Identification And Bioinformatics Analysis Of Helitrons Transposable Element In Common Bean And Other Legumes

Legumes such as common bean and soybean are important source of vegetables,and had been sequenced one after another,therefore genome research has been deepening.As a part of genome,Helitrons have unique structure and replication,and also have been found to often insert into genes or nearby,and frequently capture gene or gene fragments during transpositional process.Based on genomics and bioinformatics methods,Helitrons were identified and analysed in Glycine max,Phaseolus vulgaris,Vigna radiate,Vigna angularis,and Medicago truncatula,in order to make full use of legume genome for research of functional genes and breeding.The main results are as follows:1.Identification and annotation of Helitrons in legumes1330,72,26,22 and 1274 Helitrons were identified in Glycine max,Phaseolus vulgaris,Vigna radiate,Vigna angularis,and Medicago truncatula respectively.With the most copies,Helitrons account for the content of 1.9%and were enriched in heterochromatin region with significant inhibition in soybean.Helitrons were mainly distributed in the AT rich region;3' end of Helitrons was very conservative with a high GC content;and contained other exogenous transposable elements,simple repeat sequences,tandem repeats,inverted repeats and other repeats.2.Relationship with functional genesSoybean helitrons were found to inserted into the intron regions of two genes,and helitrons inserted into intron regions of 11 genes in Medicago truncatula,but all those genes in both two species were orthologous genes that had no expression data.8%of soybean helitrons inserted nearby genes which are related to metabolic process,signals and regulation of stress reaction in biological process,composition of cells,organelles and polymer complexes in cellular component,and catalytic activity in molecular function.91%of soybean helitrons captured genes which were related to protein phosphorylation,pollen recognition,signal transduction and resistance in biological process,composition of protoplast in cellular component,and also activities of iron ions,transmembrane receptors,protein kinases,wood xyloglucan transferase,endopeptidase and oxidordeuctase in molecular function.86%of common bean Helitrons captured genes fragments which were related to signal transduction,pollen recognition,cell apoptosis,protein of ubiquitin and phosphorylation,defense reaction in biological process,components of ubiquitin ligase complicated in cellular component,and also the carrier of membrane,extracellular glutamate ion channels,protein kinase,ubiquitin ligase activity and ATP binding activity in molecular function.3.Phylogenetic and expression analysis of Helitrons25%of the soybean Helitrons,37%of the Helitrons in Phaseolus vulgaris and 35%of the Helitrons in Medicago truncatula have potential transcriptional activity.These activities mainly performed in root,root nodules,seeds and tissue culture in soybean and Medicago truncatula Helitrons,as far as Helitrons in common bean expressed more in seeds,leaves and under drought stress.Helitrons in soybean and Medicago truncatula can generate microRNAs which could regulate cleavage and translation of DNA.The I lineage of D5 and RC domain were lost in common bean,and the m lineage of D5 domain and RC domain were lost in soybean.The research confirms that Helitrons played important role in gene structure,function and expression regulation and evolution of the in leguminous plant genomes.