ASTER-REP, a Database of Asteraceae Sequences for Structural and Functional Studies of Transposable Elements

Transposable elements (TEs) are interspersed repetitive DNA sequences that can move independently within the genome through specific transposition mechanisms. In eukaryotes, TEs are divided into two classes: class I TEs (retrotransposons, REs), which use an RNA intermediate for the transposition, and class II TEs (DNA transposons), which move through DNA excision (Wicker et al. 2007). These classes are grouped into orders and lineages, according to sequence homology and to the ability to encode their own transposition machinery or not. Traditionally, TEs have been poorly studied also because their identification has been challenging; nevertheless, these sequences have tremendous implications for genome stability and function: first, TEs drive structural variation, as their transposition can cause deletions, inversions (i.e., homologous recombination of TEs with an opposite orientation) and duplications (Cordaux and Batzer 2009), making TEs activity strongly associated with dynamics of genome reduction/expansion. Second, TEs may drastically affect the expression of other genes (Lisch 2013, Fambrini et al. 2018), either by disrupting the coding sequence or by altering the gene regulation when transposing into the upstream region with different effects, such as the disruption of regulatory sites, epigenetic silencing of neighboring regions or providing new regulatory elements (Morgante et al. 2007, Slotkin and Martienssen 2007). Finally, TEs can originate novel genes through exaptation mediating neofunctionalization with a selective advantage to the host (Ventimiglia et al. 2022).