Identification and characterization of novel retrotransposons of the gypsytype in rice

We found that two DNA fragments, which were obtained from Oryza sativa L cv . IR36 by PCR using degenerate primers designed for amplification of a rice gene, showed homology with the rt gene encoding reverse transcriptase of t he Drosophila retrotransposon gypsy. We named the element from which they o riginated RIRE3 (for rice retrotransposon No. 3) and analyzed it further by isolating various clones containing segments of RIRE3. Nucleotide sequenci ng of the clones revealed that RIRE3 has LTRs (2316 bp) and that the intern al sequence (5775 bp) includes a large ORF with gag and pol regions; the po l region includes the rt gene as well as the int gene encoding integrase in this order, as in gypsy. Interestingly, the region upstream of gag in RIRE 3 contained another open reading frame, here called orf0, which does not ex ist in gypsy or in other retrotransposons related to it. In the course of c haracterizing RIRE3, we obtained a further clone, which showed less homolog y with the pol region of RIRE3. This clone was found to be derived from ano ther gypsy-type retrotransposon (named RIRE8) containing the LTR sequence a nd orf0 both of which were only weakly homologous to that in RIRE3. Further characterization of RIRE8 revealed that there were actually two subtypes o f RIRE8 (:named RIRE8A and RIRE8B), which show little homology to each othe r in the orf0 region. Although the LTRs of RIRE3 and RIRE8 elements show ve ry weak homology with each other, there exists a conserved sequence at thei r termini. We therefore carried out PCR using primers which hybridize to th e rt gene of RIRE3, and total genomic DNA from various monocot and dicot pl ants as templates, and found that a family of RIRE3 elements was present in all plants tested.