ARS | Publication request: Recent Segmental Duplications in the Cattle Genome

Submitted to: BARC Poster Day
Publication Type: Abstract
Publication Acceptance Date: March 23, 2007
Publication Date: April 25, 2007
Citation: Liu, G., Matukumalli, L.K., Van Tassell, C.P., Sonstegard, T.S., Gasbarre, L.C., Eichler, E.E. 2007. Recent segmental duplications in the cattle genome. [abstract]. BARC Poster Day.Abstracat #25, p. 32.

Technical Abstract: We assessed the content, structure, and distribution of segmental duplications (> or =90% sequence identity, > or =5 kb length) within the newest public version of the Bos taurus genome assembly (bta_3.1). The overall fraction of duplicated sequence within the cattle assembly is approximately equivalent to those of the rodents (mouse 1.2-2.0% and rat 2.9%) but significantly less than that of human (~5.0%). 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 discrete large genomic regions, termed "duplication blocks." These appear to have been the target of extensive duplication over millions of years of evolution. We are currently estimating the gene content within duplicated regions as compared to the expected value based on the genome representation. Interestingly, sequence contigs lacking chromosome assignment ("chrUnAll: the unplaced chromosome") showed a marked enrichment for segmental duplication, indicating that segmental duplications have been problematic for sequence and assembly of the cattle genome. Further targeted efforts are required to resolve the organization and complexity of these regions.