Abstract
BackgroundHelitrons are DNA transposable elements that are proposed to replicate via a rolling circle mechanism. Non-autonomous helitron elements have captured gene fragments from many genes in maize (Zea mays ssp. mays) but only a handful of genes in Arabidopsis (Arabidopsis thaliana). This observation suggests very different histories for helitrons in these two species, but it is unclear which species contains helitrons that are more typical of plants.ResultsWe performed computational searches to identify helitrons in maize and rice genomic sequence data. Using 12 previously identified helitrons as a seed set, we identified 23 helitrons in maize, five of which were polymorphic among a sample of inbred lines. Our total sample of maize helitrons contained fragments of 44 captured genes. Twenty-one of 35 of these helitrons did not cluster with other elements into closely related groups, suggesting substantial diversity in the maize element complement. We identified over 552 helitrons in the japonica rice genome. More than 70% of these were found in a collinear location in the indica rice genome, and 508 clustered as a single large subfamily. The japonica rice elements contained fragments of only 11 genes, a number similar to that in Arabidopsis. Given differences in gene capture between maize and rice, we examined sequence properties that could contribute to differences in capture rates, focusing on 3' palindromes that are hypothesized to play a role in transposition termination. The free energy of folding for maize helitrons were significantly lower than those in rice, but the direction of the difference differed from our prediction.ConclusionMaize helitrons are clearly unique relative to those of rice and Arabidopsis in the prevalence of gene capture, but the reasons for this difference remain elusive. Maize helitrons do not seem to be more polymorphic among individuals than those of Arabidopsis; they do not appear to be substantially older or younger than the helitrons in either species; and our analyses provided little evidence that the 3' hairpin plays a role.
Highlights
Helitrons are DNA transposable elements that are proposed to replicate via a rolling circle mechanism
Our search began with a training set of 12 maize 'seed' elements from the literature [12,15,21,22], from which we isolated both 5' and 3' ends as BLAST queries
We combined our predicted helitrons with the 12 query sequences to produces a total set of 35 maize helitrons (Table S1)
Summary
Helitrons are DNA transposable elements that are proposed to replicate via a rolling circle mechanism. Helitrons are DNA elements that are proposed to move via a rolling circle replication mechanism similar to that of some prokaryotic transposable elements [8] They are unique in that they do not duplicate host insertion sites and do not contain terminal repeats. They tend to insert between Adenine and Thymidine residues They have conserved ends consisting of TC on the 5' end and CTRR on the 3' end, often with a palindromic sequence of 16–20 bp near the 3' terminus. Because they do not replicate by the "cut and paste" method of most class II elements, helitrons were initially difficult to classify and were considered their own class. They have been assigned as a separate subclass of class II TEs [1]
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