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Published on November 21, 2007; 10.1104/pp.107.110353

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Received October 8, 2007
Accepted November 15, 2007

TE nest: Automated chronological annotation and visualization of nested plant transposable elements

Brent A. Kronmiller and Roger P. Wise *

Bioinformatics and Computational Biology, Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA 50011-1020; Corn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020

* Corresponding author; email: rpwise{at}iastate.edu.

Organisms with a high density of transposable elements (TEs) exhibit nesting, with subsequent repeats found inside previously inserted elements. Nesting splits the sequence structure of TEs and makes annotation of repetitive areas challenging. We present TEnest, a repeat identification and display tool made specifically for highly repetitive genomes. TEnest identifies repetitive sequences and reconstructs separated sections to provide full length repeats, and for long terminal repeat (LTR) retrotransposons calculates age since insertion based on LTR divergence. TEnest provides a chronological insertion display, to give an accurate visual representation of TE integration history showing timeline, location and families of each TE identified, thus creating a framework from which evolutionary comparisons can be made among various regions of the genome. A database of repeats has been developed for maize (Zea mays), rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare) to illustrate the potential of the TEnest software. All currently finished maize BACs totaling 29.3 Mb were analyzed with TEnest to provide a characterization of the repeat insertions. Sixty-seven percent of the maize genome was found to be made up of TEs, of these 95% are LTR retrotransposons. The rate of solo LTR formation is shown to be dissimilar across retrotransposon families. Phylogenetic analysis of TE families reveals specific events of extreme TE proliferation, which may explain high quantities of certain TE families found throughout the maize genome. The TEnest software package is available for use on PlantGDB under the tools section (http://www.plantgdb.org/prj/TE_nest/TE_nest.html), the source code is available from http://wiselab.org/.




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