Complete sequencing of ape genomes

Dong Ahn 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; Evan E. Eichler

doi:10.1038/s41586-025-08816-3

Complete sequencing of ape genomes

Dong Ahn 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 BankevichChristine 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, Evan E. Eichler

Research output: Contribution to journal › Article › peer-review

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Abstract

The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies^{1, 2–3}. 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 (<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.

Original language	English (US)
Article number	aae0344
Pages (from-to)	401-418
Number of pages	18
Journal	Nature
Volume	641
Issue number	8062
DOIs	https://doi.org/10.1038/s41586-025-08816-3
State	Published - May 8 2025

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Yoo, D. A., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G. A., Solar, S. J., Antipov, D., Pickett, B. D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J. M., Lin, J., Sequeira, A. N., Mangan, R. J., Hickey, G., Monfort Anez, G., Balachandran, P., ... Eichler, E. E. (2025). Complete sequencing of ape genomes. Nature, 641(8062), 401-418. Article aae0344. https://doi.org/10.1038/s41586-025-08816-3

@article{9bbf13d35d5d4643ad6323e86a172141,

title = "Complete sequencing of ape genomes",

abstract = "The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1, 2–3. 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 (<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.",

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

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = may,

day = "8",

doi = "10.1038/s41586-025-08816-3",

language = "English (US)",

volume = "641",

pages = "401--418",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "8062",

}

Yoo, DA, Rhie, A, Hebbar, P, Antonacci, F, Logsdon, GA, Solar, SJ, Antipov, D, Pickett, BD, Safonova, Y, Montinaro, F, Luo, Y, Malukiewicz, J, Storer, JM, Lin, J, Sequeira, AN, Mangan, RJ, Hickey, G, Monfort Anez, G, Balachandran, P, Bankevich, A, Beck, CR, Biddanda, A, Borchers, M, Bouffard, GG, Brannan, E, Brooks, SY, Carbone, L, Carrel, L, Chan, AP, Crawford, J, Diekhans, M, Engelbrecht, E, Feschotte, C, Formenti, G, Garcia, GH, de Gennaro, L, Gilbert, D, Green, RE, Guarracino, A, Gupta, I, Haddad, D, Han, J, Harris, RS, Hartley, GA, Harvey, WT, Hiller, M, Hoekzema, K, Houck, ML, Jeong, H, Kamali, K, Kellis, M, Kille, B, Lee, C, Lee, Y, Lees, W, Lewis, AP, Li, Q, Loftus, M, Loh, YHE, Loucks, H, Ma, J, Mao, Y, Martinez, JFI, Masterson, P, McCoy, RC, McGrath, B, McKinney, S, Meyer, BS, Miga, KH, Mohanty, SK, Munson, KM, Pal, K, Pennell, M, Pevzner, PA, Porubsky, D, Potapova, T, Ringeling, FR, Rocha, JL, Ryder, OA, Sacco, S, Saha, S, Sasaki, T, Schatz, MC, Schork, NJ, Shanks, C, Smeds, L, Son, DR, Steiner, C, Sweeten, AP, Tassia, MG, Thibaud-Nissen, F, Torres-González, E, Trivedi, M, Wei, W, Wertz, J, Yang, M, Zhang, P, Zhang, S, Zhang, Y, Zhang, Z, Zhao, SA, Zhu, Y, Jarvis, ED, Gerton, JL, Rivas-González, I, Paten, B, Szpiech, ZA , Huber, CD, Lenz, TL, Konkel, MK, Yi, SV, Canzar, S, Watson, CT, Sudmant, PH, Molloy, E, Garrison, E, Lowe, CB, Ventura, M, O’Neill, RJ, Koren, S, Makova, KD, Phillippy, AM & Eichler, EE 2025, 'Complete sequencing of ape genomes', Nature, vol. 641, no. 8062, aae0344, pp. 401-418. https://doi.org/10.1038/s41586-025-08816-3

TY - JOUR

T1 - Complete sequencing of ape genomes

AU - Yoo, Dong Ahn

AU - Rhie, Arang

AU - Hebbar, Prajna

AU - Antonacci, Francesca

AU - Logsdon, Glennis A.

AU - Solar, Steven J.

AU - Antipov, Dmitry

AU - Pickett, Brandon D.

AU - Safonova, Yana

AU - Montinaro, Francesco

AU - Luo, Yanting

AU - Malukiewicz, Joanna

AU - Storer, Jessica M.

