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

Abstract

Background: Sadhu 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.

Results: 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.

Conclusions: 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.

Figure 1

Phylogenetic analysis of Arabidopsis thaliana Sadhu sequences. Maximum parsimony phylogram of full-length Sadhu elements. Taxa are color coded according to ontological grouping. See Table 1 for gene ID numbers corresponding to Sadhu numbers. Bootstrap values (percentages) were calculated from 500 bootstrap replicates.

Figure 2

Schematic alignment of selected Sadhu subfamilies in strain Col. TSD sequences are different at different elements. Sizes of TSDs: TSD1, 11 base pairs (bp); TSD2, 12 bp; TSD3, 12 bp; TSD4, 10 bp; TSD5, 13 bp. Percentages correspond to sequence identity to the longest element in the subfamily. Sizes marked above each line represent positions relative to the gapped alignment and might be slightly different from the nucleotide length of element. (a) Sadhu5; (b) Sadhu6; (c) Sadhu2; (d) Sadhu3; (e) Sadhu8-1 versus Sadhu8L3. TSD = target site duplication.

Figure 3

Empty sites detected in Arabidopsis thaliana strains at positions occupied in Col by (a) Sadhu5-1 and (b)Sadhu5-1d1. Multiple sequence alignments of Col 5' and 3' sequences flanking the site of insertion along with sequences of strains that do not contain the insertion. Sequences corresponding to Sadhu element insertions have been removed. Genbank accession numbers for Sadhu5-1 sequences are EF535531 and EF535532. Genbank accession numbers for Sadhu5-1d1 sequences are EF535533, EF535534, EF535535, EF535536, EF535537, EF535538, EF535539, EF535540, EF535541, EF535542, EF535543, EF535544, EF535545, EF535546, EF535547, EF535548, and EF535549.

Figure 4

Logo diagrams of consensus sequences at Sadhu insertion sites, based on 14 insertions in the Col reference genome. Nine nucleotides proximal to the target site were examined as the 5' nicking site, while nine nucleotides distal to the target site were examined as the 3' nicking site. The first seven nucleotides within the target site duplication were examined.

Figure 5

Phylogenetic analysis of Sadhu sequences from Arabidopsis arenosa and Arabidopsis lyrata relative to Arabidopsis thaliana. (a) Maximum parsimony phylogram of A. arenosa (Aa) internal Sadhu sequence clones and related A. thaliana elements. A. arenosa sequences are in blue. (b) Maximum parsimony phylogram of A. lyrata Sadhu sequences >350 bp (Al, purple) and full-length A. thaliana elements. Shaded large numbers indicate Sadhu subfamilies. See to Additional file 4 for DNA sequences of A. lyrata elements. Bootstrap values (percentages) were calculated from 500 bootstrap replicates.