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 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
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Nature. 2025 May;641(8062):401-418. doi: 10.1038/s41586-025-08816-3. Epub 2025 Apr 9.
The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies. 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.
传统上，类人猿基因组中最具动态性和重复性的区域被排除在比较研究之外。因此，我们对人类物种进化的理解并不完整。在此，我们展示了单倍型解析的参考基因组，并对六种猿类物种进行了比较分析：黑猩猩、倭黑猩猩、大猩猩、婆罗洲猩猩、苏门答腊猩猩和合趾猿。我们实现了染色体水平的连续性，并具有较高的序列准确性（每270万个碱基中误差小于1个），并完整地测序了215条无间隙的端粒到端粒的染色体。我们解析了具有挑战性的区域，如主要组织相容性复合体和免疫球蛋白基因座，以提供深入的进化见解。比较分析使得能够对以前未表征或研究不充分的区域的进化和多样性进行研究，而不受映射到人类参考基因组的偏差影响。这些区域包括谱系特异性片段重复中的新产生的基因家族、着丝粒DNA、近端着丝粒染色体和亚端粒异染色质。这一资源为未来人类及其最亲近的现存猿类亲属的进化研究提供了全面的基线。
