Identification and characterization of novel retrotransposons of the gypsy type 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 the Drosophila retrotransposon gypsy. We named the element from which they originated RIRE3 (for rice retrotransposon No. 3) and analyzed it further by isolating various clones containing segments of RIRE3. Nucleotide sequencing of the clones revealed that RIRE3 has LTRs (2316 bp) and that the internal sequence (5775 bp) includes a large ORF with gag and pol regions; the pol 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 RIRE3 contained another open reading frame, here called orf0, which does not exist in gypsy or in other retrotransposons related to it. In the course of characterizing RIRE3, we obtained a further clone, which showed less homology with the pol region of RIRE3. This clone was found to be derived from another gypsy-type retrotransposon (named RIRE8) containing the LTR sequence and orf0 both of which were only weakly homologous to that in RIRE3. Further characterization of RIRE8 revealed that there were actually two subtypes of RIRE8 (named RIRE8A and RIRE8B), which show little homology to each other in the orf0 region. Although the LTRs of RIRE3 and RIRE8 elements show very weak homology with each other, there exists a conserved sequence at their termini. We therefore carried out PCR using primers which hybridize to the rt gene of RIRE3, and total genomic DNA from various monocot and dicot plants as templates, and found that a family of RIRE3 elements was present in all plants tested.