Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
            

GENE ENRICHMENT TECHNOLOGIES FOR SELECTIVE SEQUENCE ANALYSIS OF THE MAIZE GENOME

¹ Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA

² Purdue University Genomics Center, S004 WSLR, Purdue University, West Lafayette, IN 47907, USA

Like other grass genomes, the nuclear DNA of maize is mostly composed of highly repetitive sequences. Over 60% of the maize genome is composed of LTR retrotransposons that are often found as nested blocks of 10-100 kb intermixed with short genic regions. The large size and the similarity of these retrotransposons will make it very difficult to assemble shotgun sequence data from the maize genome into long contiguous sequences (contigs). In order to avoid the inefficiency of sequencing the unwanted repetitive DNA, we and others have developed various gene enrichment technologies based on methylation pattern differences and copy number differences between repetitive DNAs and genes. These techniques will allow a shotgun approach for relatively efficient sequencing of gene-rich regions in the maize genome and other higher plant genomes. We will discuss and compare these technologies, indicating their respective strengths and weaknesses, especially with regard to the genic components that might be missed and their representation of the boundaries between repetitive DNAs and genic regions. Several of these techniques appear to be highly complementary. If used in a combined approach, these gene enrichment techniques should produce almost all genes in sequence contigs, and will also locate these contigs on genetic and physical maps.