Segmental Duplications (SDs) can be defined as blocks of DNA ranging from 1-400kb in length with copies found in multiple sites and typically share high sequence similarity (>90%). Studies based in both experimental and computational analyses show that ~5% of the human genome is composed of duplicated sequences. More generally, primate genomes have been found enriched for this complex patterns of interspersed segmental duplications.This 5% of euchromatin differs in structure and content between closely related primates and is not easily resolved by whole-genome shotgun sequence assembly methods.This proposal focuses on this 5% of the genome that historically has been the most difficult for sequence and assembly.The aim of this research is to reconstruct the evolutionary history of all primate segmental duplications in 6 species of primates (Human, Chimpanzee, Orangutan, Gibbon and Macaque and Marmoset) and to understand gene innovations that have emerged within these dynamic genomic regions. The Main goals of the proposal are: 1.SDs detection and analysis of non-human primate genomes. 2.SDs validation (by means of FISH and CGH arrays hybridizations) 3.Analyze species-specific functional elements and their polymorphism and divergence patterns The proposed work not only can assist/direct efforts in these regions but serve as a benchmark of the quality of the final sequenced genomes, and, as such, benefit the genomics/evolutionary/genetics community as a whole. The long-term goal is to create an integrated view of the evolution of primate segmental duplications by studying changes in the composition, frequency, size and location at the major branchpoints in the primate phylogeny. This work has the ancillary benefit that it will provide inssight the origin of SD structure associated with genomic disease and characterize lineage-specific genes relevant to realization of these primates as models of human disease and to the adaptation of these species.
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