Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 110, Issue 39, Pages 15764-15769Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1305904110
Keywords
genome evolution; retrotransposons; neofunctionalization; copy-number variation
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Funding
- European Molecular Biology Organization Short-Term Fellowship ASTF [150-2013]
- National Institutes of Health [F32 AG 039979]
- National Institutes of Health Grants National Institute of Allergy and Infectious Diseases [5 R01 AI 089246-01A1]
- National Institute of General Medical Sciences [5 R01 GM081533]
- European Molecular Biology Laboratory Genomics Core Facility
- Information Technology Unit
- Deutsche Forschungsgemeinschaft [KO 4037/1-1]
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Although nucleotide resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact of phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing, we constructed fine-resolution genomic structural variation maps in five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, which are comprised of thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques compared with great apes. By comparison, nonallelic homologous recombination is specifically active in the great apes, which is correlated with architectural differences between the genomes of great apes and macaque. Transcriptome analyses across nonhuman primates and humans revealed effects of species-specific whole-gene duplication on gene expression. We identified 13 gene duplications coinciding with the species-specific gain of tissue-specific gene expression in keeping with a role of gene duplication in the promotion of diversification and the acquisition of unique functions. Differences in the present day activity of SV formation mechanisms that our study revealed may contribute to ongoing diversification and adaptation of great ape and Old World monkey lineages.
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