A new MITE family, Pangrangja, in Gramineae species

The miniature inverted-repeat transposable element (MITE) is a type of class II transposon. We have isolated a new MITE, Pangrangja, from the species Oryza. Although Pangrangja elements are present in a number of Gramineae species, they are more prevalent in A genome Oryza species, Triticum, Aegilops, Hordeum, and Tripsacum. The Pangrangja has a 16 bp terminal inverted repeat (TIR) and conserved trinucleotides 5'-TTG-3' and 5'-AAA-3' at both ends. The TIR starts with 5'-CAGT-3', similar to the MITEs of the Emigrant family. The sequences between TIRs are very AT-rich and vary in length from 161 bp in A genome Oryza species to 513 bp in Hordeum vulgare. While the size and sequence of Pangrangia elements are conserved in the A genome Oryza species, there is some sequence variation in other plants. In an analysis of the mobile history of Oryza sativa, eight RESites (related to empty sites) were found and grouped into three types depending on the presence or absence of the conserved trinucleotides 5'-TTG-3' and 5'-AAA-3'. Since one of the RESites showed a perfect palindromic 22 bp sequence into which 180 bp of the Pangrangja element was inserted, the possible role of secondary structure of the palindromic sequences is discussed. We also suggest that as Pangrangja MITE-AFLP has been successful in many different Gramineae, Pangrangja elements may be useful in the genomic analysis of grasses.