Investigation of rice (Oryza sativa L.) retrotransposons in different taxa

Abstract

Retrotransposons are the subclass of transposable elements and they can increase their copy numbers in the genome through their copy-paste transposition mechanism. Throughout evolutionary process, their transposition events result in mutations. Thus, they cause the formation of new gene alleles and, in the long term, speciation. In contrast, their transposition events might have harmful effects. Therefore most of the organisms have been developing various mechanisms for silencing retrotransposons throughout evolutionary processes. By this way they protect their genome from harmful transposition events. In this study, we investigated transposition events of four Oryza sativa LTR-retrotransposons (Hopi, Houba, Osr30 and RIRE1) in Oryza sativa L. (rice), Brachypodium distachyon (L.) P. Beauv., Hordeum vulgare L., (barley) and Triticum aestivum L. (wheat) by PCR based IRAP marker technique. PCR resulted in different band profiles and polymorphism ratios between individuals of each species. In four species, only rice showed significant polymorphisms between individuals. This result indicates that all tested retrotransposons are still active and cause genomic polymorphism between individuals of rice while they were silenced with various mechanisms in other species. Although these four plant species have a common ancestor, rice was distinguished from others more than 40 million years ago. This result might show that the mechanisms that repress the transposition events of retrotransposons were developed after this point.