菊花EST-SNP的发掘与特征分析

Detection and Characteristic Analysis EST-SNP in Chrysanthemum

下载GenBank数据库中已公布的菊花EST序列7 087条,利用GS De nove Assembler软件进行叠连群构建,EST序列构建275个叠连群,长度共计142 713 bp,发现候选SNP位点214个,SNP平均出现频率为0.15%,共有52个contigs含有SNP位点,每个contig含有4.12个SNP位点,一个contig含有的SNP位点数最多的是40个,40.39%的contigs只含有1个SNP位点;不同叠连群所含SNP位点的数量差异较大,且转换类型明显高于颠换类型;Contigs的总长度是142 713 bp,平均666.9 bp含有1个SNP位点。另外,还应用Primer Premier5.0,按照引物设计要求,共设计出1 322对EST-SNP引物。

7 087 EST sequences of Chrysanthemum published in GenBank databases were downioaded as materials. The contigs by GS De nove Assembler software forstack were constructed, 275 contigs by EST sequences was constructed, the total length was 142 713 bp with 214 andidate SNP bit points, and the average appear frequency of SNP was 0.15%. The total number of contigs containing SNP bit points was 52, and each contig contained 4.12 SNP loci on average. The number of SNP was up to 40 in a contig, the percent of contigs containing only one SNP loci was 40.39%. Different contigs con- tained a different number of SNP, and the conversion type was significantly higher than the transversion type of mutation type and quantity. The total length of the contigs was 142 713 bp, 666.9 bp containing one SNP loci on average. 1 322 pairs of EST-SNP primers were designed by Primer Premier 5.0 following the basic search criteria.