中华鳖表达序列标签资源中的微卫星信息分析

Analysis of Simple Sequence Repeats(SSR) Information in Expressed Sequence Tag(EST) Resources of Pelodiscus sinensis

从NCBI下载中华鳖表达序列标签(Expressed sequence tag,EST)序列178条及浙江省水产农业新品种选育重大科技专项课题组构建的中华鳖腐皮病肝脏cDNA文库测序得到的4 146条EST序列中,通过去除片段长度过短和冗余的序列,得到全长为1 630.26 kb的2644条无冗余EST。采用MISA软件从这些序列中搜索到197个SSR,分布于137条EST序列中,出现频率为7.45%,平均分布频率为8.28 kb。2和3碱基重复是中华鳖主要的重复类型,分别占EST-SSR总数的60.91%和35.53%。AC/GT和AGC/CTG是2、3碱基重复中的优势类型,分别占2、3碱基重复的44.17%和62.86%。结果显示,中华鳖EST数据库中SSR序列出现频率较高,类型较丰富,根据中华鳖EST数据发掘SSR标记是一条可行的途径。

A total of 4324 Pelodiscus sinensis ESTs,178 obtained from NCBI database and 4 146 from sequencing cDNA library of ulcer disease infected liver,were analyzed.And 2 644 non-reduntant ESTs with total length about 1 630.26 kb were obtained.One hundred ninty-seven EST-SSRs distributed in 137 ESTs were mined out by MISA.The frequency of these EST-SSRs was 7.45% and the mean distance of distribution was 8.28 kb in non-redundant ESTs.Dinucleotide and trinucleotide repeats were the main types in Pelodiscus sinensis,accouting for 60.91% and 35.53% of all the SSRs,respectively.AC/GT and AGC/CTG were the most frequent motifs,accounting for 44.17% and 62.86% in dinucleotide and trinucleotide repeats,respectively.The results showed that EST-SSRs and types of tandem repeats were rich in the Pelodiscus sinensis ESTs,and it was applicable to develop SSRs from its EST resources.