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United States Department of Agriculture

Agricultural Research Service

Title: Novel porcine repetitive elements

Authors
item Wiedmann, Ralph
item Nonneman, Danny
item Keele, John

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 1, 2006
Publication Date: December 1, 2006
Citation: Wiedmann, R.T., Nonneman, D.J., Keele, J.W. 2006. Novel porcine repetitive elements. Biomed Central (BMC) Genomics. 7:304 (12 pp). Online. BMC Genomics doi:10.1186/1471-2164/7/304. Available: http://www.biomedcentral.com/1471-2164/7/304.

Interpretive Summary: Roughly half of a typical mammalian genome is composed of repeated sequences. Some of the repeated sequence is obvious – strings of A's or other simple patterns. Much of the repeated sequence is more difficult to recognize – complex strings of nucleotides that occur once each in many different locations spread throughout the genome. This paper identifies and characterizes previously unreported examples of this latter type of repeat element in the pig genome. This new knowledge will help scientists solve the puzzle of assembling the entire pig genome from the many small pieces that are currently known. It will also help laboratory scientists to know if all or part of the sequence that they are studying has many copies within the genome because some of the most commonly used laboratory techniques do not work as expected if they are applied to repetitive sequence.

Technical Abstract: An analysis of 220 fully sequenced porcine BACs generated by the Comparative Vertebrate Sequencing Initiative (http://www.nisc.nih.gov/) revealed 27 distinct, novel porcine repetitive elements ranging in length from 55 to 1059 nucleotides. This set of fully sequenced BACs covers approximately 1% of the entire porcine genome, with an emphasis on areas important to comparative genomics. To obtain copy numbers for the novel repeat elements, we used the BAC-end sequences submitted by Sanger, that had approximately 10% coverage of the porcine genome. The observed copy numbers of these novel repeat elements in BAC-ends were as follows: 6 appear less than 100 times, 16 between 100 and 1000 times, 5 appear between 1000 and 10,000 times. Several of the repeat elements were found in the bovine genome and there are examples of two in particular that occur in long orthologous stretches of sequence in pig and cow. The presence of both orthologous and non-orthologous sites indicates that some sites existed prior to speciation and some were generated later. The identification of low to moderate copy number repetitive DNA will be critical in the assembly of livestock genomes and studies of comparative genomics.

Last Modified: 12/21/2014