摘要
表达序列标签(Expressed sequence tags,EST)中存在广泛的微卫星或简单重复序列(Simple sequence re-peats,SSR),为SSR标记的开发提供了宝贵的资源。以NCBI中与番茄(Solanum lycopersicum)果实性状相关EST序列为材料,对EST序列进行聚类去冗余、拼接等前期处理后,再进行EST-SSR搜寻及分析。结果表明:NCBI中与番茄果实性状相关的83 613条EST序列经CAP3拼接后获得18 878个UniGene,其中9 650个Contigs,9 228个Singlets。对UniGene利用MISA软件进行SSR位点搜寻,获得2 039条含有EST-SSR的序列,拼接后的UniGene的检出率为12.62%,包括97种重复基元。其中单核苷酸、二核苷酸、三核苷酸重复占主导地位,三者占总SSR位点数的98.91%。SSR在番茄果实EST上的分布密度为每5 451.6 mer出现1个SSR。
Expressed sequence tags（ESTs）are important resources for development of new SSR markers.83 613 ESTs of the tomato fruit in the database of NCBl were downloaded and early treatmented,such as being clusterd to redundancy and spliced,and so on.It is concluted that there were 18 878 UniGene after being spliced by CAP3 tool,in which of 9 650 Contigs and 9 228 Singlets.2 039 EST-SSRs were gotten by using MISA tool searched SSR,accounting for 12.62% of the UniGene and including 97 repeat motifs.Mononucleotide,Dinucleotide and Trinuclotide were the dominant repeat motifs and occupied 98.91% in all the number of SSR.Every 5 451.6 mer appeared a SSR in the ESTs of the tomato fruit of containing SSR.
出处
《华北农学报》
CSCD
北大核心
2011年第4期213-217,共5页
Acta Agriculturae Boreali-Sinica
基金
岗位专家课题资助项目:国家现代农业产业体系建设专项(Nycytx-35-gw23)
国家“863”计划项目(2006AA100108-3-1)
辽宁省教育厅科学技术研究项目(2008623)
沈阳农业大学博士后基金项目(62658)
