Studies of the novel retrotransposable elements appeared on rice chromosomes

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We have identified and characterized various retrotransposons with or without LTR in the genome of O.sativa. RIRE1, a retrotransposon of copia type, was originally found in wild rice O.austrariensis in an extraordinary number of copies. RIRE2, RIRE3 and RIRE8 were isolated from O.sativa IR36. These elements turned out to be retrotransposons of gypsy type with LTR.These elements were often nested one another on rice chromosomes. RIRE2 was originally found as a sequence associated with TrsA,a tandem repeat sequence at the subtelomeric regions of the O.sativa chromosome. The gag and the pol regions of RIRE2 show high homology with those of Grande1, a teosinte retrotransposon with LTR.The amino acid sequences of rt genes of these gypsy-type retrotransposons revealed that they were divided into two groups, such as RIRE3-RIRE8 family and RIRE2-Grande1 family. We have also identified LINE elements, non-LTR retrotransposons, from the various members of the higher plants including rice. Sequence analysis revealed that these elements contained amino acid sequence motifs conserved in the region. Phylogenetic analysis indicated that these elements were transmitted vertically unlike other retrotransposons with LTR,which were believed to be transmitted horizontally.