New transposable elements identified as insertions in rice transposon Tnr1

Tnr1 (235 bp long) is a transposable element in rice. Polymerase chain reac tions (PCRs) done with a primer(s) that hybridizes to terminal inverted rep eat sequences (TIRs) of Tnr1 detected new Tnr1 members with one or two inse rtions in rice genomes. Six identified insertion sequences (Tnr4, Tnr5, Tnr 12,Tnr12, Tnr13 and RIRE9) did not have extensive homology to known transpo sable elements, rather they had structural features characteristic of trans posable elements. Tnr4 (1767 bp long) had imperfect 64-bp TIRs and appeared to generate duplication of a 9-bp sequence at the target site. However, th e TIR sequences were not homologous to those of known transposable elements , indicative that Tnr4 is a new transposable element;. Tnr5 (209 bp long) h ad imperfect 46-bp TIRs and appeared to generate duplication of sequence TT A like that of some elements of the Tourist family. Tnr11 (811 bp long) had 73-bp TIRs with significant homology to those of Tnr1 and Stowaway? and ap peared to generate duplication of sequence TA, indicative that Tnr11 is a t ransposable element of the Tnr1/Stowaway family. Tnr12 (2426 bp long) carri ed perfect 9-bp TIRs, which began with 5'-CACTA- -3' from both ends and app eared to generate duplication of a 3-bp target, sequence, indicative that T nr12 is a transposable element of the En/Spm family. Tnr13 (347 bp long) ha d 31-bp TIRs and appeared to generate duplication of an 8-bp target sequenc e. Two sequences, one the transposon-like element Crackle, had partial homo logy in the Tnr13 ends. All five insertions appear to be defective elements derived from autonomous ones encoding the transposase gene. All had charac teristic tandem repeat sequences which may be recognized by transposase. Th e sixth insertion sequence, named RIRE9 (3852 bp long), which begins with 5 '-TG- -3' and ends with 5'- -CA-3', appeared to generate duplication of a 5 -bp target sequence. These and other structural features indicate that this insertion is a solo LTR (long terminal repeat) of a retrotransposon. The t ransposable elements described above could be identified as insertions into Tnr1, which do not deleteriously affect the growth of rice cells.