大豆HGm1 helitron转座元件的鉴定与生物信息学分析

Identification and bioinformatics analysis of HGm1 helitrons in Glycine max

[目的]helitron转座元件是近年来发现的一种结构新颖和转座方式独特的DNA转座子。我们从全基因组水平上对大豆基因组中拷贝数最多的helitron HGm1家族进行深入分析,旨在为后续进一步明确helitron转座元件在大豆及其近缘种基因和基因组演化中所起的作用提供帮助。[方法]利用基因组学和生物信息学的研究手段,我们对大豆HGm1家族的数量、结构特征、染色体分布、插入基因情况,基因片段的捕获及表达模式等进行了详细的研究。[结果]从公开发表的大豆基因组序列中共鉴定出254个HGm1转座元件。这些元件的3'末端十分保守,主要由GC含量较高的碱基组成。HGm1元件主要分布在AT丰富的区域,并在重组受到显著抑制的异染色质区域富集。研究还发现,68个元件被83个外源的转座元件插入;64个元件插入到编码蛋白的基因附近(<2 kb);115个元件携带154个完整的外源基因;52个元件有潜在的转录活性,在根、茎、叶、花和种子中,以及干旱胁迫和组织培养条件都有所表达。[结论]与玉米中有关helitron的研究结果相似,HGm1家族在大豆基因组中经常以巢式的结构存在,具有频繁插入到基因附近和捕获基因的现象,并且部分成员具有潜在的转录活性。而与玉米helitron不同的是,大豆HGm1 helitron家族主要分布在基因贫乏的异染色质区域。因此,HGm1家族在改变大豆基因结构和调节基因表达以及影响大豆基因组的演化过程中具有较为重要的作用。

[Objectives] As a new type of DNA transposons,helitrons have new structure and unique transpositional mechanism. In this study,we have comprehensively analyzed the HGm1 family with the most highest copies in the whole soybean genome,and hope that these efforts will facilitate our further understanding regarding the role of helitrons in the gene and genome evolution of soybean and its relatives.[Methods] We have investigated the copy numbers,structural characteristics,chromosomes distribution,relationship with genes,captured gene fragments,and expression patterns of HGm1 family through genomic and bioinformatic approaches.[Results] A total of 254 HGm1 elements had been identified. These elements had very conserved 3’terminator with high GC contents. The identified HGm1 elements were mainly found in the AT-rich regions and were usually enriched in the heterochromatin regions,where the recombination rates were usually highly suppressed. The data also showed that 68 HGm1 elements were inserted by 83 external transposons;64 elements inserted into the regions close to the encoding genes （〈2 kb）;115 elements had carried 154 intact host genes;52 elements had potential transcript activities,because they could express in the tissues of root,stem,leaf,flower,and seed,and also express in the conditions of drought stress,and tissue culture.[Conclusions] Similar to maize helitrons,the soybean helitrons are usually present in nested patterns,frequently capturing gene or gene fragments,and some copies have potential transcriptional activities. Different from helitrons in maize,however,the soybean helitrons are usually found in gene-poored regions. Therefore,the HGm1 helitrons play an important role in altering gene structure,regulating gene expression,and affecting genome evolution history in the soybean genome.