HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

• DOI: 10.1073/pnas.1410068111
• Publication Date: 2014-07-01T14:07:52Z
• Authors: Wenwei Xiong; Limei He; Jinsheng Lai; Hugo K. Dooner; Chunguang Du
• Keywords: Rolling circle replication

Significance Helitrons are unusual rolling-circle eukaryotic transposons with a remarkable ability to capture gene sequences, which makes them of considerable evolutionary importance. Because lack typical transposon features, they challenging identify and estimated comprise at most 2% sequenced genomes. Here, we describe HelitronScanner, generalized tool for their identification based on motif-extracting algorithm proposed initially in study natural languages. HelitronScanner overcomes the divergence Helitron termini among species by using conserved nucleotides potentially variable locations. Many new were identified all organisms examined, resulting major reassessment abundance In maize, make up >6% genome abundant DNA identified.