Complete sequencing of ape genomes
May 8, 2025·
D Yoo, A Rhie, P Hebbar, F Antonacci, GA Logsdon, SJ Solar, D Antipov, BD Pickett, Y Safonova, F Montinaro, Y Luo, J Malukiewicz, JM Storer, J Lin, AN Sequeira, RJ Mangan, G Hickey, GM Anez, P Balachandran, A Bankevich, CR Beck, A Biddanda, M Borchers, GG Bouffard, E Brannan, SY Brooks, L Carbone, L Carrel, AP Chan, J Crawford, M Diekhans, E Engelbrecht, C Feschotte, G Formenti, GH Garcia, L de Gennaro, D Gilbert, RE Green, A Guarracino, I Gupta, D Haddad, J Han, RS Harris, GA Hartley, WT Harvey, M Hiller, K Hoekzema, ML Houck, H Jeong, K Kamali, M Kellis, B Kille, C Lee, Y Lee, W Lees, AP Lewis, Q Li, M Loftus, YHE Loh, H Loucks, J Ma, Y Mao, JFI Martinez, P Masterson, RC McCoy, B McGrath, S McKinney, BS Meyer, KH Miga, SK Mohanty, KM Munson, K Pal, M Pennell, PA Pevzner, D Porubsky, T Potapova, FR Ringeling, JL Rocha, OA Ryder, S Sacco, S Saha, T Sasaki, MC Schatz, NJ Schork, C Shanks, L Smeds, DR Son, C Steiner, AP Sweeten, MG Tassia, F Thibaud-Nissen, E Torres-González, M Trivedi, W Wei, J Wertz, M Yang, P Zhang, S Zhang, Y Zhang, Z Zhang, SA Zhao, Y Zhu, ED Jarvis, JL Gerton, I Rivas-González, B Paten, ZA Szpiech, CD Huber, TL Lenz, MK Konkel, SV Yi, S Canzar, CT Watson, PH Sudmant, E Molloy, E Garrison, CB Lowe, M Ventura, RJ O’Neill, S Koren, KD Makova, AM Phillippy, EE Eichler
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Abstract
We 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.
Type
Publication
Nature
Authors
Prof. Carrel focuses on genetic, epigenetic, and genomic regulation of expression on the mammalian X chromosome.
Authors
Computational Scientist
Kaivan is a computer scientist/software engineer, specializing in AI/ML. He enjoys data analysis and applying AI/ML techniques to bioinformatics data. Currently, his research focuses on non-B DNA data.
Authors
Ph.D. Student
Saswat is interested in understanding the evolution of non-B-DNA structures in primates. Currently, he is working mainly on a specific type of non-B-DNA structure called the G-quadruplex or G4, for example, developing bioinformatic tools to analyze genome-wide distribution of these structures.
Authors
Postdoctoral Scholar
Karol has a Computer Science background but also enjoys the biological aspect of his work. He did his PhD in Oncology analyzing clonal evolution in leukemias. Currently he is focusing on a more standard type of evolution, that of the primate sex chromosomes. He enjoys creating interactive visual representations of his findings. Outside of the lab Karol likes playing music and scuba diving.
Authors
Dr. Oliver Ryder serves San Diego Zoo Wildlife Alliance as the Kleberg Endowed Director of Conservation Genetics. He oversees research activities in the areas of molecular genetics, genomic studies, and genetic rescue efforts, including stem cell applications – all focused on reducing extinction risk and contributing to species recovery and sustainable populations. He guides the strategic development of efforts to develop and expand a global network of cryobanking facilities, especially for viable tissue culture cells.
Authors
Postdoctoral Scholar
Linnéa’s research in the Makova lab involves investigating selection in non-canonical DNA from primates, especially G4 quadruplexes, using bioinformatics methods. Linnéa worked for 8 years as a bioinformatician in Dr. Hans Ellegren’s lab, developing approaches to study speciation, mutation rate and sex chromosome evolution in birds, before taking on a Ph. D. in evolutionary genetics. Her thesis “Conservation genomics in inbred Scandinavian wolves using bioinformatic methods” involved work on Y chromosome evolution, admixture, genetic load and structural variation.
Authors
Ph.D. student
Before starting his PhD in the Makova lab, Edmundo worked on regional human variation as an undergraduate in Puerto Rico and on translational cancer genomics as a postdoc in NIH. As part of this thesis work, he focuses on mitochondrial genomics that cover its evolution, and
relation to complex phenotypes.
Authors
Professor
Kateryna is interested in genomics, evolution, and human genetics.
Her lab studies mutations using both computational and experimental
approaches. Additional topics of interest include sex chromosome
evolution and genomics of childhood obesity.
Authors
Dr. Adam Phillippy is a Senior Investigator and head of the Genome Informatics Section at the National Human Genome Research Institute. His lab develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. He is a pioneer of single-molecule sequencing for the reconstruction of complete genomes and is best known for his work on completing the human genome from “telomere to telomere”.