: University of Washington School of Medicine
Peter A. Audano: University of Washington School of Medicine
Ludovica Mercuri: University of Bari
Ilaria Piccolo: University of Bari
Francesca Antonacci: University of Bari
Katherine M. Munson: University of Washington School of Medicine
Alexandra P. Lewis: University of Washington School of Medicine
Carl Baker: University of Washington School of Medicine
Jason G. Underwood: Pacific Biosciences (PacBio) of California
Kendra Hoekzema: University of Washington School of Medicine
Tzu-Hsueh Huang: University of Washington School of Medicine
Melanie Sorensen: University of Washington School of Medicine
Jerilyn A. Walker: Louisiana State University
Jinna Hoffman: National Institutes of Health
Françoise Thibaud-Nissen: National Institutes of Health
Sofie R. Salama: University of California, Santa Cruz
Andy W. C. Pang: Bionano Genomics
Joyce Lee: Bionano Genomics
Alex R. Hastie: Bionano Genomics
Benedict Paten: University of California, Santa Cruz
Mark A. Batzer: Louisiana State University
Mark Diekhans: University of California, Santa Cruz
Mario Ventura: University of Bari
Evan E. Eichler: University of Washington School of Medicine

Nature, 2021, vol. 594, issue 7861, 77-81

Abstract: Abstract 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.

Date: 2021
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41586-021-03519-x Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:594:y:2021:i:7861:d:10.1038_s41586-021-03519-x

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-021-03519-x

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().