Complete sequencing of ape genomes.
DongAhn YooArang RhiePrajna HebbarFrancesca AntonacciGlennis A LogsdonSteven Jared SolarDmitry AntipovBrandon D PickettYana SafonovaFrancesco MontinaroYanting LuoJoanna MalukiewiczJessica M StorerJiadong LinAbigail N SequeiraRiley J ManganGlenn HickeyGraciela Monfort AnezParithi BalachandranAnton BankevichChristine R BeckArjun BiddandaMatthew BorchersGerard G BouffardEmry BrannanShelise Y BrooksLucia CarboneLaura CarrelYongwook ChoiJuyun CrawfordMark DiekhansEric EngelbrechtCedric FeschotteGiulio FormentiGage H GarciaLuciana de GennaroDavid M GilbertRichard E GreenAndrea GuarracinoIshaan GuptaDiana HaddadJunmin HanRobert S HarrisGabrielle A HartleyWilliam T HarveyMichael HillerKendra HoekzemaMarlys L HouckHyeonsoo JeongKaivan KamaliManolis KellisBryce KilleChul LeeYoungho LeeWilliam D LeesAlexandra P LewisQiuhui LiMark LoftusYong Hwee Eddie LohHailey LoucksJian MaYafei MaoJuan F I MartinezPatrick MastersonRajiv C McCoyBarbara McGrathSean McKinneyBritta S MeyerKaren H MigaSaswat Kumar MohantyKatherine M MunsonKarol PalMatthew W PennellPavel A PevznerDavid PorubskyTamara PotapovaFrancisca R RingelingJoana L RochaOliver A RyderSamuel SaccoSwati SahaTakayo SasakiMichael C SchatzNicholas J SchorkCole ShanksLinnéa SmedsDongmin R SonCynthia SteinerAlexander P SweetenMichael G TassiaFrançoise Thibaud-NissenEdmundo Torres-GonzálezMihir TrivediWenjie WeiJulie WertzMuyu YangPanpan ZhangShilong ZhangYang ZhangZhenmiao ZhangSarah A ZhaoYixin ZhuErich D JarvisJennifer L GertonIker Rivas-GonzálezBenedict PatenZachary Alfano SzpiechChristian D HuberTobias L LenzMiriam K KonkelSoojin V YiStefan CanzarCorey T WatsonPeter H SudmantErin K MolloyErik GarrisonCraig B LoweMario VenturaRachel J O'NeillSergey KorenKateryna D MakovaAdam M PhillippyEvan E EichlerPublished in: bioRxiv : the preprint server for biology (2024)
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.