猕猴桃EST序列的SSR信息分析

Analysis of SSR Information in EST Resources of Kiwifruit(Actinidia ssp.)

【研究目的】通过筛查猕猴桃EST数据库中的SSR重复序列,可为开发出新型的猕猴桃EST-SSR标记和分子生物学研究奠定理论基础;【方法】从NCBI公共数据库中最新公布的猕猴桃表达序列标签(Expressed Sequence Tag,EST)中随机抽取56400条序列,应用SSRHunter软件查找微卫星(Microsatellite,SSR)重复序列;【结果】研究结果表明,从猕猴桃EST序列中获得了7939条SSR,其中包括二核苷酸重复5131条(64.63%),三核苷酸重复1237条(15.58%),四核苷酸重复284条(3.58%),五核苷酸重复397条(5.00%),六核苷酸重复890条(11.21%)。在二核苷酸重复序列中,AG/CT共分布4654条(90.70%)。大约每2.48kb长度的单一基因序列中即存在1个SSR,即平均7个单一基因中存在1个SSR;【结论】在猕猴桃EST序列中,二核苷酸重复序列是最丰富的重复单元,其次为三核苷酸重复和六核苷酸重复。在所获得的SSR重复单元中,AG/CT为优势重复。

[OBJECTIVE]We screened and mined the SSR repeats in the EST database of kiwifruit （Actinidia spp.） in order to make better use of the EST-SSR resources of kiwifruit for further molecular biological studies and new EST-SSR marker development; [METHOD]56,400 EST sequences were randomly selected from EST （Expressed Sequence Tag）sequences of kiwifruit in the database of NCBI. EST sequences were analyzed and the SSR （Microsatellite）could be found out by using the SSRHunter software;[RESULTS]The resuhs showed that the 7939 SSRs were identified from the randomly selected kiwifruit EST resources. Among which there were 5131 （64.63%） dinucleotide,1237 （15.58%） trinucleotide, 284 （3.58%） tetra nucleotide, 397 （5.00%） pentanucleotide and 890 （11.21%） hexanucleotide SSRs. Among the dinucleotide sequences, AG/CT repeat motif was accounted for 4654 （90.70%）.The frequency of SSRs was approximately 1/2.48 kb, which could exist to 1 SSR in 7 unigenes; [CONCLUSION]The dinucleotide repeats appeared to be the most abundant SSRs, followed by the trinucleotide and hexanucleotide repeats. Among them the repeat motif such as AG/CT was predominant in each type of SSRs.