摘要
[Objective]The aim was to obtain effective microsatellite markers from the public strawberry ESTs data.[Method]The distribution frequency and density of simple sequence repeats（SSRs） in strawberry EST was analyzed by MISA（Microsatellite） software,and the redundancy was analyzed with CAP3 software.[Result]A total of 10 129 SSR sequence was received in 17 565 of EST sequences,and the distance among SSRs was about 0.90 kb,in which the Hexanucleotide repeats gained the greatest abundance,which was accounted for 61.0%,while the Trimeric,Monomeric,Dimeric,Tetrameric and Pentameric repeats accounted for 14.3%,13.1%,6.2%,4.3% and 1.1% respectively.The most abundant motif was A/T,AG,AAG and AAAG in the Monomeric,Dimeric,Trimeric and Tetrameric repeat motifs,while the CG was not found in the coding region.In these six types of repeat motifs,there was no significant difference between redundant and non redundant ESTs.[Conclusion]The availability of microsatellite markers could be expected to be achieved in the public strawberry database.
[目的]从现有的草莓ESTs数据中获取有效的微卫星标记。[方法]利用MISA(Microsatellite)软件分析简单重复序列(simple sequence repeats,SSRs)在草莓EST中的分布频率与密度,用CAP3软件进行冗余分析。[结果]在17565条EST序列中,共获得10129条SSR序列,SSRs之间的距离约为0.90kb。其中,六碱基重复丰度最大,占61.0%,而三碱基、单碱基、二碱基、四碱基和五碱基重复丰度分别为14.3%,13.1%,6.2%,4.3%和1.1%。在单碱基、二碱基、三碱基和四碱基重复模体中,丰度最大的分别是A/T,AG,AAG和AAAG,而CG在编码区内没有。在这6种类型的重复模体中,冗余与非冗余的草莓EST之间没有显著差异。[结论]从现有的草莓ESTs数据中可以方便地获取有效的微卫星标记。
基金
Supported by the National Natural Science Foundation of China(30370743)
Foundation of Jiangxi Normal University (2441,2732)~~
