Genome-Wide Analysis of Transposon Insertion and Excision Patterns in the Two Rice Species O. sativa and O. glaberrima

We have aligned approximately 65% of the genomes of the two rice species Oryza sativa and O. glaberrima. The two species diverged about 600,000 years ago and are thus close enough to allow good sequence alignments and yet distant enough to have accumulated numerous mutations and rearrangements. Our goal was to survey polymorphisms caused by the movements of Class 2 (DNA) transposons. We identified over 3,000 potential excisions and insertions in both species. We analysed in detail almost 500 insertions and excisions. Interestingly, we found a large excess of insertions over excisions. Our data indicate that excisions cause many large rearrangements (e.g. large deletions). We conclude that many excisions can not be detected because the affected regions have changed so strongly that they can not be properly aligned anymore. Additionally, our data indicate that excisions of transposons of the HAT and Mutator superfamilies are particularly prone to cause large rearrangements. Furthermore, we identified multiple cases where families of potential autonomous and non-autonomous elements had been active since the divergence of the two species 600,000 years ago.