Comparative analysis of repetitive DNA sequences in genus Oryza

Repetitive DNA sequences play a major architectonic role in higher order physical structuring of genomes. To be able to understand how these sequences shape plant genomes during evolution, BAC-end sequences representing ∼10% of ten Oryza genomes were used to sample their repetitive fraction. 36-76% of these genomes was repetitive and was correlated to the genome size (r=0.96). Analysis of the largest and smallest diploid genomes indicated their role in determining genome size of a species. Repetitive sequences specific to each species were identified for potential use as molecular markers in practical breeding and cytogenetic studies. Comparison of orthologous regions identified genomic rearrangements and conserved/variable regions with implications for changes at these loci both pre and post-genome differentiation from a common ancestor. Fragments of transposable elements were also found associated with conserved noncoding sequences, some of which were mapped to the untranslated regions and introns of genes, implying possible roles in gene regulation. Thus, the data suggests an evolutionary as well as functional significance of transposable elements in the host genomes. These determinations will be used to improve our understanding of the processes that might have played a role in shaping Oryza genomes