Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 USA
Due to the small insert sizes for most cloning vectors, comparisons of genome structure between cloned segments were limited to orthologous genes and their adjacent sequences. In most higher eukaryotes, however, we have long known that genes make up a minority of the nuclear DNA. A full understanding of genome structure, and its relationship to genome function and evolution, requires an understanding of both genic and intergenic DNA organization. With the advent of artificial chromosome libraries, we can now compare large regions of plant genomes. My lab has concentrated on analyses of maize, sorghum and rice, grasses that differ greatly in genome size, segmental ploidy, and degree of relatedness. Our results indicate that all genic regions are more gene rich than predicted by a model of random gene distribution. In maize, most genes are separated from other genes by large (5 kb to >50 kb) blocks of nested retrotransposons. In rice and sorghum, retrotransposons are less abundant and do not separate most of the genes analyzed. Instead, the intergenic regions of rice and sorghum are composed of small, hypervariable transposable elements (MITEs) plus a large amount of low copy number DNA of unknown origin. Despite major and rapid changes in intergenic DNA content, gene composition and order have been conserved in segments of these three genomes and (to a very limited degree) in the dicot Arabidopsis. However, small rearrangements appear to be quite frequent, indicating that genomic colinearity observed with recombinational maps may not be present in sub-centiMorgan analyses of the same regions.
Plant & Animal Genome VII Conference Plant & Animal Genome VII Conference