A new gypsy-type retrotransposon, RIRE7: preferential insertion into the tandem repeat sequence TrsD in pericentromeric heterochromatin regions of rice chromosomes

A portion of an insertion sequence present in a member of the RIRE3 family of retrotransposons in Oryza sativa L. cv. IR36 was found to have an LTR se quence following by PBS sequence complementary to the 3 ' -end region of tR NA(Met), indicative of another rice retrotransposon (named RIRE7). Cloning and sequencing of PCR-amplified fragments that made up all parts of the RIR E7 sequence showed that RIRE7 is a gypsy-type retrotransposon with partial homology in the pol region to the rice gypsy-type retrotransposons RIRE2 an d RIR3 identified in rice previously. Interestingly, various portions of th e RIRE7 sequence were homologous to several DNA segments present in the cen tromere regions of cereal chromosomes. Further cloning and nucleotide seque ncing of fragments flanking RIRE7 copies showed that RIRE7 was inserted int o a site within a tandem repeat sequence that has a unit length of 155 bp. The tandem repeat sequence, named TrsD, was homologous to tandem repeat seq uences RCS2 and CentC, previously identified in the centromeric regions of rice and maize chromosomes. Fluorescence in situ hybridization (FISH) analy sis of the metaphas chromosomes of O. sativa cv. Nipponbare showed that bot h RIRE7 and TrsD sequences were present in the centromere regions of the ch romosomes. The presence of RIRE7 and the TRsD sequences in the centromere r egions of several chromosomes was confirmed by the identification of severa l YAC clones whose chromosomal locations are known. Further FISH analysis o f rice pachytene chromosomes showed that the TrsD sequences were located in a pericentromeric heterochromatin region. These findings strongly suggest that RIRE7 and TrsD are components of the pericentromeric heterochromatin o f rice chromosomes.