Structurally 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. [Display omitted] • Long-read sequence assembly of eight primate genomes • Atlas of lineage-specific and recurrent structural variation • Structurally divergent regions (SDRs) associate with lineage-specific genes • Recurrent duplications diversify primate genes and predispose to human disease Analysis of high-quality, haplotype-resolved primate genomes provides a more complete understanding of lineage-specific, recurrent mutations and structurally divergent regions associated with primate adaptive evolution and human diseases. [ABSTRACT FROM AUTHOR]