藏茵陈川西獐牙菜转录组SSR信息分析  

Data mining of simple sequence repeats in transcriptome sequences of Tibetan medicinal plant Zangyinchen Swertia mussotii

作　　者：刘越[1,2] 岳春江 王翊[3] 马加强[1] 孙洪波[1] 罗敏[1] 马鹏举[1] 张琳霞[1] 马徐 陈川川[1] 李华[1] 唐丽[1] 

机构地区：[1]中央民族大学生命与环境科学学院,北京100081 [2]中国中医科学院中药资源研究中心道地药材国家重点实验室培育基地,北京100700 [3]美国加州大学戴维斯分校植物科学系,加利福尼亚州95616

出　　处：《中国中药杂志》2015年第11期2068-2076,共9页China Journal of Chinese Materia Medica

基　　金：国家自然科学基金项目(30801554;81274185;81373765);教育部新世纪优秀人才支持计划项目(NCET-12-0578;NCET-13-0624);2013年度人社部留学人员科技活动项目;中国博士后科研基金项目(20110490556);高等学校学科创新引智计划项目(2008-B08044);中央民族大学一流大学一流学科建设项目(YLDX01013);北京市大学生创新项目(BEIJ2014110008)

摘　　要：利用MISA（Micro SAtelite）软件对藏茵陈川西獐牙菜转录组序列68 787条跨叠群（contigs）进行简单重复序列（SSR）位点的挖掘,发现5 099条序列中含有5 610个SSR位点,发生频率为7.41%,共有220种重复基元,平均每12.60 kb出现1个SSR位点。三核苷酸重复基元SSR出现频率最高（45.99%）,其次是二核苷酸（41.62%）。AT/TA和AAT/TTA是二、三核苷酸中的优势重复基元。藏茵陈川西獐牙菜转录组SSR以5-10次重复为主,基序长度主要集中于12-30 bp。在藏茵陈川西獐牙菜转录组中注释的30 651个contigs中,有1447个SSRs位于编码区,主要以三核苷酸重复为主（928,64.13%）。藏茵陈川西獐牙菜转录组SSR的出现频率高,重复类型丰富,理论表明这些转录组SSR具有较高的可用性。该文通过对藏茵陈川西獐牙菜转录组资源的SSR信息的研究,为分子水平和生物信息学角度上开发藏茵陈川西獐牙菜的SSR功能性标记提供了丰富的候选序列。MISA （MicroSAtelite） software was employed to screen SSRs in 68 787 contigs of Swertia mussotii transcriptome sequences. 5 610 SSRs were distributed in 5 099 contigs which accounted for 7.41% of 68 787 contigs. There are 220 kinds of SSR motifs existing in S. mussotii transcriptome. On average, SSRs occurred every 12.60 kb in length. In the SSRs, the tri-nucleotide repeat motif was the most abundant （45.99%）, followed by the di-nucleotide （41.62%）. AT/TA and AAT/TTA were the main types of motif in di-, tri-nucleotide repeats. The repeat numbers of SSRs which from S. mussotii transcriptome SSRs were mainly from 5 to 10 and motif length of them mostly ranged from 12 bp to 30 bp. A total of 30 651 contigs were annotated, and only 1 447 SSRs were occurred in protein-coding regions. In the six repeat motifs, tri-nucleotide repeats were the most abundant in coding regions （928）. There are abundant SSRs in S. mussotii transcriptome with high frequency and various types, indicating their usefulness in theory. This research may lay the foundation for designing the targeted SSR primers and developing SSR molecular markers by mining the information of SSRs loci in S. mussotii transcriptome sequences data.

关 键 词：藏茵陈川西獐牙菜 转录组 SSR信息分析 

分 类 号：S567.239[农业科学—中草药栽培]