Complete sequencing of ape genomes

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.; de Gennaro, Luciana; 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.

Complete sequencing of ape genomes

DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar, Dmitry Antipov, Brandon D. Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Joanna Malukiewicz, Jessica M. Storer, Jiadong Lin, Abigail N. Sequeira, Riley J. Mangan, Glenn Hickey, Graciela Monfort Anez, Parithi Balachandran, Anton Bankevich, Christine R. Beck, Arjun Biddanda, Matthew Borchers, Gerard G. Bouffard, Emry Brannan, Shelise Y. Brooks, Lucia Carbone, Laura Carrel, Agnes P. Chan, Juyun Crawford, Mark Diekhans, Eric Engelbrecht, Cedric Feschotte, Giulio Formenti, Gage H. Garcia, Luciana de Gennaro, David Gilbert, Richard E. Green, Andrea Guarracino, Ishaan Gupta, Diana Haddad, Junmin Han, Robert S. Harris, Gabrielle A. Hartley, William T. Harvey, Michael Hiller, Kendra Hoekzema, Marlys L. Houck, Hyeonsoo Jeong, Kaivan Kamali, Manolis Kellis, Bryce Kille, Chul Lee, Youngho Lee, William Lees, Alexandra P. Lewis, Qiuhui Li, Mark Loftus, Yong Hwee Eddie Loh, Hailey Loucks, Jian Ma, Yafei Mao, Juan F. I. Martinez, Patrick Masterson, Rajiv C. McCoy, Barbara McGrath, Sean McKinney, Britta S. Meyer, Karen H. Miga, Saswat K. Mohanty, Katherine M. Munson, Karol Pal, Matt Pennell, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Francisca R. Ringeling, Joana L. Rocha, Oliver A. Ryder, Samuel Sacco, Swati Saha, Takayo Sasaki, Michael C. Schatz, Nicholas J. Schork, Cole Shanks, Linnéa Smeds, Dongmin R. Son, Cynthia Steiner, Alexander P. Sweeten, Michael G. Tassia, Françoise Thibaud-Nissen, Edmundo Torres-González, Mihir Trivedi, Wenjie Wei, Julie Wertz, Muyu Yang, Panpan Zhang, Shilong Zhang, Yang Zhang, Zhenmiao Zhang, Sarah A. Zhao, Yixin Zhu, Erich D. Jarvis, Jennifer L. Gerton, Iker Rivas-González, Benedict Paten, Zachary A. Szpiech, Christian D. Huber, Tobias L. Lenz, Miriam K. Konkel, Soojin V. Yi, Stefan Canzar, Corey T. Watson, Peter H. Sudmant, Erin Molloy, Erik Garrison, Craig B. Lowe, Mario Ventura, Rachel J. O’Neill, Sergey Koren, Kateryna D. Makova (), Adam M. Phillippy () and Evan E. Eichler ()
Additional contact information
DongAhn Yoo: University of Washington School of Medicine
Arang Rhie: National Institutes of Health
Prajna Hebbar: University of California, Santa Cruz
Francesca Antonacci: University of Bari
Glennis A. Logsdon: University of Washington School of Medicine
Steven J. Solar: National Institutes of Health
Dmitry Antipov: National Institutes of Health
Brandon D. Pickett: National Institutes of Health
Yana Safonova: Pennsylvania State University
Francesco Montinaro: University of Bari
Yanting Luo: Duke University Medical Center
Joanna Malukiewicz: University of Hamburg
Jessica M. Storer: University of Connecticut
Jiadong Lin: University of Washington School of Medicine
Abigail N. Sequeira: Penn State University
Riley J. Mangan: Massachusetts Institute of Technology
Glenn Hickey: University of California, Santa Cruz
Graciela Monfort Anez: Stowers Institute for Medical Research
Parithi Balachandran: The Jackson Laboratory for Genomic Medicine
Anton Bankevich: Pennsylvania State University
Christine R. Beck: University of Connecticut
Arjun Biddanda: Johns Hopkins University
Matthew Borchers: Stowers Institute for Medical Research
Gerard G. Bouffard: National Institutes of Health
Emry Brannan: University of Connecticut
Shelise Y. Brooks: National Institutes of Health
Lucia Carbone: Oregon Health Sciences University
Laura Carrel: Penn State University School of Medicine
Agnes P. Chan: City of Hope National Medical Center
Juyun Crawford: National Institutes of Health
Mark Diekhans: University of California, Santa Cruz
Eric Engelbrecht: University of Louisville
Cedric Feschotte: Cornell University
Giulio Formenti: The Rockefeller University
Gage H. Garcia: University of Washington School of Medicine
Luciana de Gennaro: University of Bari
David Gilbert: San Diego Biomedical Research Institute
Richard E. Green: University of California, Santa Cruz
Andrea Guarracino: University of Tennessee Health Science Center
Ishaan Gupta: University of California, San Diego
