刺叶苏铁EST序列中SSR信息分析

Analysis of SSR Information in EST Resource of Cycas rumphii Miq.

基于NCBI数据库中刺叶苏铁的21 997条EST序列,统计分析了其EST-SSR的组成与分布特点。经过剔除冗余和低质量序列后,得到长度为7 926 783 bp的无冗余EST序列13 640条。在这些序列中共搜索出了875条EST序列含有1 176个SSR,出现频率为8.6%。这些SSR的主要重复基序有A/T,C/G,AC/GT,AG/CT,AT/AT,CG/CG,AAC/GTT,AAG/CTT,AAT/ATT,ACC/GGT,ACG/CGT,AGC/CTG,AGG/CCT,ATC/ATG,AAAT/ATTT,AAGG/CCTT,AATT/AATT,ACAT/ATGT和AAACCC/GGGTTT。一、二、三核苷酸重复类型是主体,三者共占总数的99.1%。A/T、AT/AT、AG/CT、AAG/CTT和AAT/ATT分别是其优势重复基元,分别占总数的41.7%、11.5%、11.9%、2.6%和2.5%。该研究为刺叶苏铁EST-SSR标记的开发与应用奠定了基础。

This study analyzed the distribution pattern and compared the characters of EST-SSR,which were derived from a total of 21 997 ESTs of Cycas rumphii Miq.downloaded from the NCBI database.After removing redundant and poor quality sequences,13 640 non-redundant ESTs with 7 926 783 bp length were obtained,and 875 EST sequences,which accounted for 8.6% the total number of non-redundant ESTs,were detected to contain 1 176 SSRs.In these SSRs,the major repeat motifs included A/T,C/G,AC/GT,AG/CT,AT/AT,CG/CG,AAC/GTT,AAG/CTT,AAT/ATT,ACC/GGT,ACG/CGT,AGC/CTG,AGG/CCT,ATC/ATG,AAAT/ATTT,AAGG/CCTT,AATT/AATT,ACAT/ATGT and AAACCC/GGGTTT,and the major repeat types were mononucleotide,dinucleotide and trinucleotide,which were accounted for 99.1% of the total number of acquired SSRs.Among these repeats,A/T、AT/AT、AG/CT、AAG/CTT and AAT/ATT were the most frequent motifs,accounting for 41.7%,11.5%,11.9%,2.6% and 2.5%,respectively.The present study laid the foundation for the development and further use of EST-SSR markers in Cycas rumphii Miq..