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A genome-wide comparison of recent chimpanzee and human segmental duplications
Abstract
We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (> 94% sequence identity) are not duplicated in chimpanzee, including some human disease-causing duplications. Combining experimental and computational approaches, we estimate a genomic duplication rate of 4-5 megabases per million years since divergence. These changes have resulted in gene expression differences between the species. In terms of numbers of base pairs affected, we determine that de novo duplication has contributed most significantly to differences between the species, followed by deletion of ancestral duplications. Post-speciation gene conversion accounts for less than 10% of recent segmental duplication. Chimpanzee-specific hyperexpansion (> 100 copies) of particular segments of DNA have resulted in marked quantitative differences and alterations in the genome landscape between chimpanzee and human. Almost all of the most extreme differences relate to changes in chromosome structure, including the emergence of African great ape subterminal heterochromatin. Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%).
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“since the chimpanzee chromosomes 2A and 2B are capped with hyper-expanded segmental duplications and tandem repeats (StSats) not existing in the human genome [8, 40], we cannot measure the magnitude of the accumulation of BCS in those fragments comparing to the human reference.”
From Revised time estimation of the ancestral human chromosome 2 fusion (2022) · cites this paper as [8]
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Metadata
- Authors
- Cheng, Z., Ventura, M., She, X., Khaitovich, P., Graves, T., Osoegawa, K., Church, D., DeJong, P., Wilson, R. K., Pääbo, S., Rocchi, M., & Eichler, E. E.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Bari Aldo Moro (IT)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Washington University in St. Louis (US)
- National Institutes of Health (US)
- Corresponding author
- Eichler, Evan E.
- ORCID
- Venue
- Nature
- Published
- 2005-09
- Volume
- 437
- Issue
- 7055
- Pages
- 88-93
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1971369643
- Cited by
- 398
- References
- 31
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 17 · 2023: 4 · 2022: 4 · 2021: 5 · 2020: 17 · 2019: 10 · 2018: 11 · 2017: 13 · 2016: 6 · 2015: 10 · 2014: 15 · 2013: 22 · 2012: 18
- FWCI
- 27.23
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Funders
- European Commission
- Bundesministerium für Bildung und Forschung
- National Institute of General Medical Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- segmental duplication, human-chimpanzee comparison, de novo duplication, gene conversion, subtelomeric heterochromatin, gene expression differences, primate genome evolution, human evolution, chimpanzee genome, Y-linked genes, chromosome structure, comparative genomics
- MeSH terms
- Animals, Pan troglodytes, Gene Conversion, Humans, Species Specificity, Time Factors, Genome, Human, Evolution, Molecular, Computational Biology, Gene Duplication, Genomics, Chromosomes, Mammalian
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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