基于转录组数据的印度谷螟微卫星位点分析

Analysis of microsatellite loci in Plodia interpunctella based on transcriptome dataset

基于印度谷螟转录组测序数据筛选其功能微卫星(EST-SSR)分子标记,设计该虫的微卫星(SSR)引物并验证其适用性。用MicroSAtellite微卫星搜索软件查找印度谷螟转录组中微卫星的数量、重复次数以及所有微卫星的位置信息,采用Primer Premier 5软件设计SSR引物,并进行PCR验证。结果表明含EST-SSR的序列3 173个,占总搜索序列的8.52%,平均每13kb中就出现1个EST-SSR。共发现192种微卫星类型,其中重复单元为单碱基、二碱基和三碱基的比例较高,依次是28.21%、39.84%、25.43%。除单碱基重复单元外,出现频率最高的是AT/AT,有593次。在66对印度谷螟EST-SSR引物中,有28对PCR扩增成功。这说明基于印度谷螟转录组数据开发微卫星标记是可行的,本研究获得的印度谷螟EST-SSR位点为今后开展该虫的种群遗传学研究提供了基础数据。

This study is aimed to identify gene microsatellite（EST-SSR）loci from the transcriptome database of Plodia interpunctella.Based on these SSR sequences,the selected SSR primer pairs were validated.The number,repetition time and location information of all microsatellites obtained with the microsatellite search tool MicroSAtellite were analyzed.Primer Premier 5 was used to design P.interpunctella SSR primers,and then these primer pairs were verified by PCR.A total of 3 173 SSRs were identified in 37 246 Unigenes,with one SSR per 13 kb.The majority of microsatellite loci consisted of mono-,di-and tri-nucleotide motifs（28.21%,39.84% and 25.43%,respectively）.However,different types of repeat SSRs had considerably different distribution.Except mono-nucleotide,AT/AT was the most frequent repeat motif（593 repeats）among all SSR motifs.Among the 66 designed primer pairs,28 pairs were amplified successfully.Our study shows that it is feasible to develop microsatellite markers based on P.interpunctella transcriptome.The EST-SSRs of P.interpunctella obtained in this study are helpful for population genetics studies of this important stored-product pest.