Scientific Objectives and Approaches:
Transposable elements (TEs) are the most abundant component of all characterized genomes of higher eukaryotes and the genome of maize is recognized as having the most dynamic TE component. As such, it is the organism of choice for understanding how TEs contribute to gene and genome evolution. Over the past two decades, members of our group have been at the forefront of the first descriptions of the maize genome and have pioneered the genome-wide computational analyses of TEs in many plant genomes. Our collective experiences put us in the unique position of knowing what to look for in maize and how to look. In addition to identifying all TEs in maize, this project will pay particular attention to the characterization of TEs such as Pack-MULEs and Helitrons that routinely capture and amplify gene fragments and thereby confound gene annotation. This project will generate a comprehensive and rigorously annotated TE database that will greatly assist all future maize genome annotations. As such, this project will set the standard for how plant TEs should be sought, catalogued and described. Computational analysis will serve to identify candidate active TEs whose mobility will be validated using the transposon display technique in conjunction with a wide spectrum of maize genomic DNAs. This project will, for the first time, extend the analysis of TEs to the pericentromere, a region that in other sequenced genomes has been unfinished and/or unannotated. To facilitate the analysis, this project will finish the sequence of a ~59 Mb region of chromosome 9S that extends from the euchromatic portion of the arm into the edge of the centromere. The boundaries of the centromere, pericentromere, and euchromatin will be mapped using specific chromatin antibodies. The finished region of 9S will provide an important new resource for TE discovery and allow us to assess how TEs contribute and respond to different chromatin environments. All information from this project will be made freely available to the Maize Genome Sequencing Project and to long-term repositories such as Maize GDB. Software and other tools generated will be freely available at the project website.