AU - Lin, Jiadong

AU - Sequeira, Abigail N.

AU - Mangan, Riley J.

AU - Hickey, Glenn

AU - Monfort Anez, Graciela

AU - Balachandran, Parithi

AU - Bankevich, Anton

AU - Beck, Christine R.

AU - Biddanda, Arjun

AU - Borchers, Matthew

AU - Bouffard, Gerard G.

AU - Brannan, Emry

AU - Brooks, Shelise Y.

AU - Carbone, Lucia

AU - Carrel, Laura

AU - Chan, Agnes P.

AU - Crawford, Juyun

AU - Diekhans, Mark

AU - Engelbrecht, Eric

AU - Feschotte, Cedric

AU - Formenti, Giulio

AU - Garcia, Gage H.

AU - de Gennaro, Luciana

AU - Gilbert, David

AU - Green, Richard E.

AU - Guarracino, Andrea

AU - Gupta, Ishaan

AU - Haddad, Diana

AU - Han, Junmin

AU - Harris, Robert S.

AU - Hartley, Gabrielle A.

AU - Harvey, William T.

AU - Hiller, Michael

AU - Hoekzema, Kendra

AU - Houck, Marlys L.

AU - Jeong, Hyeonsoo

AU - Kamali, Kaivan

AU - Kellis, Manolis

AU - Kille, Bryce

AU - Lee, Chul

AU - Lee, Youngho

AU - Lees, William

AU - Lewis, Alexandra P.

AU - Li, Qiuhui

AU - Loftus, Mark

AU - Loh, Yong Hwee Eddie

AU - Loucks, Hailey

AU - Ma, Jian

AU - Mao, Yafei

AU - Martinez, Juan F.I.

AU - Masterson, Patrick

AU - McCoy, Rajiv C.

AU - McGrath, Barbara

AU - McKinney, Sean

AU - Meyer, Britta S.

AU - Miga, Karen H.

AU - Mohanty, Saswat K.

AU - Munson, Katherine M.

AU - Pal, Karol

AU - Pennell, Matt

AU - Pevzner, Pavel A.

AU - Porubsky, David

AU - Potapova, Tamara

AU - Ringeling, Francisca R.

AU - Rocha, Joana L.

AU - Ryder, Oliver A.

AU - Sacco, Samuel

AU - Saha, Swati

AU - Sasaki, Takayo

AU - Schatz, Michael C.

AU - Schork, Nicholas J.

AU - Shanks, Cole

AU - Smeds, Linnéa

AU - Son, Dongmin R.

AU - Steiner, Cynthia

AU - Sweeten, Alexander P.

AU - Tassia, Michael G.

AU - Thibaud-Nissen, Françoise

AU - Torres-González, Edmundo

AU - Trivedi, Mihir

AU - Wei, Wenjie

AU - Wertz, Julie

AU - Yang, Muyu

AU - Zhang, Panpan

AU - Zhang, Shilong

AU - Zhang, Yang

AU - Zhang, Zhenmiao

AU - Zhao, Sarah A.

AU - Zhu, Yixin

AU - Jarvis, Erich D.

AU - Gerton, Jennifer L.

AU - Rivas-González, Iker

AU - Paten, Benedict

AU - Szpiech, Zachary A.

AU - Huber, Christian D.

AU - Lenz, Tobias L.

AU - Konkel, Miriam K.

AU - Yi, Soojin V.

AU - Canzar, Stefan

AU - Watson, Corey T.

AU - Sudmant, Peter H.

AU - Molloy, Erin

AU - Garrison, Erik

AU - Lowe, Craig B.

AU - Ventura, Mario

AU - O’Neill, Rachel J.

AU - Koren, Sergey

AU - Makova, Kateryna D.

AU - Phillippy, Adam M.

AU - Eichler, Evan E.

PY - 2025/5/8

Y1 - 2025/5/8

N2 - The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1, 2–3. 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 (<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.

AB - The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1, 2–3. 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 (<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.

UR - http://www.scopus.com/inward/record.url?scp=105002176999&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=105002176999&partnerID=8YFLogxK

U2 - 10.1038/s41586-025-08816-3

DO - 10.1038/s41586-025-08816-3

M3 - Article

C2 - 40205052

AN - SCOPUS:105002176999

SN - 0028-0836

VL - 641

SP - 401

EP - 418

JO - Nature

JF - Nature

IS - 8062

M1 - aae0344

ER -

Complete sequencing of ape genomes

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