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SeqmanPro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≥20bp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9.28×10。bp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9.64kbEST出现1个SSR位点。二核苷酸重复基元SSR出现频率最高(43.dl%),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。
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 nonredundant 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 CTF/GAA were the main types of motif in drinu cleotide 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 abun- dant 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.