biostudies-literatureMao YOregon National Primate Research CenterHoward Hughes Medical InstituteNIDA NIH HHSNIAID NIH HHSNHGRI NIH HHSNational Natural Science Foundation of ChinaNational Institutes of HealthNIH HHSNIGMS NIH HHSShanghai Jiao Tong University1547-1562.e13https://www.ebi.ac.uk/biostudies/studies/S-EPMC10947866biostudies-literatureUnknown187(6)We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.CellStructurally divergent and recurrently mutated regions of primate genomes.PMC10947866R01 HG010485P51 OD011092R01 AI137011U24 HG011853K99 GM147352R00 GM147352R01 HG002385U01 HG010961R01 HG010169R01 HG010333DP1 AI175471DP1 DA046108R01 OD034046U41 HG010972Audano PAFair TPaten BYoo DHaukness MFeng GWei XPollen AAZhang SDel Rosario RShi YLogsdon GASun QSawyer SLLewis APWarren WCMao YDishuck PCGordon DSBakken TEHoekzema KFattor WTJeong HPorubsky DBauer VLCarbone LMunson KMYang XRozanski AHarvey WTEichler EEWilkerson GKLu QfalseStructurally divergent and recurrently mutated regions of primate genomes.We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.2024-01-01T00:00:00Z2024 Mar2026-06-01T19:20:20.801Z2025-04-04T09:07:10.61ZS-EPMC109478663842842410.1016/j.cell.2024.01.052