Genome-Wide Identification of MITEs and their Role on Genome Evolution

Miniature inverted-repeat transposable elements (MITEs) are prevalent in eukaryotic species including plants. Studies on MITEs have been advanced considerably in the last two decades. However, their evolutionary genomics including their origin, transposition and roles on genome evolution remains poorly explored. Using computer programs MITE-hunter, MITE Digger and RSPB, MITEs were genome-wide de novo identified from 41 plant species, including seven lower plants. More than 3,000 MITE families were identified, most of which are novel ones. Comparative analysis of MITEs in related species was performed to study the origin, amplification and evolution of MITEs. The number of MITEs (538-237,302) or the proportion of MITE sequences (0.006%-9.984%) varies dramatically among higher plants. The vast majority of MITE families are not active. However, four MITE groups with more than 20 identical elements were found in 4 species, which are very likely transposing currently. Sequences important for the transposing ability of these MITEs were predicted. MITEs are frequently transcribed with plant genes. At least 7,887 MITEs in the rice genome are transcribed and more than 3,463 are transcribed with rice genes. The MITE sequences transcribed with rice coding genes form 1,130 pairs of potential natural sense/antisense transcripts. MITEs generate 23.5% (183,837 of 781,885) of all small RNAs identified from rice. Small RNAs were produced mainly from the terminals of some MITE families, while from the central regions of other MITE families. The abundance of MITE-derived small RNAs along MITE sequences were largely determined by GC content, mainly from regions with high GC content. Considering that different sets of genes may be regulated by MITE-derived small RNAs in different genotypes, MITEs provide considerable diversity for O. sativa.