摘要
表达序列标签(expressed sequence tags,ESTs)是开发微卫星标记的一个重要的资源。褐飞虱Nilaparvata lugens(Sta°l)EST序列的公布为开发EST-SSRs提供了宝贵的数据资源,本研究利用生物信息学对NCBI公共数据库中的37398条褐飞虱ESTs序列进行EST-SSRs特征分析,得到全长为7619.324kb的无冗余EST9852条。按照3个不同的查找标准在这些序列中搜索SSR。查找结果显示:褐飞虱EST-SSRs主要重复基元以1～3碱基为主,占总EST-SSR的95%以上。在单碱基重复基元中,A/T是占优势的重复基元,在二相重复类型中,AG/CT重复基元出现的频率最多,而AAG/CTT是三相重复中占绝对优势的重复基元。在褐飞虱EST-SSRs中未查找到GC重复基元。以100bp为参照,在3种查找标准下含有SSR的EST序列中两端侧翼序列均≥100bp的序列分别为738,89和42个。通过分析褐飞虱EST-SSRs标记可以为褐飞虱和近缘种的SSR标记的开发提供信息,同时通过分析褐飞虱EST-SSRs的分布频率和分布特征可以为昆虫EST-SSRs的研究提供借鉴和参考。
Expressed sequence tags （ESTs） are important resources for development of new SSR markers.In this study,37 398 ESTs of Nilaparvata lugens （St。l） were downloaded from NCBI and analyzed.After the pre-procession,9 852 non-redundant ESTs with the total length about 7 619.324 kb were obtained.The EST-SSRs were detected under three search qualifications.The search results indicated that the 1-3 repeat motifs were the major repeats among all the SSRs,which accounted for above 95% of all EST-SSRs.A/T was the most frequent motif in the mononucleotide.AG/CT and AAG/CTT were the major motifs in the dinucleotide and trinucleotide,respectively.The GC repeat motif was not found in the EST-SSRs of N.lugens.When 100 bp was used as the comparison,the numbers of sequences with both flanking regions ≥100 bp under three search qualifications were 738,89,and 42,respectively.The analysis of EST-SSRs markers can provide the information for the SSR development of N.lugens and related species.Furthermore,the analysis of the distribution frequency and character of N.lugens EST-SSRs can provide help for the EST-SSRs study of insects.
出处
《昆虫学报》
CAS
CSCD
北大核心
2010年第3期239-247,共9页
Acta Entomologica Sinica
基金
广东省野生动物保护与利用公共实验室基金资助项目(2008-003)
国家自然科学基金项目(30700537)
