RIRE2, a novel gypsy-type retrotransposon from rice

The 441-bp DNA segment in a PCR-amplified fragment from Oryza sativa cv. IR36 was found to have a sequence with features characteristic of LTRs of retroelements, which was named RIRE2 (Rice retroelement #2) and further analyzed. Cloning and sequencing analyses of the DNA segments connected to LTR-like sequence showed that RIRE2 has a long internal region almost 10 kb long that is flanked by LTR-like sequences. This internal region carries a primer binding site (PBS) and polypurine tract (PPT) which are necessary for cDNA synthesis of retroelements. The PBS sequence is complementary to the 3' end region of tRNA^Arg . The internal region has an rt gene homologous to that of gypsy-type retrotransposons, evidence that RIRE2 is indeed a retrotransposon related to gypsy from Drosophila. RIRE2 has an extra sequence more than 4 kb long in the region downstream of gag-pol. Phylogenetic analysis of the putative amino-acid sequences of the rt gene as well as the int gene showed that RIRE2 is related to a group of gypsy-type retrotransposons of a large size that include Grande1-4 of teosinte, Tat4-1 and Athila1-1 of Arabidopsis thaliana, and Cyclops-2 of pea, but distantly related to any other group of gypsy-type retrotransposons, including RIRE3 and RIRE8 of rice. RIRE2 and Grande1-4 had the highest homology in the gag-pol region, but the nucleotide sequences of the LTR regions differed. Both elements had significant homology in the middle area of the extra regions downstream of gag-pol, in which they had an open reading frame encoding a protein with no known function on the opposite strand from that coding for gag-pol.