栲属EST序列中微卫星含量及特征

Characteristics of microsatellites in EST sequence of Castanopsis

采用生物信息学方法对栲属Castanopsis（D.Don）Spach EST序列中微卫星DNA的含量、分布、碱基组成和频率等进行了分析。通过搜索,在3354条栲属EST序列中共查找到802个SSR位点,平均1.733 kb核苷酸序列分布一个SSR位点,其中有74.56%的SSR位点分布于长度为500～799 bp的EST序列。栲属EST-SSR的主要重复类型为二核苷酸,占SSR总数的42.39%。此外,A/T（97%）、AG/CT（80%）、AAG/CTT（30%）分别为单核苷酸、二核苷酸和三核苷酸的优势重复基元。现有栲属EST-SSR的长度分布于10-224 bp之间,重复数总平均为9.11次,其中有29.30%的EST-SSR长度大于20 bp。研究结果表明,栲属EST-SSR具有丰富的多态性,可利用栲属EST-SSR序列开发一批具有应用价值的SSR分子标记供遗传多样性研究所用。

In this study, the quantity, distribution, bases motif and frequency of EST-SSRs in Castanopsis （D. Don） Spach were analyzed using bioinformatics approaches. Using MISA analysis, a total of 802 SSRs with an average of one SSR per 1.733 kb EST sequence were identified from 3354 EST sequences and 73.69% of EST-SSRs were distributed in ESTs with the length from 500 to 799 bp. The major types of EST-SSR were dinucleotide repeats, accounting for 42.39%. The dominating motifs were A/T（accounting for 97%）in mononucleotide repeats, AG/CT （80%） in dinucleotide repeats, and AAG/CTT （30%） in trinucleotide repeats. In addition, the length of the EST-SSRs ranged from 10 to 224 bp and 29.30% of them were longer than 20 bp. The average repetition of the EST-SSRs was 9.11. The results showed that there were abundent SSRs in Castanopsis EST, and more useful microsatellites could be screened for further genetic diversity studies.