A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications

Genome Res. 2006 May;16(5):576-83. doi: 10.1101/gr.4949406. Epub 2006 Apr 10.

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.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Pair Mismatch*
  • Base Pairing
  • Base Sequence
  • Chromosomes*
  • Databases, Factual
  • Evolution, Molecular
  • Gene Duplication*
  • Genome, Human
  • Hominidae / genetics
  • Humans
  • In Situ Hybridization, Fluorescence
  • Molecular Sequence Data
  • Pan troglodytes / genetics*
  • Papio / genetics*
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid