Although short interspersed elements (SINEs) were discovered nearly 30 years ago, the studies of these genomic repeats were mostly limited to animal genomes. Very little is known about SINEs in legumes--one of the most important plant families. Here we report identification, genomic distribution and molecular features of six novel SINE elements in Lotus japonicus (named LJ_SINE-1, -2, -3) and Medicago truncatula (MT_SINE-1, -2, -3), model species of legume. They possess all the structural features commonly found in short interspersed elements including RNA polymerase III promoter, polyA tail and flanking repeats. SINEs described here are present in low to moderate copy numbers from 150 to 3000. Bioinformatic analyses were used to searched public databases, we have shown that three of new SINE elements from M. truncatula seem to be characteristic of Medicago and Trifolium genera. Two SINE families have been found in L. japonicus and one is present in both M. truncatula and L. japonicus. In addition, we are discussing potential activities of the described elements.
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