Recent Segmental Duplications in the Working Draft Assembly of the Brown Norway Rat

Abstract

We assessed the content, structure, and distribution of segmental duplications (Ն90% sequence identity, Ն5 kb length) within the published version of the Rattus norvegicus genome assembly (v.3.1). The overall fraction of duplicated sequence within the rat assembly (2.92%) is greater than that of the mouse (1%-1.2%) but significantly less than that of human (∼5%). Duplications were nonuniformly distributed, occurring predominantly as tandem and tightly clustered intrachromosomal duplications. Regions containing extensive interchromosomal duplications were observed, particularly within subtelomeric and pericentromeric regions. We identified 41 discrete genomic regions greater than 1 Mb in size, termed "duplication blocks." These appear to have been the target of extensive duplication over millions of years of evolution. Gene content within duplicated regions (∼1%) was lower than expected based on the genome representation. Interestingly, sequence contigs lacking chromosome assignment ("the unplaced chromosome") showed a marked enrichment for segmental duplication (45% of 75.2 Mb), indicating that segmental duplications have been problematic for sequence and assembly of the rat genome. Further targeted efforts are required to resolve the organization and complexity of these regions.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

“…In marked contrast to observations for mammalian genome assemblies [129][130][131][132] , of the confirmed segmental duplications in chicken (see above), few exceeded 10 kb in length (Fig. 13), and none greater than 50 kb were detected.…”

Congenic Interval Mapping of RNO10 Reveals a Complex Cluster of Closely-Linked Genetic Determinants of Blood Pressure

“…Segmental duplications are reported on RNO 10. 39 Chen et al have demonstrated segmental duplications flanking the multiple sclerosis locus on human chromosome 17q and suggested that segmental duplications could affect the biological activity of the genes on a chromosome. 40 However, such segmental duplications may not be genetic determinants underlying Region 1 because it does not appear to contain segmental duplications (http:// ratparalogy.gs.washington.edu/cgi-bin/hgTracks).…”

Diagnosing duplications – can it be done?

“…Because reports conflict on the gene content of LCRs [20,21,[67][68][69][70], depending on methodology, species and the quality of the data, it is not clear to what extent LCRs have a role in the duplication of entire genes. However, there is substantial evidence that LCRs contain fragments of coding sequence and are likely to be the sites of new gene formation by domain shuffling.…”