Complete sequencing of ape genomes
Authors: Yoo DongAhn , Rhie Arang , Hebbar Prajna , Antonacci Francesca , Logsdon Glennis A. , Solar Steven J. , Antipov Dmitry , Pickett Brandon D. , Safonova Yana , Montinaro Francesco , Luo Yanting , Malukiewicz Joanna , Storer Jessica M. , Lin Jiadong , Sequeira Abigail N. , Mangan Riley J. , Hickey Glenn , Anez Graciela Monfort , Balachandran Parithi , Bankevich Anton , Beck Christine R. , Biddanda Arjun , Borchers Matthew , Bouffard Gerard G. , Brannan Emry , Brooks Shelise Y. , Carbone Lucia , Carrel Laura , Chan Agnes P. , Crawford Juyun , Diekhans Mark , Engelbrecht Eric , Feschotte Cedric , Formenti Giulio , Garcia Gage H. , Gennaro Luciana de , Gilbert David , Green Richard E. , Guarracino Andrea , Gupta Ishaan , Haddad Diana , Han Junmin , Harris Robert S. , Hartley Gabrielle A. , Harvey William T. , Hiller Michael , Hoekzema Kendra , Houck Marlys L. , Jeong Hyeonsoo , Kamali Kaivan , Kellis Manolis , Kille Bryce , Lee Chul , Lee Youngho , Lees William , Lewis Alexandra P. , Li Qiuhui , Loftus Mark , Loh Yong Hwee Eddie , Loucks Hailey , Ma Jian , Mao Yafei , Martinez Juan F. I. , Masterson Patrick , McCoy Rajiv C. , McGrath Barbara , McKinney Sean , Meyer Britta S. , Miga Karen H. , Mohanty Saswat K. , Munson Katherine M. , Pal Karol , Pennell Matt , Pevzner Pavel A. , Porubsky David , Potapova Tamara , Ringeling Francisca R. , Rocha Joana L. , Ryder Oliver A. , Sacco Samuel , Saha Swati , Sasaki Takayo , Schatz Michael C. , Schork Nicholas J. , Shanks Cole , Smeds Linnéa , Son Dongmin R. , Steiner Cynthia , Sweeten Alexander P. , Tassia Michael G. , Thibaud-Nissen Françoise , Torres-González Edmundo , Trivedi Mihir , Wei Wenjie , Wertz Julie , Yang Muyu , Zhang Panpan , Zhang Shilong , Zhang Yang , Zhang Zhenmiao , Zhao Sarah A. , Zhu Yixin , Jarvis Erich D. , Gerton Jennifer L. , Rivas-González Iker , Paten Benedict , Szpiech Zachary A. , Huber Christian D. , Lenz Tobias L. , Konkel Miriam K. , Yi Soojin V. , Canzar Stefan , Watson Corey T. , Sudmant Peter H. , Molloy Erin , Garrison Erik , Lowe Craig B. , Ventura Mario , O’Neill Rachel J. , Koren Sergey , Makova Kateryna D. , Phillippy Adam M. , Eichler Evan E. 
Published: August 2024

ABSTRACTWe present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.