应用石斛EST序列对SNP位点开发与分析

Development and Analysis of Dendrobium SNP Based on EST Sequence

利用生物信息学手段,从NCBI中db EST数据库获取大量的石斛属(Dendrobium Sw.)EST序列,对SNP与EST的数量及拼接结果之间的关系、SNP碱基置换的偏好性进行了分析。采用DNASTAR软件中的SeqMan程序对获取的16 183条石斛EST序列构建叠连群,得出2 267个叠连群,长度计628 444 bp,发现342个叠连群共含有1 083个候选SNP位点。经统计分析SNP位点平均出现频率为0.17%,平均580.28个bp含有1个SNP位点,每个叠连群含有3.25个SNP位点。不同叠连群SNP位点个数差异较大,其中含SNP位点最多的叠连群共有22个SNP位点。突变中转换和颠换类型差异较大,数量分别为655和408,插入缺失为20个,分别占SNP位点总数的60.5%、37.7%、1.8%。通过对SNP位点所在核酸序列的同源比对分析发现共有1 021个SNP位点所在的核酸序列与同属植物铁皮石斛(D.candidum)的302个基因同源,且同源性基本都在89%以上。

In order to develop Dendrobium SNPs,related traits and variety identification of Dendrobium,16 183 Dendrobium EST sequences published in db EST database of NCBI were downloaded and assembled into contigs by Seq Man program of DNASTAR software. The results showed that,2 267 contigs were constructed by 16 183 EST sequence,and 342 of which contained SNP sites. The total length was 628 444 bp with 1 083 SNP sites. By statistical analysis,the average frequency of SNP sites was 0.17%. The average 580.28 BP contained 1 SNP site and each contig contained 3.25 SNP sites on average. Different contigs contained diferent SNP sites,and the largest number of SNP sites in all cotings was 22. The difference between transformation type and transversion type in mutation was great. The number of transformation,transversion and indel were655,408 and 20,respectively,which accounted for 60.5%,37.7% and 1.8% of the SNP total number. By sequence homology analysis,1 021 SNP sites were derived from 302 Dendrobium candidum genes,and the homology was all above 89%.