Comparative analysis of segmental duplications in human and great ape genomes

Studies on human and great ape genomes have shown that recent segmental duplications (SDs) have more differences in both content and structure when compared to other euchromatic regions. To reveal the origin of phenotypic difference between human and great apes, researchers analyze shared SDs and species-specific SDs between human and great apes. We compared SDs in human and great ape genomes, and detected 132 Mb, 85 Mb, and 124 Mb of human SDs that are shared with SDs in chimpanzee, orangutan, and gorilla genomes, respectively. Due to duplication events that happened after speciation, shared SDs between two species may vary in copy numbers across these species. We also revealed that 61 Mb of the shared human-chimpanzee SDs, 29 Mb of the shared human-orangutan SDs, and 44 Mb of the shared human-gorilla SDs that existed in the ancestor genome before speciation and are still conserved in both genomes after speciation. Finally, we constructed the breakpoint graph of SDs between two species to represent how species-specific SDs interacted with shared SDs between two species at the whole genome scale. (This study was supported in part by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel-Aviv University)