摘要
目的获得银线草Chloranthusjaponicus根茎转录组信息特征。方法用高通量测序平台IlluminaHiSeq TM2000150PE进行银线草根茎转录组测序分析。结果转录组测序共获得68458750条高质量序列(cleanreads),Trinitydenovo组装获得56 096个unigenes,平均长度801 nt。BLAST分析显示分别有25 773(45.94%)、17 801(31.73%)、16 082(28.67%)、9649(17.20%)个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40分支,涉及131个KEGG标准代谢通路,其中包括16个次生代谢标准通路。进一步分析获得170个基因参与单萜、二萜、倍半萜、三萜等萜类化合物生物合成通路。同时,转录组预测编码蛋白框序列1 887个;高等植物转录因子54个家族。借助MISA软件发现8 987个简单重复序列(SSRs),二碱基重复SSRs数量最丰富,有5 948个,出现频率为66.2%,五碱基重复SSRs相对较少,占1.3%。结论基于RNA-seq分析获得银线草根茎转录组信息特征及萜类合成代谢通路关键基因,为后期银线草活性成分次生代谢途径解析及调控研究奠定基础。
Objective To obtain the transcriptome dataset of Chloranthus japonicas.Methods Using the Illumina HiSeqTM 2000 150 PE,a rhizome transcriptome of C.japonicus was generated,followed by systemic bioinformatics analyses.Results A total of 68 458 750 high quality clean reads were produced by the transcriptome sequencing.Trinity de novo assembling resulted in a total of 56 096 unigenes with an average length of 801 nt.BLAST analysis indicated that 25 773(45.94%),17 801(31.73%),16 082(28.67%),and 9 649(17.20%) unigenes were successfully annotated in the NR,Swiss-port,KOG,and KEGG databases,respectively.All unigenes were classified into three major groups by GO,including biological process,cellular component,and molecular function,and then,grouped into 40 subgroups.And 131 KEGG standard pathways were designated,16 of which were defied as the secondary metabolism.Further analysis revealed that a total of 170 unigenes were involved in the biosynthesis of mono-,di-,sesqui-,or triterpene.Meantime,1 887 unigenes were predicted to contain protein coding sequences.Totally 54 families of transcription factors of higher plant were identified.Using MISA prediction,8 987 simple sequence repeats(SSRs) were obtained,among which the di-nucleotide SSRs were abundant with 5 948(66.2%),whereas the penta-nucleotide SSRs were relatively less,accounting for 1.3%.Conclusion The transcriptome of C.japonicus rhizome was generated by RNA-seq along with the identification of unigenes implicated in various terpenes biosynthesis,which will provide a fundamental basis for secondary metabolism pathway dissections and their regulatory mechanisms in this plant species.
作者
李依民
胡本祥
彭亮
沈霞
高静
王昌利
颜永刚
张岗
LI Yi-min;HU Ben-xiang;PENG Liang;SHEN Xia;GAO Jing;WANG Chang-li;YAN Yong-gang;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)
出处
《中草药》
CAS
CSCD
北大核心
2018年第21期4967-4974,共8页
Chinese Traditional and Herbal Drugs
基金
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
咸阳市中青年科技领军人才项目
陕西省科技厅项目(2016KTTSSF01-01-01)
国家中医药管理局项目(ZYBZH-C-QIN-45)
关键词
银线草
转录组
功能基因
代谢通路
简单重复序列
RNA-SEQ
Chloranthusjaponicus Sieb.
transcriptome
functional gene
metabolim pathway
simple sequence repeats
RNA-seq
