Recent segmental duplications in the working draft assembly of the brown Norway rat.

Segmental duplications have long been recognized as important mediators of both gene and genome evolution (Muller 1936; Ohno 1970). From the genic perspective, such duplications often encode protein products which, although not essential for viability of the organism, are important for the adaptation of the species to specific ecological niches (Duda and Palumbi 1999). Among mammalian species, commonly duplicated genes include those associated with the recognition of environmental molecules and include genes associated with innate immunity, drug detoxification, olfaction, and sperm competition. From the perspective of genome structure, lineage-specific segmental duplications or large repeats often delineate regions of recurrent evolutionary lability (Eichler and Sankoff 2003). Recent comparative sequencing efforts among closely related eukaryotes, for example, shows that highly homologous repetitive sequence frequently associate with the breakpoints of large-scale chromosomal rearrangement (Dehal et al. 2001; Kellis et al. 2003). Understanding the nature and pattern of segmental duplications provides fundamental insight into functional redundancy, adaptive evolution, and the structural dynamics of chromosomal evolution. One of the surprising findings from the analysis of the Human Genome Project data was the relevant abundance of large blocks of sequence with a high degree of sequence identity (Bailey et al. 2001; International Human Genome Sequencing Consortium [IHGSC] 2001). A variety of computational and experimental methods (Bailey et al. 2001, 2002; Cheung et al. 2001) now estimate 5%–6% of the human as duplicated (≥1kb and ≥90%). Compared to other sequenced organisms such as fly and worm, the human genome is enriched for recent segmental duplications, particularly interspersed duplications (Bailey et al. 2002). Such comparisons, however, typically assess duplication content with lower-bound estimates of length. For example, these cross-species comparisons rarely characterize duplications less than 500 bp in length. This may introduce an ascertainment bias, particularly among invertebrates, whose genomes can be orders of magnitude smaller compared to human. Larger genomes may simply harbor larger segmental duplications. The purported “unique” properties of the human genome can only be assessed by detailed comparison with other mammalian genomes where genome sizes are equivalent. With the whole-genome shotgun sequence assembly of the rat genome, we can now assess the nature and pattern of segmental duplication of a third mammalian genome (Rat Genome Sequencing Project Consortium [RGSPC] 2004; Waterston et al. 2002). We present a preliminary, genome-wide analysis of the segmental duplication content of the rat (Rattus norvegicus). Any assessment of segmental duplication content is highly dependent on the methodology and quality of the sequence assembly (Bailey et al. 2001; Eichler 2001; Cheung et al. 2003a). Discrimination between highly paralogous copies and allelic regions that have not been properly assembled requires an estimate of the levels of both allelic variation and sequencing error. For most regions, paralogous sequences are more divergent than allelic copies. Another consideration is the method of genome assembly. Assembly algorithms based on sequence overlap from working-draft BAC clones were shown to overestimate the frequency of segmental duplication, due to a failure to properly merge allelic overlaps (Bailey et al. 2001; IHGSC 2001). Alternatively, assembly strictly from whole-genome shotgun sequence reads tends to over-collapse and therefore underrepresent such regions due to the recruitment of both paralogous and allelic sequence reads (Eichler 1998; Bailey et al. 2002; Estivill et al. 2002). Interestingly, the assembly algorithm of the rat genome represents a hybrid of whole-genome- and clone-ordered-based approaches. The ability of this approach to resolve segmental duplications has not been tested previously. In light of these inherent difficulties associated with the assembly of highly similar duplications, the analysis should be considered a first approximation of the recent duplication properties of the rat genome. Such initial analyses, however, are essential in providing a more accurate and robust “final” version of the rat genome as well as insight into genome-assembly approaches. The results of the present study have been made publicly available through the UCSC genome browser as well as through our own local database (http://ratparalogy.cwru.edu), providing a resource for the rat sequencing and genetics community.