绿豆Copia类反转座子全基因组注释及进化分析  

Annotation and evolutionary analysis of the Copia retrotransposons in mung bean

作　　者：李阳 袁娜[2] 刘大亮 翟小杰 徐照龙[2] 程静 杜建厂[1,2] LI Yang;YUAN Na;LIU Da-liang;ZHAI Xiao-jie;XU Zhao-long;CHENG Jing;DU Jian-chang(College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing 210095,China;Institute of Germplasm Resoueces and Biotechnology, Jiangsu Academy of Agricultural Sciences/Jiangsu Provincial Key Laboratory of Agrobiology, Nanjing 210014, China)

机构地区：[1]南京农业大学园艺学院/作物遗传与种质创新国家重点实验室,江苏南京210095 [2]江苏省农业科学院种质资源与生物技术研究所/江苏省农业生物学重点实验室,江苏南京210014

出　　处：《江苏农业学报》2020年第4期858-867,共10页Jiangsu Journal of Agricultural Sciences

基　　金：国家自然科学基金项目(31370266);江苏省农业科技自主创新基金项目(CX17-3004)。

摘　　要：利用基于结构从头寻找和同源比对的方法,从绿豆基因组中鉴定出插入位置明确的1198个完整的Copia类反转座子和1038个solo LTR转座子元件。这些元件不均匀分布在绿豆的22条染色体上,并和功能基因的分布呈现显著的负相关关系。绝大部分Copia类反转座子(91.8%)在最近5.0 MYA内插入到寄主基因组中,并在1.0~2.0 MYA呈现1个明显的活跃峰值。此外,每个家族的solo LTR转座元件数量与完整转座元件数量的比值与进化时间无关,而与LTR的长度呈现显著的正相关关系。尽管这些Copia类反转座子可划分为Angela、Ale、Bianca、Ivana、Maximus和TAR等6个谱系,但各谱系内所包含的家族数和元件数差异较大。通过染色体上的位置比较,发现67个Copia类反转座子家族的713个元件插入到629个功能基因的内部或附近区域(<1 kb),提示这些元件可能对基因的结构、表达和功能产生一定的影响。Using structure-based and homology search approaches,1198 intact Copia retrotransposons and 1038 solo LTR retrotransposons with well-defined insertion positions were identified from the mung bean genome.These elements were unevenly distributed along 22 chromosomes of mung bean,and showed a significant negative correlation with the distribution of functional genes.The vast majority of Copia retrotransposons(91.8%)were inserted into the host genome in the last 5.0 MYA,and showed a significant active peak during 1.0-2.0 MYA.In addition,the ratio of the number of solo LTRs to the number of intact elements in each family had no correlation with the evolutionary time,but had a significant positive correlation with the size of the LTR.Although these Copia retrotransposons could be divided into six lineages,such as Angela,Ale,Bianca,Ivana,Maximus and TAR,the number of families and elements in each lineage varied greatly.By comparing the positions on the chromosomes,it was found that 713 elements of 67 Copia retrotransposon families were inserted into or close to the 629 functional genes(<1 kb),suggesting that these elements may affect the structure,expression and function of genes.

关 键 词：Copia类反转座子 插入时间 进化树 绿豆 

分 类 号：Q754[生物学—分子生物学]