P-MITE: a database for plant miniature inverted-repeat transposable elements

Miniature inverted-repeat transposable elements(MITEs) are prevalent in eukaryotic speciesincluding plants. MITE families vary dramaticallyand usually cannot be identified based onhomology. In this study, we de novo identifiedMITEs from 41 plant species, using computerprograms MITE Digger, MITE-Hunter and/orRepetitive Sequence with Precise Boundaries(RSPB). MITEs were found in all, but one(Cyanidioschyzon merolae), species. Combinedwith the MITEs identified previously from the ricegenome, >2.3 million sequences from 3527 MITEfamilies were obtained from 41 plant species. Ingeneral, higher plants contain more MITEs thanlower plants, with a few exceptions such aspapaya, with only 538 elements. The largestnumber of MITEs is found in apple, with 237 302MITE sequences. The number of MITE sequencesin a genome is significantly correlated withgenome size. A series of databases (plant MITEdatabases, P-MITE) was constructedto host all MITE sequences from the 41 plantgenomes. The databases are available forsequence similarity searches (BLASTN), and MITEsequences can be downloaded by family or bygenome. The databases can be used to study theorigin and amplification of MITEs, MITE-derivedsmall RNAs and roles of MITEs on gene andgenome evolution.

Chen, J., Hu, Q., Zhang, Y., Lu, C., and Kuang, H. (2014). P-MITE: a database for plant miniature inverted-repeat transposable elements. Nucleic Acids Res. 42, 1176-1181.