中医学报2017，Vol.32Issue(10)：1954-1958,5.DOI:10.16368/j.issn.1674-8999.2017.10.513
白花前胡转录组简单重复序列位点分析
Analysis on SSR Information in Transcriptome of Peucedani Radix
摘要
Abstract
Objective:The simple sequence repeats (SSR) information in the transcriptome data of Peucedani Radix was analyzed in this study,in order to design the SSR primers and lay the foundation for further developing new SSR markers.Methods:The SSR loci were searched in the transcriptome of Peucedani Radix (70 752 Unigenes) by using MISA (Microsatellite) software.The SSR primers were designed using Primer 3 software,and SSR primers were screened according to the primer screening standards.Results:A total 12 267 SSRs (the SSR frequency of occurrence was 17.34％) wcrc dctccted in the transcriptome of Peucedani Radix,distributed in 10 674 Unigenes.the distribution density of SSR was on average 1/3.78 kb.Single nucleotide to six nucleotide repeat types were present in the transcriptome data,the dinucleotide repeat was the main type and accounting for 61.57％ of all SSRs,followed by mononucleotide repeat (16.82％) and trinucleotide repeat (15.73％),the remaining only 0.73％,and the average distance between different repetition types is quite different.There were 93 different kinds of SSR motifs existing in Peucedani Radix transcriptome,there were 2,6,30,40,8,7 species from single to six nucleotide repeat motif,the AT/TA repeat motif,A/T repeat motif and CTT/GAA repeat motif were the most frequent motifs accounting for 38.21％,16.59％ and 1.14％ respectively of the total SSRs,the rest of the nucleotide repeat motif were more,but the number was less.A total of 10 254 primer pairs were successfully designed and 841 primer pairs were selected according to the standard of SSR sequence length greater than 20 bp.Conclusion:The SSR loci in Peucedani Radix transcriptome showed high frequency of occurrence and diverse types of repeat.Especially in the single,two,three nucleotide repeat SSR in the polymorphism potential has a high value,can be targeted for primer design and application.关键词
白花前胡/简单重复序列信息分析/中药Key words
Peucedani Radix/simple sequence repea analysis/Chinese medicine分类
医药卫生引用本文复制引用
时博,赵乐,霍常青..白花前胡转录组简单重复序列位点分析[J].中医学报,2017,32(10):1954-1958,5.基金项目
2013年度国家级大学生创新创业训练计划项目(201310471027) （201310471027）
