Emiliani G, Paffetti D, Giannini R-Identification and molecular characterization of LTR and LINE retrotransposable elements in Fagus sylvatica L

Introduction Transposable elements (TEs) are ancient (retro)-virus insertions inside a host genome and are peculiar mobile genetic elements accounting for a large proportion of repetitive DNA regions (SanMiguel et al. 1996). TEs (Fig. 1) are classified according to their origin and structure (Craig et al. 2002, Wicker et al. 2007). Class II DNA mediated TEs are usually in low copy number as they transpose with a “cut and paste” process (Casacuberta & Santiago 2003) and are particularly important in prokaryotic and animal genetics (Craig et al. 2002, Kazazian 2004, Biémont & Vieira 2005). Miniature Inverted TEs (MITEs) are defective, non autonomous forms of DNA transposons and are the predominant TE type in or near plant genes (Feschotte et al. 2002). Retrotransposons (RNA mediated Class I TEs) are the most widespread class of eukaryotic TE, particularly relevant in shaping plant genomes (Feschotte et al. 2002, Wicker et al. 2007). Retrotransposons can be classified in two main classes (Feschotte et al. 2002): nonLTR and LTR elements characterized, respectively, by the absence or presence of long repeated regions flanking the ORFs core. LTR retrotransposons, if still active, increase their copy number with their copyand-paste mode of transposition. Non-LTR retrotransposons can be divided in several subclasses, such as LINE (Long INterspersed Elements) and SINE (Short INterspersed Elements Wicker et al. 2007). Both LINEs and SINEs elements, despite the differences in structure and transposition mechanisms (Wicker et al. 2007), are ubiquitous components of eukaryotic genomes, playing a major role in their evolution. LTR and non-LTR retrotransposons are common in plant genomes where they can be present in high copy number, ranging from 20000 to 200000 copies of copia-like LTR elements in barley and maize (Vicient et al. 1999, Meyers et al. 2001); the gypsy LTR element is present in 20000 copies in maize. There are 250000 copies of LINE elements in Lilium (Leeton & Smyth 1993) and SINEs are represented, for example, by 50000 copies in tobacco (Yoshioka et al. 1993). It is therefore clear that retrotransposable elements build large parts of eukaryotic genomes (Vitte et al. 2007). They represent, for example, a 20% genomic fraction in Drosophila melanogaster (Kapitonov & Jurka 2003), 45% in human (TIHGSC 2001) and over 80% in maize (SanMiguel et al. 1996). The observed differences in genome size in plants are accompanied by variations in the content of LTR retrotransposons, demonstrating that such elements might be important players in the evolution of plant genomes, along with polyploidy (Flowers & Purugganan 2008). The analysis of these elements have also revealed that plant genomes underwent genome amplifications (retrotransposition) and contractions (homologous or illegitimate recombination) leading Vitte & Panaud (2005) to the definition of the increase/decrease model of genome evolution. TEs have also an important role in gene evolution and regulation (Xiao et al. 2008). Even if they usually integrate into intergenic regions, in maize both LTR-retrotransposons and MITEs elements have been frequently found associated to genes (Wessler 1998). Retrotransposition can directly affects gene expression by integrating into coding or regulatory regions (White et al. 1994, Durbin et al. 2001); it also acts on tissue specific alternative splicing if inserted in intron regions (Leprince et al. 2001). Deleterious effects of TEs movement and replication are controlled by the development of mechanisms limiting their mutagenic activity, being silencing, probably, the most general and effective one (Vance & Vaucheret 2002). Since retrotransposable elements are abundant, ubiquitous and highly conserved (especially the LTR elements), they have drawn much attention for the development of genetic diversity and mapping markers; se-