Complete sequencing of ape genomes
The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies<sup>1-3</sup>. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.
Authors
- Marlys L. Houck (ORCID: https://orcid.org/0000-0002-3879-9511)
- Wenjie Wei (ORCID: https://orcid.org/0000-0003-4105-9693)
- William Lees (ORCID: https://orcid.org/0000-0001-9834-6840)
- Zachary A. Szpiech (ORCID: https://orcid.org/0000-0001-6372-8224)
- Mihir Trivedi (ORCID: https://orcid.org/0000-0001-6506-2390)
- Agnes P. Chan (ORCID: https://orcid.org/0000-0003-2373-9580)
- Yana Safonova (ORCID: https://orcid.org/0000-0002-9634-4216)
- Francesco Montinaro (ORCID: https://orcid.org/0000-0002-4506-963X)
- Miriam K. Konkel (ORCID: https://orcid.org/0000-0002-3190-1667)
- Parithi Balachandran (ORCID: https://orcid.org/0000-0003-3256-1403)
- Erik Garrison (ORCID: https://orcid.org/0000-0003-3821-631X)
- Glennis A. Logsdon (ORCID: https://orcid.org/0000-0003-2396-0656)
- Iker Rivas-González (ORCID: https://orcid.org/0000-0002-0515-0628)
- Evan E. Eichler (ORCID: https://orcid.org/0000-0002-8246-4014)
- Rachel J. O’Neill (ORCID: https://orcid.org/0000-0002-1525-6821)
- Jennifer L. Gerton (ORCID: https://orcid.org/0000-0003-0743-3637)
- Barbara C. McGrath
- Giulio Formenti (ORCID: https://orcid.org/0000-0002-7554-5991)
- Eric Engelbrecht (ORCID: https://orcid.org/0000-0002-4122-3425)
- Gage H. Garcia (ORCID: https://orcid.org/0009-0005-2383-722X)
- Peter H. Sudmant (ORCID: https://orcid.org/0000-0002-9573-8248)
- Christian D. Huber (ORCID: https://orcid.org/0000-0002-2267-2604)
- David M. Gilbert (ORCID: https://orcid.org/0000-0001-8087-9737)
- Hyeonsoo Jeong (ORCID: https://orcid.org/0000-0002-5565-2685)
- Mark Loftus (ORCID: https://orcid.org/0000-0002-6279-6855)
- Dmitry Antipov (ORCID: https://orcid.org/0000-0002-6087-0660)
- Zhenmiao Zhang (ORCID: https://orcid.org/0000-0003-3748-1664)
- Juyun Crawford (ORCID: https://orcid.org/0009-0006-4430-7751)
- Ishaan Gupta (ORCID: https://orcid.org/0000-0001-8934-9919)
- Shelise Brooks
- Pavel A. Pevzner (ORCID: https://orcid.org/0000-0002-0418-165X)
- Andrea Guarracino (ORCID: https://orcid.org/0000-0001-9744-131X)
- Erich D. Jarvis (ORCID: https://orcid.org/0000-0001-8931-5049)
- Luciana de Gennaro (ORCID: https://orcid.org/0009-0007-9572-7630)
- Alexander P. Sweeten (ORCID: https://orcid.org/0000-0002-5316-2973)
- Tamara Potapova (ORCID: https://orcid.org/0000-0003-2761-1795)
- Gerard G. Bouffard (ORCID: https://orcid.org/0000-0001-8744-6440)
- Cole Shanks (ORCID: https://orcid.org/0009-0009-9633-6695)
- Julie Wertz
- Brandon D. Pickett (ORCID: https://orcid.org/0000-0001-8235-4440)
- Oliver A. Ryder (ORCID: https://orcid.org/0000-0003-2427-763X)
- Britta Meyer (ORCID: https://orcid.org/0000-0002-2549-1825)
- Edmundo Torres-González (ORCID: https://orcid.org/0000-0001-8844-2855)
- Richard E. Green (ORCID: https://orcid.org/0000-0003-0516-5827)
- Muyu Yang (ORCID: https://orcid.org/0000-0002-0142-0328)
- Françoise Thibaud‐Nissen (ORCID: https://orcid.org/0000-0003-4957-7807)
- Linnéa Smeds (ORCID: https://orcid.org/0000-0002-8415-9259)
- Swati Saha (ORCID: https://orcid.org/0009-0004-7210-6338)
- Michael Hiller (ORCID: https://orcid.org/0000-0003-3024-1449)
