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目的为了在裂叶牵牛中开发功能性EST-SSR分子标记,分析裂叶牵牛EST-SSRs特征。方法从NCBI公共数据库中下载裂叶牵牛EST序列,运用DNAstar软件中的Seqman Pro程序,对下载序列进行拼接和聚类,去除冗余序列,利用SSRIT软件筛选重复序列长度≥20 bp的二、三、四、五、六、七、八核苷酸7种类型的SSR,统计分析裂叶牵牛EST-SSRs的特征。结果从NCBI公共数据库中下载62 388条裂叶牵牛EST序列,剔除冗余序列,得到全长为8.35×106 bp的无冗余EST序列11 569条。在这些序列中搜索出985条EST序列含有1 132个SSRs,占无冗余EST序列的9.78%,平均每7.37 kb EST出现1个SSR位点。二核苷酸重复基元SSR出现频率最高(51.06%),其次是三核苷酸(33.57%),AG/TC、GA/CT和AAG/TTC是二、三核苷酸中的优势重复基元。裂叶牵牛EST-SSRs以4～10次重复为主,基序长度主要集中于20～30 bp。结论裂叶牵牛EST-SSR的出现频率高,重复类型丰富,理论上表明这些EST-SSRs具有较高的可用性。本实验通过对裂叶牵牛EST资源的SSR信息的研究,为分子水平和生物信息学角度上开发裂叶牵牛的SSR功能性标记提供了候选序列。
Objective To develop functional EST-SSR molecular markers in Crassostrea burgdorferi. METHODS: The EST sequences of Cunninghamia lanceolata were downloaded from the NCBI public database, the downloaded sequence was spliced and clustered by using the Seqman Pro program in DNAstar software to remove redundant sequences. SSRIT software was used to screen the sequences with length of 20 bp or more. Three, four, five, six, seven, eight nucleotides seven types of SSR, statistical analysis of the characteristics of EST-SSRs. Results A total of 62 388 EST sequences were isolated from the NCBI public database and the redundant sequences were deleted. A total of 11 569 non-redundant EST sequences with a total length of 8.35 × 106 bp were obtained. Among these sequences, 985 ESTs were found to contain 1 132 SSRs, accounting for 9.78% of the non-redundant EST sequences, with an average of 1 SSR loci per 7.37 kb EST. The SSR frequency of dinucleotide repeats was highest (51.06%), followed by trinucleotide (33.57%). AG / TC, GA / CT and AAG / TTC were the dominant repeat bases yuan. The EST-SSRs of Fagus morningifolia were mainly repeated 4 to 10 times with the length of motifs mainly ranging from 20 to 30 bp. Conclusions EST-SSR of Crassostrea burgdorferi has high frequency of occurrence and abundance of repetitive types, and theoretically shows that EST-SSRs have high usability. In this study, we studied the SSR information of EST in Crassostrea annua, and provided a candidate sequence for the development of SSR functional markers in Crataegus plantain from the perspective of molecular biology and bioinformatics.