title: A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications.
abstract: Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence divergence estimates of human duplications have suggested an expansion relatively recently during hominoid evolution. Based on primate comparative sequence analysis of 37 unique duplication-transition regions, we establish a molecular clock for their divergence that shows a significant increase in their effective substitution rate when compared with unique genomic sequence. Fluorescent in situ hybridization (FISH) analyses from 1053 random nonhuman primate BACs indicate that great-ape species have been enriched for interspersed segmental duplications compared with representative Old World and New World monkeys. These findings support computational analyses that show a 12-fold excess of recent (>98%) intrachromosomal duplications when compared with duplications between nonhomologous chromosomes. These architectural shifts in genomic structure and elevated substitution rates have important implications for the emergence of new genes, gene-expression differences, and structural variation among humans and great apes.
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.
authors.forename: Xinwei
authors.initials: X
authors.lastname: She
authors.forename: Ge
authors.initials: G
authors.lastname: Liu
authors.forename: Mario
authors.initials: M
authors.lastname: Ventura
authors.forename: Shaying
authors.initials: S
authors.lastname: Zhao
authors.forename: Doriana
authors.initials: D
authors.lastname: Misceo
authors.forename: Roberta
authors.initials: R
authors.lastname: Roberto
authors.forename: Maria Francesca
authors.initials: MF
authors.lastname: Cardone
authors.forename: Mariano
authors.initials: M
authors.lastname: Rocchi
authors.forename: Eric D
authors.initials: ED
authors.lastname: Green
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Archidiacano
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
mesh_terms: D000818:Animals; D020137:Base Pair Mismatch; D020029:Base Pairing; D001483:Base Sequence; D002875:Chromosomes; D016208:Databases, Factual; D019143:Evolution, Molecular; D020440:Gene Duplication; D015894:Genome, Human; D015186:Hominidae / Q000235:genetics; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D002679:Pan troglodytes / Q000235:genetics*; D010215:Papio / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid