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Complete sequencing of ape genomes.

Publication ,  Journal Article
Yoo, D; Rhie, A; Hebbar, P; Antonacci, F; Logsdon, GA; Solar, SJ; Antipov, D; Pickett, BD; Safonova, Y; Montinaro, F; Luo, Y; Malukiewicz, J ...
Published in: Nature
May 2025
Published version (DOI) Link to item

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 (<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.

Duke Scholars

Craig Lowe
Author Craig Lowe Molecular Genetics and Microbiology
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Published In

Nature

DOI

10.1038/s41586-025-08816-3

EISSN

1476-4687

Publication Date

May 2025

Volume

641

Issue

8062

Start / End Page

401 / 418

Location

England

Related Subject Headings

  • Whole Genome Sequencing
  • Telomere
  • Segmental Duplications, Genomic
  • Phylogeny
  • Pan troglodytes
  • Pan paniscus
  • Humans
  • Hominidae
  • Heterochromatin
  • Haplotypes
 

Citation

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Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G. A., Solar, S. J., … Eichler, E. E. (2025). Complete sequencing of ape genomes. Nature, 641(8062), 401–418. https://doi.org/10.1038/s41586-025-08816-3
Yoo, DongAhn, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar, Dmitry Antipov, et al. “Complete sequencing of ape genomes.” Nature 641, no. 8062 (May 2025): 401–18. https://doi.org/10.1038/s41586-025-08816-3.
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, et al. Complete sequencing of ape genomes. Nature. 2025 May;641(8062):401–18.
Yoo, DongAhn, et al. “Complete sequencing of ape genomes.” Nature, vol. 641, no. 8062, May 2025, pp. 401–18. Pubmed, doi:10.1038/s41586-025-08816-3.
Yoo D, 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. Complete sequencing of ape genomes. Nature. 2025 May;641(8062):401–418.
Journal cover image

Published In

Nature

DOI

10.1038/s41586-025-08816-3

EISSN

1476-4687

Publication Date

May 2025

Volume

641

Issue

8062

Start / End Page

401 / 418

Location

England

Related Subject Headings

  • Whole Genome Sequencing
  • Telomere
  • Segmental Duplications, Genomic
  • Phylogeny
  • Pan troglodytes
  • Pan paniscus
  • Humans
  • Hominidae
  • Heterochromatin
  • Haplotypes