| Helitrons are a new class of DNA transposable elements, which have the ability to capture gene fragments and transpose by means of rolling-circle replication. As one of the most important cereal crops, common wheat possess a huge polyploid genome and provides an ideal resource to explore the roles of Helitron elements in genome expansion and polyploidization. With the release of genome sequence of the hexaploid wheat and its two progenitor genomes T.urartu and A.tauschii, computational prediction and characterization of Helitron elements in these genomes are possible.Based on the local combinational variables algorithm, we improved the HelitronScanner program and identified 38546, 36362 and 32636 putative Helitron elements in the hexaploid bread wheat, Triticum urartu and Aegilops tauschii. Helitrons were estimated accounting for 6.3%, 3.8% and 4.1% of each genome. According to the sequence similarity of 5’ and 3’ends, these transposons were classified into 90 families containing 424 subfamilies. By analyzing Helitron sequence divergence, more than 90% Helitrons in three genomes had amplified in recent 8 million years. Generally, Helitrons experienced a burst of expansion at 2 million years ago in all three genomes, and another dramatic amplification was observed within recent 0.5 million years in the hexaploid wheat, which strongly supports the opinion that polyploidization promoted Helitrons expansion in common wheat genome. Further, the number of Helitron generated during second hybridization was larger than that during the first hybridization, suggesting the second hybridization event stimulated Helitrons expansion more strongly during the speciation of the hexaploid wheat.The gene capture analysis found that Helitrons in three genomes totally captured 14332 different gene fragments, with an average of 1.2~1.3 gene fragments per Helitron element. The majorities of them were annotated with functioning in binding and metabolic process. More than 84% Helitron transposons captured noly one gene fragment. Intriguingly, the gene encoding DnaQ_like exonuclease, chromosome segregation ATPase and histone methyltransferase SUVH1 were preferentially captured suggesting Helitrons expansion is helpful for maintaining genome integrity and epidemic regulation.We identified 43, 36 and 15 putative autonomous elements in the hexaploid wheat, Triticum urartu and Aegilops tauschii respectively. In addition to the classical Helicase and Rep domain, RVT and Peptidase_C48 domains were also found in some autonomous elements, which are probably involved in DNA transposon. Multiple sequence alignment for autonomous Helitrons in Triticeae with that in other species found two conserved motifs “ExQKRGLPHxH†and “KYLxKYxxKG†in Rep domain, which may be critical for Helitron transposion. Multiple sequence alignment for Helicase domain encoded by these autonomous elements displayed 7 conserved motifs, which was homologous with Helicase SF1.Based on the diversity of transposable elements in different Triticeae breeds and the principle of PCR, we totally validated 763 Helitron elements in the hexaploid wheat while absent in its two progenitors. This result further supports the opinion that Helitrons expanded during the speciation of the hexaploid wheat. Further, we carried on PCR amplification assay and validated some Helitron transposable elements with diversity among 8 different Triticum species.According to the above results, Helitron elements experienced a dramatic expansion at 2 million years ago in three Triticeae genomes, while another Helitron dramatic expansion in the hexaploid wheat was observed in recent 0.5 million years which may result from polyploidization. The analysis of gene capture showed that the genes related to genome stability and epidemic regulation were preferentially captured by Helitron elements, suggesting that the functional genes amplification droved by Helitrons can balance the instability and gene abnormal expression. |
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