一个毛竹典型LTR转座子的克隆、鉴定及进化分析

Cloning,Characterization and Phylogenetic Analysis of a Typical Long Terminal Repeat Retrotransposon in Phyllostachys heterocycla cv. pubescens

LTR反转录转座子普遍存在于植物界中。为了进一步了解LTR反转录转座子及探索毛竹中存在的可能具有潜在活性的LTR反转录转座子,研究借助毛竹基因组草图数据库,通过LTR-structure软件分析得到一个典型LTR反转录转座子Ph-LTR1,并对其进行鉴定及插入时间的估算,结果表明PhLTR1属于Ty3-gypsy类反转录转座子,其两端长末端重复序列同源性高达98.78%,插入时间约为47.9万年,是一个自身具备转座条件的年轻反转录转座子,并且极有可能具有潜在活性。采用同源性搜索方法搜索到52条Ph-LTR1家族元件,并对这些元件结构及其所在基因组的位置进行分析,结果表明PhLTR1家族元件中存在大量缺失的元件,且Ph-LTR1家族元件偏向分布于远离基因的区域。研究结果为后续具有潜在活性的LTR反转录转座子转化拟南芥实验奠定了基础,Ph-LTR1家族元件结构及进化分析促进了对于LTR反转录转座子在基因组进化角色的认识与理解。

LTR Retro-transposons were widely distributed in plant.In order to further understand LTR Retro-transposons and explore LTR retro-transposons with potential activity in Phyllostachys heterocycla cv.pubescens,a typical long terminal repeat retro-transposon named Ph-LTR1 from Phyllostachys heterocycla draft genome database has been identified by using LTR-structure software.Structure analysis showed that Ph-LTR1 belonged to Ty3-gypsy retrotransposon.The homology of the long terminal repeat of PhLTR amounted to 98.78％ and its insertion time was 0.479 million years.Ph-LTR1 was a young and potentially active transposon which had all indispensable component for transposition.Based on these results,52 Ph-LTR1 family elements in the genome database were extracted using blast method,then structure and location of 52 Ph-LTR1 family elements were analyzed.Most of the 52 elements were the deletion sequences of Ph-LTR1.The elements in Ph-LTR1 family were prone to distribute in the distal region of gene.This may provide a basis for further investigation of transposition activities of Ph-LTR1 and better understanding the role of LTR Retro-transposons on the evolution of Moso bamboo genome.