苦参转录组SSR位点及基因功能注释分析
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摘要
分析苦参转录组中的简单重复序列(SSR)位点信息,为开发分子标记奠定基础。利用Fastqc软件对苦参转录组测序的原始读长(reads)进行质量评估,再用Trimmomatic软件对reads质量较差的碱基进行过滤,利用Trinity软件对Trimmomatic处理后的reads进行序列组装,之后使用基因组装完整性评估(BUSCO)软件对转录组组装的序列进行质量评估,并分析组装的conting序列的开放阅读框(open reading frame,简称ORF);利用MicroSAtellite(MISA)软件对无冗余独立基因(unigene)进行SSR搜索。利用Trinity软件最终筛选得到23074条ORF信息;使用MISA软件从unigenes序列中发现8 798个SSR位点,分布于7 339条unigene中,总体上unigenes序列中SSR占比为2.16%,SSR位点平均间隔是5.28 bp,其中占比最高的是单核苷重复基序,为50.53%;其次是出现频率分别为22.28%、24.73%的二、三核苷酸。苦参转录组中SSR类型众多,出现频率高,在后续的苦参遗传性状分析,及次生代谢(苦参碱和黄酮等次生代谢产物)途径等相关基因定位等方面具有很好的应用潜力。
引文
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[17]Dreisigacker S,Zhang P,Warburton M L,et al.SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments[J].Crop Science,2004,44(2):381-388.
[2]张贵君.精编中草药彩色图谱[M].北京:中国医药科技出版社,2016.
[3]张翅.苦参茎叶中化学成分的研究[D].天津:天津中医药大学,2013.
[4]段永红,渠云芳,王长彪,等.药用植物苦参SSR-PCR体系的优化与验证[J].中国农业大学学报,2014,19(5):95-100.
[5]He J Y,Zhu S,Komatsu K,et al.Genetic polymorphism of medicinally-used Codonopsis species in an internal transcribed spacer sequence of nuclear ribosomal DNA and its application to authenticate Codonopsis Radix[J].Journal of Natural Medicines,2014,68(1):112-124.
[6]Han R,Takahashi H,Nakamura M,et al.Transcriptome analysis of nine tissues to discover genes involved in the biosynthesis of active ingredients in Sophora flavescens[J].Biological and Pharmaceutical Bulletin,2015,38(6):876-883.
[7]Staff S.Using the SRA Toolkit to convert .sra files into other formats[EB/OL].(2015-08-22)[2017-12-06].http://www.ncbi.nlm.nih.gov/books/NBK158900/.
[8]Bonnal R J P,Ranzani V,Arrigoni A,et al.De novo transcriptome profiling of highly purified human lymphocytes primary cells[J].Scientific Data,2015,2:150051.
[9]Grabherr M G,Haas B J,Yassour M,et al.Trinity:reconstructing a full-length transcriptome without a genome from RNA-Seq data[J].Nature Biotechnology,2011,29(7):644-652.
[10]王林.白色链霉菌和白背飞虱的基因组学研究[D].合肥:中国科学技术大学,2017.`
[11]舒江平,刘莉,沈慧,等.基于系统基因组学分析揭示早期陆生植物的复杂网状进化关系[J].生物多样性,2017,25(6):675-682.
[12]王希,陈丽,赵春雷.利用MISA工具对不同类型序列进行SSR标记位点挖掘的探讨[J].中国农学通报,2016,32(10):150-156.
[13]王东,曹玲亚,高建平.党参转录组中SSR位点信息分析[J].中草药,2014,45(16):2390-2394.
[14]邓科君,张勇,熊丙全,等.药用植物丹参EST-SSR标记的鉴定[J].药学学报,2009,44(10):1165-1172.
[15]杨维泽,金航,赵振玲,等.西洋参EST资源的SSR信息分析[J].西南农业学报,2011,24(1):275-278.
[16]Li C F,Zhu Y J,Guo X,et al.Transcriptome analysis reveals ginsenosides biosynthetic genes,microRNAs and simple sequence repeats in Panax ginseng C.A.Meyer[J].BMC Genomics,2013,14:245.
[17]Dreisigacker S,Zhang P,Warburton M L,et al.SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments[J].Crop Science,2004,44(2):381-388.