• 中文核心期刊
  • CSCD来源期刊
  • 中国科技核心期刊
  • CA、CABI、ZR收录期刊

畲药十二时辰基源植物重瓣铁线莲的全长转录组分析

Full-length Transcriptome of She Herbal Medicine Plant Clematis florida

  • 摘要:
    目的 重瓣铁线莲是畲药十二时辰基源植物,以根入药,含有丰富的活性成分,本研究旨在了解重瓣铁线莲基因注释信息,次级代谢产物代谢通路及基因功能,丰富其转录组信息,为进一步筛选和鉴定其药用成分代谢通路相关基因奠定基础。
    方法 利用SMRT测序技术,对重瓣铁线莲根进行全长转录组测序,并借助生物信息学工具进行功能注释、结构分析以及萜类合成途径基因的挖掘。
    结果 测序共获得高质量测序subreads数据量为62.21 Gb,通过数据处理分析,获到20540条高质量去冗余转录本。利用NR, GO, NT, Pfam, COG/KOG, SwissProt, KEGG等7个数据库对高质量去冗余序列进行基因功能注释,共有19909条转录本至少在1个数据库得到注释,有8888条转录本在NR、NT、COG/KOG、KEGG、GO等5个公共数据库中均有注释。GO注释结果显示,14911条转录本共富集在包含生物学过程、细胞组成和分子功能三大类的53个条目中。KEGG分析显示,19701条转录本序列被富集到6条主通路和44条子通路。COG/KOG注释发现,13204条转录本被注释,其中注释最多的功能类别为一般功能预测。对转录本结构分析发现,共预测到978个转录因子、224条长非编码RNA、7167个SSR。对萜类化合物生物合成途径进行挖掘,共鉴定到48个转录本(16个关键酶候选基因)参与萜类骨架生物合成。
    结论 本研究成功对畲药十二时辰基源植物重瓣铁线莲的根进行了全长转录组测序,获得该物种的全长转录组相关基因功能信息,填补了重瓣铁线莲的基因信息的空白,为深入研究重瓣铁线莲的调控网络、生物学特征、相关代谢途径、信号通路及分子机制等提供参考。

     

    Abstract:
    Objective  Transcription of herbal plant Clematis florida Thunb. var. plena D. Don was used to identify the key genes involved in the metabolic pathways of the active compounds in the famed “Shiershichen” of She medicine.
    Method  PacBio single-molecule real-time (SMRT) was employed to sequence the full-length transcriptome of the roots of the herbal plant that contains the active compounds of the She medicine. Functional annotation, gene structure, and mining of the terpenoid biosynthetic pathway were conducted using bioinformatics tools to secure the transcript data.
    Result From the 62.21 G polymerase read bases generated, 20,540 non-redundant high-quality transcript sequences were identified after data treatment. At least one of the 7 major databases including NR, NT, Pfam, COG/KOG, SwissProt, GO, and KEGG applied annotated the gene functions of 19,909 transcripts, and 8,888 were in NR, NT, COG/KOG, KEGG, and GO. The GO annotation showed 14,911 transcripts enriched in 53 terms that included biological processes, cellular components, and molecular functions. The KEGG database annotated 19,701 transcripts and classified them into 6 major pathways and 44 sub-pathways with the largest number of transcripts enriched in metabolic pathways. The COG/KOG annotation identified 13,204 transcripts with the general function prediction being the most predominant. There were 978 transcription factors, 224 LncRNAs, and 7,167 SSRs predicted, and 48 transcripts with 16 key candidate genes involved in the terpenoid backbone biosynthesis identified.
    Conclusion The full-length transcriptome sequencing on the roots of C. florida was successfully obtained with the comprehensive gene function information. It provided a basis for further studies on the regulatory network, biological characteristics, related metabolic pathways, signaling pathways, and molecular mechanisms associated with the well-known She herbal medicine.

     

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