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

2014; National Academy of Sciences; Volume: 111; Issue: 28 Linguagem: Inglês

10.1073/pnas.1410068111

1091-6490

Wenwei Xiong, Limei He, Jinsheng Lai, Hugo K. Dooner, Chunguang Du,

Plant Virus Research Studies

Significance 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. Many new Helitrons were identified in all organisms examined, resulting in a major reassessment of their abundance in eukaryotic genomes. In maize, they make up >6% of the genome and are the most abundant DNA transposons identified.