%0 Journal Article
%T Novel porcine repetitive elements
%A Ralph T Wiedmann
%A Dan J Nonneman
%A John W Keele
%J BMC Genomics
%D 2006
%I BioMed Central
%R 10.1186/1471-2164-7-304
%X We discovered 27 repetitive elements in 220 BACs covering 1% of the porcine genome (Comparative Vertebrate Sequencing Initiative; CVSI). These repeats varied in length from 55 to 1059 nucleotides. To estimate copy numbers, we went to an independent source of data, the BAC-end sequences (Wellcome Trust Sanger Institute), covering approximately 15% of the porcine genome. Copy numbers in BAC-ends were less than one hundred for 6 repeat elements, between 100 and 1000 for 16 and between 1,000 and 10,000 for 5. Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor. None of the repeat elements were found in primate, rodent or dog genomes. We were unable to identify any of the replication machinery common to active transposable elements in these newly identified repeats.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 that is specific to artiodactyls will be critical in the assembly of livestock genomes and studies of comparative genomics.Repetitive elements comprise ~45% [1] of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression [2,3] and by affecting genomic size, diversity and evolution [4-8]. The ubiquity and increasingly understood importance of repetitive elements (REs) contribute to the need to identify and annotate REs [9]. In recent years, several attempts have been made to automate the process of de novo identification and characterization of REs [10-16]. The algorithms take into account the likely evolutionary history of the REs ¨C not only genetic drift, but also the processes that lead to the juxtaposition of REs [10]. Because knowing the evolutionary history of each RE helps
%U http://www.biomedcentral.com/1471-2164/7/304