苹果EST中微卫星分析

Analysis of microsatellites derived from apple ESTs

利用MISA(microsatellite)软件分析了简单重复序列(simple sequence repeats,SSRs)在苹果EST中的分布频率与密度。结果表明,在263 820条EST序列中,共获得160 686条SSR序列,SSRs之间的距离约为0.79 kb。其中,六碱基重复丰度最大,占57.2%,而单碱基、三碱基、二碱基、四碱基和五碱基重复丰度分别为14.5%,13.1%,10.1%,4.1%和1.0%。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在编码区内丰度很低。用CAP3软件进行冗余分析表明,在这六种类型的重复模体中,冗余与非冗余的苹果EST之间没有显著差异,表明可从现有的ESTs数据中方便地获取有效的苹果微卫星标记。

database were were found in Among them, Simple sequence repeats （SSRs） of apple expressed sequence tags （EST） in public investigated by using computer program MISA （mierosatellite）. Up to 160 686 SSRs 263 820 sequences and the average distance between SSRs was approximately 0.79 kb. hexanucleotide repeats （57. 2 %） were the most abundance, while the monomerie, trimeric, dimeric, tetramerie and pentameric repeats were represented in decreasing proportions of 14.5 %, 13.1%, 10. 1 %, 4. 1% and 1.0 %, respectively. The most abundant motifs were A/T, AG, AAG and AAAG in monomeric, dimerie, trimeric and tetrameric repeats, respectively. Whereas CG rich repeats were rarely found in the coding regions. The redundancy analysis indicated that no significant differences were observed between the redundant and non-redundant set of apple ESTs in individual SSR motifs. Furthermore, the availability of microsatellite markers can be expected to enhance the power and resolution of genome analysis in apple.