A genome-wide comparison of recent chimpanzee and human segmental duplications

Ze Cheng, Mario Ventura, Xinwei She, Philipp Khaitovich, Tina Graves, Kazutoyo Osoegawa, Deanna Church, Pieter DeJong, Richard K. Wilson, Svante Pääbo, Mariano Rocchi, Evan E. Eichler

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285 Scopus citations

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%).

Original languageEnglish
Pages (from-to)88-93
Number of pages6
JournalNature
Volume437
Issue number7055
DOIs
StatePublished - Sep 1 2005

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    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. (2005). A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature, 437(7055), 88-93. https://doi.org/10.1038/nature04000