Overview of Rim2/Hipa transposon superfamily: Structure, distribution, transposition and utilization

The rice Rim2/Hipa is a unique transposon superfamily in Oryza genomes, which can be transcriptionally activated by the infection of the rice blast pathogen Magnaporthe grisea and its elicitors. Rim2/Hipa elements belong to En/Spm family, with perfect terminal inverted repeats in both ends, direct and inverted sub-terminal repeats, and 3-bp target site duplication upon insertion. Intriguingly, the typical ‘CACTG’ end sequences in the terminal inverted repeats of most Rim2/Hipa elements distinguish them from previously reported CACTA elements, such as En/Spm, Tam1, and Tgm1, which harbor ‘CACTA’ sequence in their terminal inverted repeats. In particular, the plentiful Rim2/Hipa elements unevenly distribute over all 12 chromosomes and make up at least 1% of the entire genome. Southern hybridization revealed the existence of Rim2/Hipa elements in all rice varieties examined and the Rim2/Hipa core sequence is unique to rice genomes. Evidence derived from sequence analysis indicated the occurrence of transposition events during the long evolution. The abundance and insertion polymorphisms suggested their applications as novel molecular marker in rice fingerprinting and fine chromosome mapping. This paper aims at outlining the Rim2/Hipa elements with respect to their structure, distribution, transposition and utilization.