TEOS1, a novel transposable element family from Oryza sativa

We have uncovered a novel group of transposable elements TEOS1, (Transposable Element of Oryza sativa) by repeat mining of rice genome sequence data. We first identified a TEOS1 element, 6,896 bp in length, from a PAC clone of rice chromosome 5. The presence of long terminal repeats (LTRs) and other diagnostic features, such as a primer-binding site (PBS) and a polypurine tract (PPT), indicated that TEOS1 is a group of LTR retrotransposon. The internal domain of TEOS1 containing two arrays of tandem repeats and a predicated Tf1gene was characteristically distinct from those of other LTR retrotransposons previously described. TEOS1 elements identified were flanked by 5-bp direct repeats; some identified as solo LTRs were flanked by 5-7 bp direct repeats. The PBS sequence was homologous to the 3 ́ end region of tRNAArg. The deduced amino acid sequence of Tf1 is dissimilar to that of any known mobility related proteins. TEOS1 is probable to be trans-activated by other retrotransposons in the rice genome. We have estimated that there are about 300 TEOS1 elements per haploid rice genome. The presence of repeats in TEOS1 offers the potential to form secondary structure during replication and transcription, and to serve as a hot spot for transposon insertion, augmenting the dynamics of molecular interactions of the genomic sequences.