biostudies-literatureYoo DNIA NIH HHSNIAID NIH HHSNIMH NIH HHSNHGRI NIH HHSNLM NIH HHSNIH HHSNIGMS NIH HHS401-418https://www.ebi.ac.uk/biostudies/studies/S-EPMC12058530biostudies-literatureUnknown641(8062)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 previoNatureComplete sequencing of ape genomes.PMC12058530P20 GM139769R35 GM146926R56 AG056169R35 GM146886P51 OD011092R01 AG056169T15 LM007093R01 HG002385R01 MH120295R35 GM151945P01 AI152999U24 HG007497R35 GM151348R35 GM142916R01 HG007352R35 GM133600U24 HG010263U41 HG007234R35 GM133747UH3 AG064706T32 HG012344R01 HG010329R01 HG010169R35 HG011332U19 AG023122R01 GM123312Zhao SACrawford JMalukiewicz JSon DRZhang SFeschotte CTorres-Gonzalez EZhang PLees WLogsdon GABrannan ELoh YHESacco SLewis APJeong HLoftus MRocha JLCanzar SMunson KMRyder OAGuarracino ABankevich AMontinaro FLin JPotapova TEngelbrecht ERivas-Gonzalez ISchork NJSteiner CZhu YYi SVHebbar PMasterson PSasaki TSchatz MCRhie AWei WKamali KThibaud-Nissen FMeyer BSMcGrath BLowe CBDiekhans MLee CHiller MKoren SBiddanda APickett BDde Gennaro LWertz JHickey GMiga KHGarrison ESzpiech ZABalachandran PKellis MTassia MGPal KSaha SHuber CDPhillippy AMSequeira ANCarrel LLoucks HHan JLee YWatson CTPennell MPevzner PAHaddad DPaten BGreen REVentura MAntipov DO'Neill RJSafonova YBrooks SYMcCoy RCGupta IHouck MLSolar SJMangan RJJarvis EDGilbert DYang MGarcia GHStorer JMLi QLenz TLRingeling FRTrivedi MMolloy EBorchers MMonfort Anez GBouffard GGMcKinney SShanks CSudmant PHFormenti GSmeds LYoo DSweeten APMartinez JFIAntonacci FKille BMao YChan APHoekzema KMakova KDHarris RSPorubsky DKonkel MKCarbone LMohanty SKHartley GAZhang ZHarvey WTZhang YEichler EELuo YMa JGerton JLBeck CRfalseComplete sequencing of ape genomes.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 previo2025-01-01T00:00:00Z2025 May2026-06-01T14:51:00.536Z2026-04-08T13:28:32.586ZS-EPMC120585304020505210.1038/s41586-025-08816-3