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An ontology for transposable elements and other repetitive sequences in the age ofgenomicsKate L. Hertweck, National Evolu...
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iEvoBio Hertweck abstract 2012

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Abstract for my presentation on transposable element ontology for iEvoBio in Ottawa, July 2012

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iEvoBio Hertweck abstract 2012

  1. 1. An ontology for transposable elements and other repetitive sequences in the age ofgenomicsKate L. Hertweck, National Evolutionary Synthesis CenterAs sequencing costs decrease, researchers are incorporating large-scale genomic sequencing projectsinto their projects. The resulting data inundate the scientific community, providing ample opportunityfor myriad comparative genomic studies. A crucial step in most genome sequencing projects is to maskrepetitive sequences. This approach improves efficiency of gene assembly, but discards an informative,diverse part of the genome. The repetitive portion of a genome comprises all sequences in very highcopy number, such as transposable elements. Previously thought to be “junk” DNA, a growing body ofevidence suggests transposable elements play vital roles in genomic evolution, affecting everythingfrom chromosome structure, gene regulation, and even derivation of new genes (Biemont, 2010).Substantial work has described the classification of transposable elements (Wicker et al., 2007),although our current knowledge of such sequences is largely based on relatively few model systems.A majority of publicly available repeat libraries are built from long-read Sanger sequences or highlycurated, deep coverage genome sequencing. Available approaches to repetitive element assembly fromnext generation sequencing data relies on assumptions about the genomes repeat content, includingavailability of a reference genome, depth of sequencing, and length of reads. The results from thesealgorithms provide invaluable information about transposable elements, especially in organisms withvery large genomes. However, results from various repeat assembly methods require an extensiveamount of metadata to be useful for other researchers. Development of an appropriate ontology forrepetitive elements assembled from next generation sequencing data should include characteristics ofthe sequencing method (platform, length, number of reads) as well as details of the assembly (ab initiovs de novo, stringency thresholds) and annotation methods (library used, search parameters).BIEMONT, C. 2010. A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution. Genetics 186: 1085-1093.WICKER, T., F. SABOT, A. HUA-VAN, J. L. BENNETZEN, P. CAPY, B. CHALHOUB, A. FLAVELL, et al. 2007. A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 8: 973-982.