Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome Tatiana Zerjal Æ Johann Joets Æ Karine Alix Æ Marie-Ange `le Grandbastien Æ Maud I. Tenaillon Received: 29 October 2008 / Accepted: 31 May 2009 / Published online: 17 June 2009 Ó Springer Science+Business Media B.V. 2009 Abstract Miniature inverted-repeat transposable elements (MITEs) are short, non autonomous DNA elements that are widespread and abundant in plant genomes. The high sequence and size conservation observed in many MITE families suggest that they have spread recently throughout their respective host genomes. Here we present a maize genome wide analysis of three Tourist-like MITE families, mPIF, and two previously uncharacterized families, ZmV1 and Zead8. We undertook a bioinformatic analysis of MITE insertion sites, developed methyl-sensitive transposon dis- play (M-STD) assays to estimate the associated level of CpG methylation at MITE flanking regions, and conducted a population genetics approach to investigate MITE patterns of expansion. Our results reveal that the three MITE families insert into genomic regions that present specific molecular features: they are preferentially AT rich, present low level of cytosine methylation as compared to the LTR retrotranspo- son Grande, and target site duplications are flanked by large and conserved palindromic sequences. Moreover, the anal- ysis of MITE distances from predicted genes shows that 73% of 263 copies are inserted at less than 5 kb from the nearest predicted gene, and copies from Zead8 family are signifi- cantly more abundant upstream of genes. By employing a population genetic approach we identified contrasting pat- terns of expansion among the three MITE families. All elements seem to have inserted roughly 1 million years ago but ZmV1 and Zead8 families present evidences for activity of several master copies within the last 0.4 Mya. Keywords Maize Á MITE Á Tourist-like Á M-STD Á Methylation Á Evolution Introduction Transposable elements (TEs) are discrete DNA segments found in nearly all living organisms examined, and are particularly abundant in eukaryote genomes (Craig et al. 2002). TEs are traditionally divided into two classes (Wicker et al. 2007). Class I elements, known as retro- transposons, transpose via a RNA intermediate by a ‘‘copy and paste’’ mechanism and are distinguished in five orders on the basis of their internal genomic organization and mechanistic features. Class II elements, known as DNA transposons, transpose via a DNA intermediate and are divided into two subclasses, distinguishable by the number of DNA strands that are cut during transposition: both strands in subclass 1 and one strand in subclass 2. Subclass 1 Electronic supplementary material The online version of this article (doi:10.1007/s11103-009-9511-0) contains supplementary material, which is available to authorized users. T. Zerjal Á M. I. Tenaillon CNRS, UMR 0320/UMR 8120, Ge ´ne ´tique Ve ´ge ´tale, F-91190 Gif-sur-Yvette, France J. Joets INRA, UMR 0320/UMR 8120, Ge ´ne ´tique Ve ´ge ´tale, F-91190 Gif-sur-Yvette, France K. Alix AgroParisTech, UMR 0320/UMR 8120, Ge ´ne ´tique Ve ´ge ´tale, F-91190 Gif-sur-Yvette, France M.-A. Grandbastien INRA, Laboratoire De Biologie Cellulaire, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France T. Zerjal (&) UMR de Ge ´ne ´tique Ve ´ge ´tale, INRA/Univ Paris-Sud/CNRS/ AgroParisTech, Ferme du Moulon, F-91190 Gif-sur-Yvette, France e-mail: zerjal@moulon.inra.fr 123 Plant Mol Biol (2009) 71:99–114 DOI 10.1007/s11103-009-9511-0