Primate genome architecture influences structural variation mechanisms and functional consequences

Genomic structural variants (SVs) significantly contribute to human genetic variation and have been linked with numerous diseases. Compared with humans, the characterization of SVs occurring within and across nonhuman primates has lagged. We generated comprehensive massively parallel DNA sequencing-based SV maps in three nonhuman primate species and show that the rates of different SV formation mechanisms, such as nonallelic homologous recombination and Alu retrotransposition, vary significantly between the great apes and the rhesus macaque—leading to markedly different SV landscapes in these species. Linking gene expression data with species-specific gene duplications, we describe several instances where gene duplicates seem to lead to evolutionary innovation through the gain of gene expression in new tissues.