January 13-17, 2007
Town & Country Convention Center
San Diego, CA
Brent A Kronmiller1,3 , Karin Werner2,3 , Roger Wise1,2,3
The maize sequencing project is underway and specialized tools are necessary to resolve difficult regions. Seventy percent of the maize genome consists of transposable elements (TEs). Of these, 95% are LTR retrotransposons which greatly hinder sequence assemblies. A majority of TEs occur in clusters of nested repeats, where a TE inserts within the sequence of an existing element, creating short segments of different types. Mapping of maize TEs is therefore difficult as the resulting fragments are not easily identified, necessitating an accurate nested TE identification tool for complete annotation of the genome. Current repeat software does not address nested TEs, making it especially laborious to resolve even moderately clustered repeat regions. With use of a maize canonical TE database, TE nest identifies and maps repeat incorporations into the original genome sequence while providing chronology of insertion events in Mya based on LTR base pair substitution rate. An insertion graph is produced to give an accurate visual representation of TE integration history showing timeline, location and types of each TE identified, thus creating a framework from which evolutionary comparisons can be made among various regions of the maize genome. We have used TE nest to analyze all 165 finished maize BACs from GenBank along with in-house generated 1.5 Mb rf1-spanning sequence in the centromeric region of chr3, constructed from 19 contiguous BACs. Huck, opie, and ji retrotransposons make up 50% of all repeat insertions, showing prolific replication of single TE copies at specific time intervals during maize genome evolution.