- Hailey Loucks (ORCID: https://orcid.org/0009-0000-6956-9922)
- Kateryna D. Makova (ORCID: https://orcid.org/0000-0002-6212-9526)
- Saswat K. Mohanty (ORCID: https://orcid.org/0000-0002-1813-589X)
- Sergey Koren (ORCID: https://orcid.org/0000-0002-1472-8962)
- William T. Harvey (ORCID: https://orcid.org/0000-0003-0646-7528)
- Karen H. Miga (ORCID: https://orcid.org/0000-0002-3670-4507)
- Erin K. Molloy (ORCID: https://orcid.org/0000-0001-5553-3312)
- Michael G. Tassia (ORCID: https://orcid.org/0000-0002-5485-8155)
- Yixin Zhu (ORCID: https://orcid.org/0000-0003-4257-462X)
- Gabrielle A. Hartley (ORCID: https://orcid.org/0000-0002-5672-2171)
- Abigail N Sequeira (ORCID: https://orcid.org/0000-0003-4093-1654)
- Cynthia Steiner (ORCID: https://orcid.org/0000-0002-2131-8072)
- Riley J. Mangan (ORCID: https://orcid.org/0000-0003-3342-3934)
- Takayo Sasaki (ORCID: https://orcid.org/0000-0001-7609-9316)
- Joana L. Rocha (ORCID: https://orcid.org/0000-0003-3266-6328)
- Mark Diekhans (ORCID: https://orcid.org/0000-0002-0430-0989)
- Lucia Carbone (ORCID: https://orcid.org/0000-0002-2118-107X)
- Stefan Canzar (ORCID: https://orcid.org/0000-0003-4719-8010)
- Patrick Masterson (ORCID: https://orcid.org/0000-0001-8837-3706)
- Michael C. Schatz (ORCID: https://orcid.org/0000-0002-4118-4446)
- Corey T. Watson (ORCID: https://orcid.org/0000-0001-7248-8787)
- Sean McKinney (ORCID: https://orcid.org/0000-0002-9740-6247)
- Benedict Paten (ORCID: https://orcid.org/0000-0001-8863-3539)
- Joanna Malukiewicz (ORCID: https://orcid.org/0000-0003-0494-1089)
- Alexandra P. Lewis (ORCID: https://orcid.org/0000-0002-6195-4786)
- Yong Hwee Eddie Loh
- Prajna Hebbar (ORCID: https://orcid.org/0009-0008-9817-5330)
- Kendra Hoekzema (ORCID: https://orcid.org/0000-0002-8058-0177)
- Mario Ventura (ORCID: https://orcid.org/0000-0001-7762-8777)
- Juan Francisco Iturralde Martinez
- Cedric Feschotte
- Yafei Mao (ORCID: https://orcid.org/0000-0002-9648-4278)
- Matthew W. Pennell (ORCID: https://orcid.org/0000-0002-2886-3970)
- Steven J. Solar (ORCID: https://orcid.org/0000-0003-3051-9009)
- Anton Bankevich (ORCID: https://orcid.org/0000-0003-0609-9542)
- Francesca Antonacci (ORCID: https://orcid.org/0000-0002-5833-6186)
- Diana Haddad
- Bryce Kille (ORCID: https://orcid.org/0000-0003-2946-6915)
- Jessica M. Storer (ORCID: https://orcid.org/0000-0002-9619-5265)
- Robert S. Harris (ORCID: https://orcid.org/0000-0001-5464-6892)
- Nicholas J. Schork (ORCID: https://orcid.org/0000-0003-0920-5013)
- Samuel Sacco (ORCID: https://orcid.org/0000-0003-1227-8934)
- Glenn Hickey (ORCID: https://orcid.org/0000-0002-2280-9404)
- Rajiv C. McCoy (ORCID: https://orcid.org/0000-0003-0615-146X)
- Arang Rhie (ORCID: https://orcid.org/0000-0002-9809-8127)
- Jiadong Lin (ORCID: https://orcid.org/0000-0002-8116-5901)
- DongAhn Yoo (ORCID: https://orcid.org/0000-0003-0033-3721)
- Karol Pál (ORCID: https://orcid.org/0000-0002-7726-4691)
- Matthew Borchers (ORCID: https://orcid.org/0000-0001-5903-3489)
- Katherine M. Munson (ORCID: https://orcid.org/0000-0001-8413-6498)
- Soojin V. Yi (ORCID: https://orcid.org/0000-0003-1497-1871)
- Arjun Biddanda (ORCID: https://orcid.org/0000-0003-1861-1523)
- Christine R. Beck (ORCID: https://orcid.org/0000-0001-7821-8489)