Diana Haddad: National Institutes of Health
Junmin Han: Shanghai Jiao Tong University
Robert S. Harris: Penn State University
Gabrielle A. Hartley: University of Connecticut
William T. Harvey: University of Washington School of Medicine
Michael Hiller: LOEWE Centre for Translational Biodiversity Genomics
Kendra Hoekzema: University of Washington School of Medicine
Marlys L. Houck: San Diego Zoo Wildlife Alliance
Hyeonsoo Jeong: University of Washington School of Medicine
Kaivan Kamali: Penn State University
Manolis Kellis: Massachusetts Institute of Technology
Bryce Kille: Rice University
Chul Lee: The Rockefeller University
Youngho Lee: Seoul National University
William Lees: University of Louisville
Alexandra P. Lewis: University of Washington School of Medicine
Qiuhui Li: Johns Hopkins University
Mark Loftus: Clemson University
Yong Hwee Eddie Loh: University of California, Santa Barbara
Hailey Loucks: University of California, Santa Cruz
Jian Ma: Carnegie Mellon University
Yafei Mao: Shanghai Jiao Tong University
Juan F. I. Martinez: Pennsylvania State University
Patrick Masterson: National Institutes of Health
Rajiv C. McCoy: Johns Hopkins University
Barbara McGrath: Penn State University
Sean McKinney: Stowers Institute for Medical Research
Britta S. Meyer: University of Hamburg
Karen H. Miga: University of California, Santa Cruz
Saswat K. Mohanty: Penn State University
Katherine M. Munson: University of Washington School of Medicine
Karol Pal: Penn State University
Matt Pennell: Cornell University
Pavel A. Pevzner: University of California, San Diego
David Porubsky: University of Washington School of Medicine
Tamara Potapova: Stowers Institute for Medical Research
Francisca R. Ringeling: University of Regensburg
Joana L. Rocha: University of California, Berkeley
Oliver A. Ryder: San Diego Zoo Wildlife Alliance
Samuel Sacco: University of California, Santa Cruz
Swati Saha: University of Louisville
Takayo Sasaki: San Diego Biomedical Research Institute
Michael C. Schatz: Johns Hopkins University
Nicholas J. Schork: City of Hope National Medical Center
Cole Shanks: University of California, Santa Cruz
Linnéa Smeds: Penn State University
Dongmin R. Son: University of California, Santa Barbara
Cynthia Steiner: San Diego Zoo Wildlife Alliance
Alexander P. Sweeten: National Institutes of Health
Michael G. Tassia: Johns Hopkins University
Françoise Thibaud-Nissen: National Institutes of Health
Edmundo Torres-González: Penn State University
Mihir Trivedi: University of Washington School of Medicine
Wenjie Wei: Westlake University
Julie Wertz: University of Washington School of Medicine
Muyu Yang: Carnegie Mellon University
Panpan Zhang: Cornell University
Shilong Zhang: Shanghai Jiao Tong University
Yang Zhang: Carnegie Mellon University
Zhenmiao Zhang: University of California, San Diego
Sarah A. Zhao: Massachusetts Institute of Technology
Yixin Zhu: Cornell University
Erich D. Jarvis: The Rockefeller University
Jennifer L. Gerton: Stowers Institute for Medical Research
Iker Rivas-González: Max Planck Institute for Evolutionary Anthropology
Benedict Paten: University of California, Santa Cruz
Zachary A. Szpiech: Penn State University
Christian D. Huber: Penn State University
Tobias L. Lenz: University of Hamburg
Miriam K. Konkel: Clemson University
Soojin V. Yi: University of California, Santa Barbara
Stefan Canzar: University of Regensburg
Corey T. Watson: University of Louisville
Peter H. Sudmant: University of California, Berkeley
Erin Molloy: University of Maryland
Erik Garrison: University of Tennessee Health Science Center
Craig B. Lowe: Duke University Medical Center
Mario Ventura: University of Bari
Rachel J. O’Neill: University of Connecticut
Sergey Koren: National Institutes of Health
Kateryna D. Makova: Penn State University
Adam M. Phillippy: National Institutes of Health
Evan E. Eichler: University of Washington School of Medicine

Nature, 2025, vol. 641, issue 8062, 401-418

Abstract: Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1–3. 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 (

Date: 2025
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DOI: 10.1038/s41586-025-08816-3

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