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Title:   Author  item
                                            KRONMILLER, BRENT - IOWA STATE UNIVERSITYitem
                                            Wise, Roger
  Submitted to: Plant Physiology
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 11/15/2007
                                    Publication  Date: 11/21/2007
                                    Citation: Kronmiller, B.A., Wise, R.P. 2007. TEnest:  Automated Chronological Annotation and Visualization of Nested Plant Transposable Elements. Plant Physiology. 146(1):45-59.Interpretive Summary: Transposable elements (TEs) are mobile DNA found throughout eukaryotic organisms.  Although abundance is extremely high in some organisms, little is known about the processes governing the distribution of transposable elements across the genome.  By the nature of their mobility, transposable elements have the potential to induce change throughout an organism’s genome.  As a consequence of multiple transposable element copies, unequal cross-over and recombination can occur between chromosome regions.  Transposable element insertions can cause gene or regulatory mutations, altering levels of transcripts, or provide new genetic material for novel gene functions to evolve.  

In order to fully analyze repeat dense grass genomes, we have developed TEnest, a software package for the annotation and visualization of nested transposable elements.  TEnest calculates the estimated time since insertion of LTR (long terminal repeat) retrotransposons, providing a unique dimension to replication, movement, and evolutionary analysis of transposable elements and the genome sequence.  TEnest is available for use as a web tool, simply requiring an input sequence, or the source code is provided for download.  This is an important resource for analysis of emerging large genome sequences with high transposable element content, such as maize, wheat, and barley for researchers working in the field of genomics.
                                Technical Abstract: 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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