- Emry O. Brannan (ORCID: https://orcid.org/0009-0002-1347-8479)
- Laura Carrel (ORCID: https://orcid.org/0000-0002-5868-4228)
- Kaivan Kamali
- Adam M. Phillippy (ORCID: https://orcid.org/0000-0003-2983-8934)
- David Porubský (ORCID: https://orcid.org/0000-0001-8414-8966)
- Craig B. Lowe (ORCID: https://orcid.org/0000-0002-6838-1976)
- Manolis Kellis (ORCID: https://orcid.org/0000-0001-7113-9630)
- Yang Zhang (ORCID: https://orcid.org/0000-0002-1483-9195)
- Young Ho Lee (ORCID: https://orcid.org/0000-0003-4213-1909)
- Panpan Zhang (ORCID: https://orcid.org/0000-0002-2204-6400)
- Jian Ma (ORCID: https://orcid.org/0000-0002-4202-5834)
- Shilong Zhang (ORCID: https://orcid.org/0009-0000-8844-2273)
- Yanting Luo (ORCID: https://orcid.org/0000-0003-1227-8512)
- Francisca Rojas (ORCID: https://orcid.org/0000-0001-8776-9768)
- Chul Lee (ORCID: https://orcid.org/0000-0002-9403-0774)
- Tobias L. Lenz (ORCID: https://orcid.org/0000-0002-7203-0044)
- Qiuhui Li
- Graciela Monfort Anez
- Dongmin R. Son
- Junmin Han
- Sarah A Zhao
Institutions
- Oregon National Primate Research Center (US)
- Broad Institute (US)
- Goethe University Frankfurt (DE)
- Stowers Institute for Medical Research (US)
- Translational Genomics Research Institute (US)
- National Institutes of Health (US)
- Pennsylvania State University (US)
- Zoological Society of San Diego (US)
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- Bar-Ilan University (IL)
- University of Connecticut (US)
- University of Louisville (US)
- Johns Hopkins University (US)
- University of California, Santa Barbara (US)
- Universität Hamburg (DE)
- University of Tennessee Health Science Center (US)
- Oregon Health & Science University (US)
- Shanghai Jiao Tong University (CN)
- University of California, Santa Cruz (US)
- University of Washington (US)
- Huazhong Agricultural University (CN)
- Cornell University (US)
- German Primate Center (DE)
- Senckenberg Research Institute and Natural History Museum Frankfurt/M (DE)
- Westlake University (CN)
- University of California San Diego (US)
- National Human Genome Research Institute (US)
- Center for Human Genetics (US)
- National Center for Biotechnology Information (US)
- Jackson Laboratory (US)
- San Diego Biomedical Research Institute (US)
- Max Planck Institute for Evolutionary Anthropology (DE)
- LOEWE Centre for Translational Biodiversity Genomics (DE)
- Duke Medical Center (US)
- Institute of Molecular Biology (AM)
- Greenwood Genetic Center (US)
- Duke University Hospital (US)
- Digital Research Alliance of Canada
- University of Bari Aldo Moro (IT)
- University of Tartu (EE)
- University of Regensburg (DE)
- Chongqing Jiaotong University (CN)
- Massachusetts Institute of Technology (US)
- University of Maryland, College Park (US)
- Rice University (US)
- Carnegie Mellon University (US)
- UConn Health (US)
- Zhejiang University (CN)
- University of Pennsylvania (US)
- Clemson University (US)
- Penn State Milton S. Hershey Medical Center (US)
- Rockefeller University (US)
- University of California, Berkeley (US)
Publication Details
- Journal
- Nature
- Published
- 2025-04-09
- DOI
- https://doi.org/10.1038/s41586-025-08816-3
- Citations
- 98
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 75.77