马蹄香表达序列标签资源的SSR信息分析

Data mining for simple sequence repeats in expressed sequence tags from Saruma henryi

目的分析马蹄香EST资源的SSR信息,为开发EST-SSR标记奠定基础。方法从GenBank中获得马蹄香EST序列,用Sequencher4.8软件进行序列拼接得到Uni-EST序列,用SciRoKo3.4软件对Uni-EST序列进行SSR扫描,分析EST-SSR的分布频率和重复基元的类型特征。结果共获得10274条马蹄香EST序列,通过预处理共得到全长为5.11×106bp的无冗余Uni-EST6643条。在这些序列中共搜索出1408个SSR位点,分布在1232条Uni-EST序列中,发生频率为18.55%,EST-SSR的平均长度为22.30bp,平均每3.63kb含1个SSR位点。单核苷酸重复在马蹄香EST-SSR中占主导地位,发生频率为12.24%,其次为二核苷酸重复,发生频率为5.01%。在所有重复基元中,A/T基元出现频率最高,其次为AG/CT。结论马蹄香EST中SSR出现的频率较高,并且类型较为丰富。

Objective To analyze the simple sequence repeat （SSR） information in expressed sequence tag （EST） resource of Saruma henryi and lay a solid foundation for the development of EST-SSR markers in this species. Methods ESTs of S. henryi were downloaded from GenBank and used to perform the conrig assembly using Sequencher 4.8. Uni-ESTs were obtained and screened for SSR-containing unigenes using SciRoKo 3.4. The distributing frequency of the EST-SSRs and the basic characteristics of motifs were analyzed. Results A total of 10 274 ESTs of S. henryi were retrieved and were assembled into 6 643 nonredundant Uni-ESTs with a total length of 5.11× 10^6 bp. In all, the data mining yielded 1 408 SSR loci, which corresponded to 1 232 Uni-ESTs （18.55%）. On average, EST-SSRs spanned 22.30 bp, and occurred every 3.63 kb in length. In S. henryi, mononucleotide repeats predominated with an occurrence frequency of 12.24%. Dinucleotide repeats followed with a frequency of 5.01%. The most frequent one was A/T among all the repeat motifs, then followed by AG/CT. Conclusion SSRs in ESTs of S. henryi display a relatively high level of occurrence frequency and show abundance of types.