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A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos
Biorxiv : the Preprint Server for Biology
|June 22, 2026
Summary
Population-scale pangenomics of chimpanzees and bonobos reveals extensive genetic diversity and identifies structural variants impacting human disease and pathogen resistance. This research deepens our understanding of hominin evolution and biodiversity.
Area of Science:
- Genomics
- Evolutionary Biology
- Primate Genetics
Background:
- Haplotype-resolved genome assemblies offer insights into complex genomic regions.
- Population-scale pangenomes of chimpanzees and bonobos are crucial for understanding hominin evolution.
Purpose of the Study:
- To generate high-contiguity pangenome assemblies for four Pan clades.
- To characterize genetic variation, structural variants, and evolutionary patterns in chimpanzees and bonobos.
Main Methods:
- Sequencing and assembly of 58 haplotypes from four distinct Pan clades.
- High-contiguity genome assembly (median contig NG50=54 Mb), including eight near-T2T genomes.
- Comparative analysis of structural variants (SVs) and single nucleotide variants (SNVs) across species.
Main Results:
- Increased estimates of genome-wide genetic diversity (6-37%) in Pan populations.
- Recurrent structural polymorphisms impact immune response and host-pathogen interaction genes; SVs have higher impact than SNVs.
- Human disease-associated short tandem repeat loci show unique expansion in humans; parallel adaptations to pathogen resistance observed in glycophorin genes.
Conclusions:
- Nonhuman primate pangenomics is vital for understanding complex genome evolution and primate biodiversity.
- Structural variants play a significant role in high-impact genetic variation across hominins.
- Ancient and recent structural variations reveal parallel adaptations to pathogen resistance in humans and chimpanzees.
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