党参转录组中SSR位点信息分析.PDFVIP

·2390 · 中草药 Chinese Traditional and Herbal Drugs 第45 卷 第16 期 2014 年8 月 党参转录组中 SSR 位点信息分析 * 王 东，曹玲亚，高建平 山西医科大学药学院，山西 太原 030001 摘 要：目的 采用生物信息学方法分析党参转录组文库 EST 序列简单重复序列（SSR ）位点，快速、大规模鉴定党参功 能性 SSR。方法 使用 MicroSAtellite （MISA ）软件分析党参高通量转录组SSR 的分布频率和重复基元的类型特征，利用 软件Primer3 设计引物，并通过SSRFinder 校验SSR，筛选SSR 引物。结果 从45 511 条Unigenes 中共搜到7 327 个SSR 位点，分布在6 017 条Unigenes 序列中，发生频率为12.22%，共有415 种重复基元，平均每4 520 bp 含1 个SSR 位点，二 核苷酸重复占主要地位，发生频率为58.67%，在所有重复基元中，AG/CT 出现频率最高。共获得4 329 条SSR 引物。结论 大规模的SSR 分子标记开发将有助于党参遗传多样性与分子育种研究。 关键词：党参；转录组；SSR；MicroSAtellite 软件；引物 中图分类号：R282.12 文献标志码：A 文章编号：0253 - 2670(2014)16 - 2390 - 05 DOI: 10.7501/j.issn.0253-2670.2014.16.021 Data mining of simple sequence repeats in Codonopsispilosula transcriptome WANG Dong, CAO Ling-ya, GAO Jian-ping College of Pharmacy, Shanxi Medical University, Taiyuan 030001, China Abstract: Objective To rapidly and largely identify the functional simple sequence repeat (SSR) in transcriptome dataset of Codonopsis pilosula based on bioinformatics analysis. Methods MicroSAtellite (MISA) sofeware was used to analyze the distributing frequency of high-flux transcriptome SSR and the basic characteristics of repeat motifs. Primers were designed using Primer3, and SSRFinder was used to check SSR and screen the SSR primers. Results SSR loci (7 327) were obtained from 45 511 unigenes, distributed in 6 017 unigenes (12.22%). There are 415 kinds of repeat motifs existing in C. pilosula transcriptome. On average, SSRs occurred every 4 520 bp in length. Dinucleotid repeats predominated with an occurrence frequency of 58.67%, and AG/CT was the most frequent one among all the repeat types. A total of 4 329 primer pairs were designed for marker development. Conclusion The large number of SSR genetic markers developed in the present study should contribute greatly to res