Complete sequencing of ape genomes

• 成果类型: Article
• 署名作者: 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; Monfort Anez, Graciela; 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, Linnea; Son, Dongmin R.; Steiner, Cynthia; Sweeten, Alexander P.; Tassia, Michael G.; Thibaud-Nissen, Francoise; Torres-Gonzalez, 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-Gonzalez, 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.
• 署名单位: University of Washington; University of Washington Seattle; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI); University of California System; University of California Santa Cruz; Universita degli Studi di Bari Aldo Moro; University of Pennsylvania; Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Pennsylvania State University - University Park; University of Tartu; Duke University; University of Hamburg; Leibniz Association; Deutsches Primatenzentrum (DPZ); University of Connecticut; Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Pennsylvania State University - University Park; Massachusetts Institute of Technology (MIT); Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; Harvard University; Harvard Medical School; Stowers Institute for Medical Research; Jackson Laboratory; University of Connecticut; Johns Hopkins University; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI); University of Connecticut; Oregon Health & Science University; Oregon Health & Science University; Oregon National Primate Research Center; Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Penn State Health; Translational Genomics Research Institute; City of Hope; University of Louisville; Cornell University; Rockefeller University; University of California System; University of California Santa Cruz; University of Tennessee System; University of Tennessee Health Science Center; University of California System; University of California San Diego; National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM); Shanghai Jiao Tong University; Leibniz Association; Senckenberg Gesellschaft fur Naturforschung (SGN); Goethe University Frankfurt; Rice University; Rockefeller University; Seoul National University (SNU); Bar Ilan University; Johns Hopkins University; Clemson University; Clemson University; University of California System; University of California Santa Barbara; Carnegie Mellon University; Zhejiang University; Shanghai Jiao Tong University; Cornell University; University of Regensburg; University of California System; University of California Berkeley; University of California System; University of California Santa Barbara; Westlake University; Huazhong Agricultural University; Howard Hughes Medical Institute; Max Planck Society; University of California System; University of California Santa Barbara; University of California System; University of California Berkeley; University System of Maryland; University of Maryland College Park
• 刊物名称: Nature
• ISSN/ISSBN: 0028-2266
• DOI: 10.1038/s41586-025-08816-3
• 发表日期: 2025-05-08
• 关键词: segmental duplications; evolutionary history; pericentric-inversion; molecular characterization; 15q13.3 microdeletion; gene family; chimpanzee; diversity; IMPACT; heterochromatin

摘要

The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies(1-3). 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.