花生EST资源的SSR信息分析

Analysis of SSR Information in EST Resource of Peanut

微卫星或简单重复序列(simple sequence repeats,SSR)存在于表达序列标签(expressedsequence tags,ESTs)中。为了在花生中开发EST-SSR功能性标记,利用生物信息学对NCBI公共数据库中的41501条花生ESTs序列进行EST-SSRs特征分析。剔除冗余序列,得到全长为5125.94kb的无冗余EST8391条。在这些序列中搜索出1109个SSR,分布于946条EST中,出现频率是11.27%。这些EST-SSR的平均长度为18.16bp,平均分布频率1/4.62kb。在1～6bp的重复基元中,三核苷酸重复基元的SSRs出现频率最高(49.23%),其次是二核苷酸(32.83%)、单核苷酸(14.88%)。AG/CT和AAG/CTT是二、三核苷酸中的优势重复基元,分别占二、三核苷酸重复的71.43%和31.50%。本研究为开发多态性花生微卫星标记提供了候选序列。

41501 ESTs of peanut in the database of NCBI were downloaded and analyzed. After the preprocession, we got 8391 non-redundant ESTs with total length about 5125.94 kb. Totally 1109 SSRs distributed in 946 ESTs were detected, accounting for 11.27% of the non-redundant ESTs. The average length and distribution distance of the EST-SSRs were about 18.16 bp and 4.62 kb, respectively. Dinucleotide and trinucleotide are the main types repeats with similar frequency, accounting for 82.06% of all the SSRs. AG/CT and AAG/CTT are the most frequent motifs, accounting for 71.43% and 31. 50% in the dinucleotide and trinucleotide repeats, respectively. These EST-SSRs will help to develop SSR markers with high polymorphism for peanut.