NDLI: Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Content Provider	PubMed Central
Author	Gazave, Elodie Fleur, Darré Carlos, Morcillo-suarez Natalia, Petit-marty Carreño, Angel Marigorta, Urko M. Ryder, Oliver A. Blancher, Antoine Rocchi, Mariano Bosch, Elena Baker, Carl Marquès-bonet, Tomàs Eichler, Evan E. Navarro, Arcadi
Copyright Year	2011
Abstract	Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV data. We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps. In addition, for bonobo and gorilla, patterns of CNV and nucleotide diversity were studied in the same individuals. We show that CNVs have been subject to different selective pressures in different lineages. Evidence for purifying selection is stronger in gorilla CNVs overlapping genes, while positive selection appears to have driven the fixation of structural variants in the orangutan lineage. In contrast, chimpanzees and bonobos present high levels of common structural polymorphism, which is indicative of relaxed purifying selection together with the higher mutation rates induced by the known burst of segmental duplication in the ancestor of the African apes. Indeed, the impact of the duplication burst is noticeable by the fact that bonobo and chimpanzee share more CNVs with gorilla than expected. Finally, we identified a number of interesting genomic regions that present high-frequency CNVs in all great apes, while containing only very rare or even pathogenic structural variants in humans.
Related Links	http://dx.doi.org/10.1101/gr.117242.110
Ending Page	1639
Page Count	14
Starting Page	1626
File Format	PDF
ISSN	10889051
e-ISSN	15495469
Journal	Genome Research
Issue Number	10
Volume Number	21
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2011-10-01
Access Restriction	Open
Rights Holder	Cold Spring Harbor Laboratory Press
Subject Keyword	Genetics(clinical) Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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