Plant Genome Reshuffling via Rolling Circle Helitrons

Helitrons are unusual rolling-circle eukaryotic transposons with a remarkable ability to capture gene sequences, which makes them of considerable evolutionary importance.  Because Helitrons lack typical transposon features, they are challenging to identify and are estimated to comprise at most 2% of sequenced genomes.  Here we describe HelitronScanner, a generalized tool for their identification based on a motif-extracting algorithm proposed initially in a study of natural languages.  HelitronScanner overcomes the divergence of Helitron termini among species by using conserved nucleotides at potentially variable locations.  We ran HelitronScanner against a wide range of plant genome sequences from Phytozome version 9.0 and identified a total of 107,367 Helitrons.  Many new Helitrons were identified in model species, such as maize, rice, and Arabidopsis, and in a variety of organisms where Helitrons had not been reported previously, leading to a major upward reassessment of their abundance in plant genomes.  The Helitron abundance revealed by our study is consistent with previous suggestions that the percentage of Helitrons in genomes was most likely underestimated.  We found no sign of correlation between Helitron abundance and genome sizes.