›› 2010, Vol. 53 ›› Issue (3): 239-247.doi:

• 研究论文 •    下一篇



  • 出版日期:2010-05-07 发布日期:2010-03-20
  • 通讯作者: 侯茂林

Analysis of microsatellite information in EST resource of Nilaparvata lugens (Homoptera: Delphacidae)

LIU Yu-Di, HOU Mao-Lin   

  • Online:2010-05-07 Published:2010-03-20

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 (Stål) 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37 398条褐飞虱ESTs序列进行EST-SSRs特征分析,得到全长为7 619 324 kb的无冗余EST 9 852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100 bp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≥100 bp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。

关键词: 褐飞虱, 生物信息学, 表达序列标签, EST-SSRs, 查找标准, 重复基元

Abstract: Expressed sequence tags (ESTs) are important resources for development of new SSR markers. In this study, 37 398 ESTs of Nilaparvata lugens (Stål) 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.

Key words: Nilaparvata lugens, bioinformatics, EST, EST-SSRs, search qualification, repeat motif