Abstract
BackgroundSadhu elements are non-autonomous retroposons first recognized in Arabidopsis thaliana. There is a wide degree of divergence among different elements, suggesting that these sequences are ancient in origin. Here we report the results of several lines of investigation into the genomic organization and evolutionary history of this element family.ResultsWe 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.ConclusionsOur 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.
Highlights
Sadhu elements are non-autonomous retroposons first recognized in Arabidopsis thaliana
We examined the region around these target sites to determine whether 5’ and 3’ nicking site consensus patterns could be identified and, if so, whether they resembled patterns previously reported for long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE)
Sequences at the target site are similar to the Arabidopsis SINE consensus, consistent with the hypothesis that the LINE machinery is responsible for the mobilization of both of these types of elements
Summary
Sadhu elements are non-autonomous retroposons first recognized in Arabidopsis thaliana. Similar to small interspersed nuclear elements (SINEs), Sadhu elements are non-protein coding and do not contain long terminal repeats (LTRs); they are expected to be non-autonomous. Sadhu elements resemble SINEs (noncoding, poly(A) tract), but unlike known SINEs, they do not contain sequence similarity to known non-coding RNAs (for example, 5SrRNA, tRNA) [2]. There is variation in the modes of silencing of various Sadhu family members highlighted by differential susceptibility to epigenetic modifier mutations and distinct cytosine methylation profiles. These findings suggest that Sadhu elements are silenced independently and individually, not coordinately [6]. Sadhu represents a unique family of non-LTR retroelements
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