基于高通量测序技术的黄三七根茎转录组数据分析  

Transcriptomic data analyses of rhizome of Souliea vaginata via Illumina high-throughput sequencing technology

作　　者：李依民 彭亮 杨冰月 张明英 任瀛 程虎印 吴海峰[2] 张岗 LI Yi-min;PENG Liang;YANG Bing-yue;ZHANG Ming-ying;REN Ying;CHENG Hu-yin;WU Hai-feng;ZHANG Gang(Shaanxi Provincial Key Laboratory for Chinese Medicine Basis &New Drugs Research,College of Pharmacy,Shaanxi University of Chinese Medicine,Xi'an 712046,China;Institute of Medicinal Plant Development,Chinese Academy of Medical Sciences &Peking Union Medical College,Beijing 100193,China)

机构地区：[1]陕西中医药大学药学院陕西省中药基础与新药研究重点实验室,陕西西安712046 [2]中国医学科学院北京协和医学院药用植物研究所,北京100193

出　　处：《中草药》2018年第21期4983-4990,共8页Chinese Traditional and Herbal Drugs

基　　金：陕西省自然科学基金项目(2017JM8030);陕西省教育厅专项(18JK0216);陕西中医药大学新进博士科研启动经费(104080001);陕西省高校首批青年杰出人才支持计划项目;中国医学科学院医学与健康科技创新重大协同创新项目(2017-I2M-1-013);咸阳市中青年科技领军人才项目;国家留学基金委浙江省药学重中之重开放课题(YKFJ3-012)

摘　　要：目的获得黄三七Soulieavaginata根茎转录组信息特征。方法以黄三七根茎为对象,采用二代高通量测序平台IlluminaHi SeqTM2000150PE进行转录组测序并进行系统的生物信息学分析。结果转录组测序分析共获得63 322 086条高质量序列(clean reads),Trinity de novo组装获得52 575个unigenes,平均长度909 nt。BLAST分析显示分别有28 842(54.86%)、10 712(20.37%)、9 245(17.58%)、11 559(21.99%)条unigenes在NR、Swiss-port、KOG、KEGG数据库得到注释信息,可归为GO分类的生物过程、细胞组分和分子功能3大类45分支,涉及126个KEGG标准代谢通路,其中包括17个次生代谢标准通路。蛋白编码框序列2 215个,包含高等植物转录因子55个家族;借助MISA软件发现4 609个SSRs,三碱基重复SSRs数量最丰富,有2106个,出现频率为45.7%,五碱基重复SSRs相对较少,占2.9%。结论利用高通量测序技术和生物信息分析获得黄三七根茎转录组信息特征,为后期黄三七功能基因鉴定、次生代谢途径解析及其调控机制研究奠定基础。Objective To obtain the transcriptome dataset of rhizome of Souliea vaginata Methods Using the high-throughput illumina sequencing platform Illumina HiSeqTM 2000 150 PE,a rhizome transcriptome dataset of S.vaginata was obtained,followed by systemic bioinformatics analyses.Results The transcriptome sequencing analyses produced to a great number of 63 322 086 high quality clean reads.Trinity de novo assembling resulted in a total of 52 575 unigenes with an average length of 909 nt.BLAST analysis indicated that 28 842(accounting for 54.86% of the total unigenes),10 712(20.37%),9 245(17.58%),and 11 559(21.99%) unigenes were successfully annotated in the NR,Swiss-port,KOG,and KEGG databases,respectively.GO classification contained the basic three major groups,including biological process,cellular component,and molecular function,and 45 subgroups.Among them126 KEGG standard pathways were designated,of which 17 were defied as the secondary metabolism.Of all unigenes,2 215 with protein coding sequences were predicted,and 55 families of plant transcription factors were also identified.MISA prediction yielded a number of 4 609 simple sequence repeats(SSRs),among which the tri-nucleotide SSRs were abundant with 2 106(45.7%),whereas the penta-nucleotide SSRs were relatively less,accounting for 2.9%.Conclusion The transcriptomic characteristics of S.vaginata rhizome were revealed by the high-throughput Illumina sequencing technology along with bioinformatics analyses,which would be of great importance for the functional gene characterization,secondary metabolism pathway dissections,and their regulatory mechanisms in S.vaginata.

关 键 词：黄三七 转录组 功能基因 代谢通路 简单重复序列 

分 类 号：R282.12[医药卫生—中药学]