Advent of a new retrotransposon structure: the long form of the Veju elements Franc¸ ois Sabot 1,2 , Pierre Sourdille 1 & Michel Bernard 1, * 1 UMR INRA/UBP 1095 Ame´lioration & Sante ´ des Plantes, 234 Avenue du Bre ´zet, F-63100 Clermont- Ferrand, France; 2 Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, Viikkinkaari 4, PO Box 56, FIN-00014, Helsinki, Finland; *Author for correspondence (Phone: +33-4-73-62-43-07; Fax: +33-4-73-62-44-53; E-mail: michel.bernard@clermont.inra.fr) Received 26 January 2005 Accepted 5 August 2005 Key words: evolution, grass, transposable elements, TRIM, Triticeae, wheat Abbreviations: BAC – Bacterial Artificial Chromosome; LARD – LArge Retrotransposon Derivative; LTR – Long Terminal Repeats; PBS – Primer Binding Site; PPT – PolyPurine Tract; TEs – Transposable elements; TSD – Target-Site Duplication; TRIM – Terminal Repeats In Miniature. Abstract Transposable elements are the main component of plant genomes, especially in grass species. In a previous analysis, we have identified two unusual types of Class I elements, two homologous Veju TRIM elements, but with an unusual long structure. They are formed by the junction of a yet unidentified segment labelled unknown DNA, flanked by the borders of the classical Veju element. Here, we show that the long (Veju_L) and the short forms (Veju_S) coexist within wheat genomes. The associated unknown DNA had always the same origin, and the Veju_L came probably from either illegitimate recombinations or ‘template switching’ between the Veju_S and another unique unknown DNA sequence. This junction then evolved differently within wheat genomes. Introduction Transposable elements (TEs) are endogenous mo- bile genetic sequences which play an important role in chromatin structure and genome plasticity (Kim et al., 1998; Kumar & Bennetzen, 1999). They are ubiquitous among all living kingdoms, and are especially numerous in plants. TEs represent 20% of the Arabidopsis genome and more than 70% of the Triticeae and Liliaceae genomes (Kumar & Bennetzen, 1999; Sabot, Simon & Bernard, 2004). Different classes are distinguished according to their transposition intermediates and their sequence homologies. Class I elements transpose via an RNA intermediate, where the corresponding reverse transcribed cDNA is inserted into a new genomic location. These elements are separated in two groups, LTR (Long Terminal Repeats) retro- transposons and non-LTR retrotransposons. Within the LTR retrotransposon group, elements are further divided into copia, gypsy, athila, TRIMs (Terminal Repeats In Miniature, Witte et al., 2001) and LARDs (LArge Retrotransposon Derivatives, Kalendar et al., 2004), according to their structures (Sabot, Simon & Bernard, 2004). In a previous analysis on homoeologous sequences from related wheats (Chantret et al., 2005), we have identified two new TEs belonging to Class I LTR retro- transposons at the homologous positions on the CR626934 and CR626926 sequences (bearing the Hardness locus of the D genome of T. aestivum and Ae. tauschii, respectively). These two elements Genetica (2005) 125: 325–332 Ó Springer 2005 DOI 10.1007/s10709-005-7926-3