论文部分内容阅读
微卫星或简单重复序列(simplesequencerepeats,SSR)存在于表达序列标签(expressedsequencetags,ESTs)中.为了在棉花中开发EST-SSR功能性标记,利用生物信息学方法对NCBI网上公开的63485条雷蒙德氏棉(GossypiumraimondiiUlbrich)ESTs序列进行EST-SSRs特征分析.剔除冗余序列,得到非冗余序列58906条.在非冗余序列中发现含不同重复基元SSRs的EST序列有2620条,共2818个EST-SSRs,EST-SSRs序列的频率是4.45%,平均相隔14.8kb出现一个SSR.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(38.31%),其次是二核苷酸(24.09%)、单核苷酸(23.35%).对所有的重复基元类型进行统计分析发现,所占比例最大的是A/T(18.67%),其次是AT/TA(14.83%).在复合型(compound)中发现三核苷酸串联三核苷酸的重复基元出现频率最高,为48.65%.利用Prime3软件,设计了1554对EST-SSRs引物,随机选用300对对本室四倍体作图亲本陆地棉TM-1和海岛棉海7124进行多态性检测,其中129对有多态性,多态性频率为43%.这些EST-SSRs将有效用于不同棉种间的分布特征比较及染色体定位等方面研究.
Microsatellite or simple sequence repeats (SSR) are found in expressed sequences tags (ESTs) .In order to develop EST-SSR functional markers in cotton, bioinformatics methods were used to analyze 63485 Raymond The EST-SSRs of Gossypium raimondii Ulbrich ESTs were analyzed in detail, and 58906 non-redundant sequences were deleted.A total of 2620 EST sequences were found in non-redundant SSRs with 2818 The frequency of EST-SSRs and EST-SSRs sequences was 4.45%, with an average of 14.8kb.Among the 1 ~ 6bp repeat motifs, the trinucleotide repeat motifs had the highest frequency of SSRs (38.31%), followed by (24.09%) and single nucleotide (23.35%) .According to statistical analysis of all the repeat types, A / T (18.67%) was the largest proportion, followed by AT / TA (14.83%) .There were 48.55% repetitive motifs of trinucleotide tandem trinucleotide found in compound, 1554 pairs of EST-SSR primers were designed by using Prime3 software and 300 On the tetraploid mapping of the parent cotton land TM-1 and island cotton sea into the 7124 The polymorphism detection, 129 were polymorphic, the polymorphism frequency of 43%. These EST-SSRs useful in the study of the distribution and chromosomal localization, etc. Comparison between different species..