title: Primate genome architecture influences structural variation mechanisms and functional consequences.
abstract: 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.
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115.
authors.forename: Omer
authors.initials: O
authors.lastname: Gokcumen
authors.forename: Verena
authors.initials: V
authors.lastname: Tischler
authors.forename: Jelena
authors.initials: J
authors.lastname: Tica
authors.forename: Qihui
authors.initials: Q
authors.lastname: Zhu
authors.forename: Rebecca C
authors.initials: RC
authors.lastname: Iskow
authors.forename: Eunjung
authors.initials: E
authors.lastname: Lee
authors.forename: Markus Hsi-Yang
authors.initials: MH
authors.lastname: Fritz
authors.forename: Amy
authors.initials: A
authors.lastname: Langdon
authors.forename: Adrian M
authors.initials: AM
authors.lastname: Stütz
authors.forename: Pavlos
authors.initials: P
authors.lastname: Pavlidis
authors.forename: Vladimir
authors.initials: V
authors.lastname: Benes
authors.forename: Ryan E
authors.initials: RE
authors.lastname: Mills
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
authors.forename: Charles
authors.initials: C
authors.lastname: Lee
authors.forename: Jan O
authors.initials: JO
authors.lastname: Korbel
mesh_terms: D000818:Animals; D020440:Gene Duplication; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics*; D056914:Genomic Structural Variation / Q000235:genetics*; D006801:Humans; D009711:Nucleotides / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics; D011323:Primates / Q000235:genetics*; D013045:Species Specificity
chemical_list: D009711:Nucleotides
keywords: copy-number variation; genome evolution; neofunctionalization; retrotransposons