Overview

Miniature inverted-repeat transposable elements (MITEs) are prevalent in eukaryotic genomes, which are believed to be truncated derivatives of DNA transposons. MITEs usually have terminal inverted repeats (TIR), flanked by short direct repeats (also called target site duplication, TSD). MITEs are often short (< 800 bp) and do not encode transposases. Full-length MITEs from sequenced plant genomes were identified using MITE-hunter and RSPB (Han and Wessler, 2010; Lu et al., 2012), and then annotated manually. All MITE sequences were classified into superfamilies and families based on structure and sequence characteristics. One or a few full-length MITE sequences (called seed sequence) from each family were used as query sequences to search for related sequences from a genome using RepeatMask.