甘薯近缘野生种三浅裂野牵牛EST资源的SSR信息分析

doi:10.3969/j.issn.1000-7091.2012.z1.006

摘要/Abstract

摘要： 利用生物信息学方法对NCBI公共数据库的1 458条三浅裂野牵牛ESTs序列进行EST-SSRs信息特征分析。结果显示，剔除低质量的和冗余的序列后，得到总长度为334.368 kb无冗余序列868条。这些无冗余序列中有35个微卫星简单重复序列(Simple sequence repeat，SSR)，分布于35条EST中，出现频率为4.03%，平均分布距离为9.55 kb。在2～6核苷酸的重复类型中，二、三核苷酸SSR之和占总EST-SSR的68.57%，其中三核苷酸SSR占总SSR数量的45.71%。在所有重复单元中，所占比例最高的是AT/AT(14.29%)，其次是TCT/AGA为11.43%，TAA/TTA为8.57%列第3位。在所有的SSR中，EST-SSRs重复次数5次的有13个，占全部SSR的37.14%，其次是重复次数为4次和7次，各有5个，占全部SSR的14.29%。结果说明，甘薯近缘野生种三浅裂野牵牛的EST-SSR出现频率较高、类型丰富、具有一定的研究利用价值。

关键词: 三浅裂野牵牛, 生物信息学, EST, SSR

Abstract: In the study， 1 458 ESTs of Ipomoea trifida in the database of NCBI were downloaded and analyzedby bioinformatics tools and method． The results showed that we got 868 non-redundant ESTs with total length about334． 368 kb after the preprocessed， some redundants and low qualities sequences were removed． Totally 35 SSRs( Simple sequence repeat) were screened and distributed in 35 ESTs， accounting for 4． 03 % of the non-redundantESTs， the average distribution distance of the EST-SSRs was about 9． 55 kb． In the different motifs ranging from 2 to6 nucleotides， except to mononucleotide， di-nucleotide and tri-nucleotide repeats were dominant repeat types and accounted for 68． 57% ， ftri-nucleotide repeats types accounted for 45． 71 % ． In addition， Among all repeat motifs ofSSRs， AT /AT was most high-frequent repeat motif and accounted for 14． 29% ， followed by TCT /AGA accounted for11 ． 43 % ， thirdly TAA /TTA accounted for 8． 57% ． Among all SSRs， SSRs which repeated overstep 5 times accounted for 37． 14% ， that of repeated 5 and 7 times accounted for 14． 29% ． The result in this paper indicated that theEST-SSR of Ipomoea trifida hadrevelance utility value in the study of sweetpotato genetic and breeding．

Key words: Ipomoea trifida, Bioinformatics, Expressed sequence tags, Simple sequence repeat

中图分类号:

S531

JIA Zhao-dong, MA Pei-yong, GUO Xiao-ding, XIE Yi-zhi. Analysis of SSR Information in ESTs Resource of Ipomoea trifida[J]. ACTA AGRICULTURAE BOREALI-SINICA, doi: 10.3969/j.issn.1000-7091.2012.z1.006.

http://www.hbnxb.net/CN/Y2012/V27/IS1/27

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