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Title:   Author  item
                                            Liu, Ge

                                                         - *George*item
                                            MATUKUMALLI, LAKSHMI - GEORGE MASON UNIVERSITYitem
                                            Van Tassell, Curtis

                                                         - *Curt*item
                                            Sonstegard, Taditem
                                            Gasbarre, Louisitem
                                            EICHLER, EVAN - U OF WASH SCHOOL OF MED
  Submitted to: BARC Poster Day
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 3/23/2007
                                    Publication  Date: 4/25/2007
                                    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.Interpretive Summary:
                                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.


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