Complete sequencing of ape genomes
DongAhn Yoo(University of Washington), Arang Rhie(National Institutes of Health), Prajna Hebbar(University of California, Santa Cruz), Francesca Antonacci(University of Bari Aldo Moro), Glennis A. Logsdon(University of Washington), Steven J. Solar(National Institutes of Health), Dmitry Antipov(National Institutes of Health), Brandon D. Pickett(National Institutes of Health), Yana Safonova(Pennsylvania State University), Francesco Montinaro(University of Bari Aldo Moro), Yanting Luo(Duke Medical Center), Joanna Malukiewicz(Universität Hamburg), Jessica M. Storer(University of Connecticut), Jiadong Lin(University of Washington), Abigail N Sequeira(Pennsylvania State University), Riley J. Mangan(Broad Institute), Glenn Hickey(University of California, Santa Cruz), Graciela Monfort Anez(Stowers Institute for Medical Research), Parithi Balachandran(Jackson Laboratory), Anton Bankevich(Pennsylvania State University), Christine R. Beck(University of Connecticut), Arjun Biddanda(Johns Hopkins University), Matthew Borchers(Stowers Institute for Medical Research), Gerard G. Bouffard(National Institutes of Health), Emry O. Brannan(University of Connecticut), Shelise Brooks(National Institutes of Health), Lucia Carbone(Oregon National Primate Research Center), Laura Carrel(Penn State Milton S. Hershey Medical Center), Agnes P. Chan(Translational Genomics Research Institute), Juyun Crawford(National Institutes of Health), Mark Diekhans(University of California, Santa Cruz), Eric Engelbrecht(University of Louisville), Cedric Feschotte(Cornell University), Giulio Formenti(Rockefeller University), Gage H. Garcia(University of Washington), Luciana de Gennaro(University of Bari Aldo Moro), David M. Gilbert(San Diego Biomedical Research Institute), Richard E. Green(University of California, Santa Cruz), Andrea Guarracino(University of Tennessee Health Science Center), Ishaan Gupta(University of California San Diego), Diana Haddad(National Institutes of Health), Junmin Han(Shanghai Jiao Tong University), Robert S. Harris(Pennsylvania State University), Gabrielle A. Hartley(University of Connecticut), William T. Harvey(University of Washington), Michael Hiller(Goethe University Frankfurt), Kendra Hoekzema(University of Washington), Marlys L. Houck(Zoological Society of San Diego), Hyeonsoo Jeong(University of Washington), Kaivan Kamali(Pennsylvania State University), Manolis Kellis(Broad Institute), Bryce Kille(Rice University), Chul Lee(Rockefeller University), Young Ho Lee(Institute of Molecular Biology), William Lees(Bar-Ilan University), Alexandra P. Lewis(University of Washington), Qiuhui Li(Johns Hopkins University), Mark Loftus(Center for Human Genetics), Yong Hwee Eddie Loh(University of California, Santa Barbara), Hailey Loucks(University of California, Santa Cruz), Jian Ma(Carnegie Mellon University), Yafei Mao(Shanghai Jiao Tong University), Juan Francisco Iturralde Martinez(Pennsylvania State University), Patrick Masterson(National Institutes of Health), Rajiv C. McCoy(Johns Hopkins University), Barbara C. McGrath(Pennsylvania State University), Sean McKinney(Stowers Institute for Medical Research), Britta Meyer(Universität Hamburg), Karen H. Miga(University of California, Santa Cruz), Saswat K. Mohanty(Pennsylvania State University), Katherine M. Munson(University of Washington), Karol Pál(Pennsylvania State University), Matthew W. Pennell(Cornell University), Pavel A. Pevzner(University of California San Diego), David Porubskỳ(University of Washington), Tamara Potapova(Stowers Institute for Medical Research), Francisca Rojas(University of Regensburg), Joana L. Rocha(University of California, Berkeley), Oliver A. Ryder(Zoological Society of San Diego), Samuel Sacco(University of California, Santa Cruz), Swati Saha(University of Louisville), Takayo Sasaki(San Diego Biomedical Research Institute), Michael C. Schatz(Johns Hopkins University), Nicholas J. Schork(Translational Genomics Research Institute), Cole Shanks(University of California, Santa Cruz), Linnéa Smeds(Pennsylvania State University), Dongmin R. Son(University of California, Santa Barbara), Cynthia Steiner(Zoological Society of San Diego), Alexander P. Sweeten(National Institutes of Health), Michael G. Tassia(Johns Hopkins University), Françoise Thibaud‐Nissen(National Institutes of Health), Edmundo Torres-González(Pennsylvania State University), Mihir Trivedi(University of Washington), Wenjie Wei(Huazhong Agricultural University), Julie Wertz(University of Washington), Muyu Yang(Carnegie Mellon University), Panpan Zhang(Cornell University), Shilong Zhang(Shanghai Jiao Tong University), Yang Zhang(Carnegie Mellon University), Zhenmiao Zhang(University of California San Diego), Sarah A Zhao(Massachusetts Institute of Technology), Yixin Zhu(Cornell University), Erich D. Jarvis(Howard Hughes Medical Institute), Jennifer L. Gerton(Stowers Institute for Medical Research), Iker Rivas-González(Max Planck Institute for Evolutionary Anthropology), Benedict Paten(University of California, Santa Cruz), Zachary A. Szpiech(Pennsylvania State University), Christian D. Huber(Pennsylvania State University), Tobias L. Lenz(Universität Hamburg), Miriam K. Konkel(Center for Human Genetics), Soojin V. Yi(University of California, Santa Barbara), Stefan Canzar(University of Regensburg), Corey T. Watson(University of Louisville), Peter H. Sudmant(University of California, Berkeley), Erin K. Molloy(University of Maryland, College Park), Erik Garrison(University of Tennessee Health Science Center), Craig B. Lowe(Duke Medical Center), Mario Ventura(University of Bari Aldo Moro), Rachel J. O’Neill(University of Connecticut), Sergey Koren(National Institutes of Health), Kateryna D. Makova(Pennsylvania State University), Adam M. Phillippy(National Human Genome Research Institute), Evan E. Eichler(Howard Hughes Medical Institute)
Cited by 120Open Access
Abstract
. 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.
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