The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species

We present a classification scheme for Sadhu elements in A. thaliana, describing derivative elements related to the full-length elements we reported previously. We characterized Sadhu5 elements in a set of A. thaliana strains in order to trace the history of radiation in this subfamily. Sequences surrounding the target sites of different Sadhu insertions are consistent with mobilization by LINE retroelements. Finally, we identified Sadhu elements grouping into distinct subfamilies in two related species, Arabidopsis arenosa and Arabidopsis lyrata.Our analyses suggest that the Sadhu retroelement family has undergone target primed reverse transcription-driven retrotransposition during the divergence of different A. thaliana strains. In addition, Sadhu elements can be found at moderate copy number in three distinct Arabidopsis species, indicating that the evolutionary history of these sequences can be traced back at least several millions of years.We previously reported a novel family of Arabidopsis retroposons, Sadhu [1]. The typical Sadhu element contains a poly(A) tract and is flanked by a direct 7 to 16 base pair (bp) target site duplication (TSD). Similar to small interspersed nuclear elements (SINEs), Sadhu elements are non-protein coding and do not contain long terminal repeats (LTRs); they are therefore expected to be non-autonomous. Although plant SINEs are thought to be mobilized by autonomous long interspersed nuclear elements (LINEs), the source of the transposase for Sadhu is not clear.Structurally, Sadhu elements resemble SINEs (non-coding, poly(A) tract), but unlike known SINEs, they do not contain sequence similarity to known non-coding RNAs (for example, 5SrRNA, tRNA) [2]. Nor do Sadhu elements carry conserved sequences similar to RNA polymerase II TATA boxes or RNA polymerase III promoter motifs (for example, A and B boxes). However, Sadhu elements share a motif near the 5' end (consensus 5' CAATCGTTSC 3') and an approximately 20 bp polypyrimidine reg