乌拉尔甘草EST资源的SSR信息分析

目的:为了在乌拉尔甘草中开发功能性EST-SSR分子标记,分析乌拉尔甘草EST-SSRs特征。方法:从NCBI公共数据库中下载乌拉尔甘草EST序列,运用DNAstar软件中的Seqman Pro程序,对下载序列进行拼接和聚类,去除冗余序列,利用SSRIT软件筛选重复序列长度≥20 bp的二、三、四、五核苷酸4种类型的SSR,统计分析乌拉尔甘草EST-SSR的特征。结果:从NCBI公共数据库中下载50666条乌拉尔甘草EST序列,剔除冗余序列,得到全长为9.28×106bp的无冗余EST序列11100条。在这些序列中搜索出752条EST序列含有963个SSR,占无冗余EST序列的8.68%,平均每9.64 kb EST出现1个SSR位点。二核苷酸重复基元SSR出现频率最高(43.41%),其次是三核苷酸(41.95%),AG/TC、GA/CT和CTT/GAA是二、三核苷酸中的优势重复基元。乌拉尔甘草EST-SSR以4～10次重复为主,基序长度主要集中于20～30bp。结论:乌拉尔甘草EST-SSR的出现频率高,重复类型丰富,理论上表明这些EST-SSR具有较高的可用性。本文通过对乌拉尔甘草EST资源的SSR信息的研究,为分子水平和生物信息学角度上开发乌拉尔甘草的SSR功能性标记提供了候选序列。

Analysis of SSR Information in EST Resource of Glycyrrhiza Uralensis

Objective:This study investigated EST-SSRs feature in EST resource of Glycyrrhiza uralensis which is a kind of Chinese medicine and wildly used in clinical practice.Methods:EST database of Glycyrrhiza uralensis downloaded from NCBI website was analyzed by DNAstar to get rid of redundant EST sequences.SSRIT software was employed in screening SSRs in these non-redundant EST sequences.The characters of Glycyrrhiza uralensis EST-SSR were analyzed by statistical methood.Results:A total of 50,666 ESTs of Glycyrrhiza uralensis were downloaded from the database of NCBI.After the preprocession,11,100 non-redundant EST sequences that totaled 9.28×106 bp length were obtained.963 SSRs were distributed in 752 EST sequences,which accounted for 8.68% of the 11,100 non-redundant ESTs.The average density of SSR was 1 SSR/9.64 kb EST sequence.In the SSRs,the di-nucleotide repeat motif was the most abundant(43.41%),followed by tri-nucleotide(41.95%).AG/TC、GA/CT and CTT/GAA were the main types of motif in di-,tri-nucleotide repeats.The repeat number of Glycyrrhiza uralensis EST-SSR was mainly 4~10 and motif length of them mostly ranged from 20 bp to 30 bp.Conclusion:The EST-SSRs are abundant in Glycyrrhiza uralensis and highly feasible in theory.This research might lay the foundation for designing the targeted EST-SSR primers and developing EST-SSR molecular markers by mining the information of EST-SSR loci in Glycyrrhiza uralensis EST sequences data.