Genome wide transcriptome profiling reveals differential gene expression in secondary metabolite pathway of Cymbopogon winterianus.
Genome wide transcriptome profiling reveals differential gene expression in secondary metabolite pathway of Cymbopogon winterianus.
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DOI：
10.1038/srep21026
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发表时间：
2016-02-15
影响因子：
4.6
通讯作者：
Sen P
中科院分区：
文献类型：
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作者：
Devi K;Mishra SK;Sahu J;Panda D;Modi MK;Sen P
转录组测序技术的发展为产生大规模表达数据集提供了快速、经济、可靠的方法，特别适用于非模式物种，以鉴定推定基因、关键途径和调控机制。香茅（Cymbopogon winterianus）是一种芳香药用草，具有抗肿瘤、抗菌、抗真菌、抗病毒、解毒和天然驱虫作用。尽管萜类化合物具有许多应用价值，但其生物合成途径中的相关基因至今仍不清楚。本研究是一个开拓性的尝试，以获得详尽的次级代谢途径的分子信息，并增加基因组资源的香茅。使用高通量RNA-Seq技术，以前所未有的深度（11.7 Gb）分析了根和叶转录组。目标搜索确定了大多数与代谢途径和其他天然产物途径即抗生素合成沿着的基因以及许多新基因。通过RT-PCR和qRT-PCR验证了15个单基因的萜类生物合成基因的比较表达结果。因此，这些转录组的覆盖范围是全面的，足以发现所有已知的主要代谢途径的基因。该转录组数据集可以作为香茅属基因表达、基因组学和功能基因组学研究的重要公共信息，并将作为未来作物改良的基准。
Advances in transcriptome sequencing provide fast, cost-effective and reliable approach to generate large expression datasets especially suitable for non-model species to identify putative genes, key pathway and regulatory mechanism. Citronella (Cymbopogon winterianus) is an aromatic medicinal grass used for anti-tumoral, antibacterial, anti-fungal, antiviral, detoxifying and natural insect repellent properties. Despite of having number of utilities, the genes involved in terpenes biosynthetic pathway is not yet clearly elucidated. The present study is a pioneering attempt to generate an exhaustive molecular information of secondary metabolite pathway and to increase genomic resources in Citronella. Using high-throughput RNA-Seq technology, root and leaf transcriptome was analysed at an unprecedented depth (11.7 Gb). Targeted searches identified majority of the genes associated with metabolic pathway and other natural product pathway viz. antibiotics synthesis along with many novel genes. Terpenoid biosynthesis genes comparative expression results were validated for 15 unigenes by RT-PCR and qRT-PCR. Thus the coverage of these transcriptome is comprehensive enough to discover all known genes of major metabolic pathways. This transcriptome dataset can serve as important public information for gene expression, genomics and function genomics studies in Citronella and shall act as a benchmark for future improvement of the crop.