Narnoliya Lokesh K, Kaushal Girija, Singh Sudhir P, Sangwan Rajender S
Center of Innovative and Applied Bioprocessing (A National Institute under the Department of Biotechnology, Govt. of India), S.A.S. Nagar, Mohali, Punjab, India.
BMC Genomics. 2017 Jan 13;18(1):74. doi: 10.1186/s12864-016-3437-0.
Rose-scented geranium (Pelargonium sp.) is a perennial herb that produces a high value essential oil of fragrant significance due to the characteristic compositional blend of rose-oxide and acyclic monoterpenoids in foliage. Recently, the plant has also been shown to produce tartaric acid in leaf tissues. Rose-scented geranium represents top-tier cash crop in terms of economic returns and significance of the plant and plant products. However, there has hardly been any study on its metabolism and functional genomics, nor any genomic expression dataset resource is available in public domain. Therefore, to begin the gains in molecular understanding of specialized metabolic pathways of the plant, de novo sequencing of rose-scented geranium leaf transcriptome, transcript assembly, annotation, expression profiling as well as their validation were carried out.
De novo transcriptome analysis resulted a total of 78,943 unique contigs (average length: 623 bp, and N50 length: 752 bp) from 15.44 million high quality raw reads. In silico functional annotation led to the identification of several putative genes representing terpene, ascorbic acid and tartaric acid biosynthetic pathways, hormone metabolism, and transcription factors. Additionally, a total of 6,040 simple sequence repeat (SSR) motifs were identified in 6.8% of the expressed transcripts. The highest frequency of SSR was of tri-nucleotides (50%). Further, transcriptome assembly was validated for randomly selected putative genes by standard PCR-based approach. In silico expression profile of assembled contigs were validated by real-time PCR analysis of selected transcripts.
Being the first report on transcriptome analysis of rose-scented geranium the data sets and the leads and directions reflected in this investigation will serve as a foundation for pursuing and understanding molecular aspects of its biology, and specialized metabolic pathways, metabolic engineering, genetic diversity as well as molecular breeding.
玫瑰天竺葵（天竺葵属）是一种多年生草本植物，因其叶片中具有特征性成分氧化玫瑰和无环单萜类化合物的混合，能产出具有重要香气价值的高价值精油。最近，该植物还被证明在叶片组织中能产生酒石酸。从经济回报以及该植物和植物产品的重要性来看，玫瑰天竺葵是顶级经济作物。然而，几乎没有关于其代谢和功能基因组学的研究，公共领域也没有任何基因组表达数据集资源。因此，为了开始从分子层面了解该植物的特殊代谢途径，对玫瑰天竺葵叶片转录组进行了从头测序、转录本组装、注释、表达谱分析及其验证。
从头转录组分析从1544万个高质量原始 reads 中得到了总共78943个独特的重叠群（平均长度：623 bp，N50长度：752 bp）。通过电子功能注释鉴定出了几个代表萜类、抗坏血酸和酒石酸生物合成途径、激素代谢以及转录因子的推定基因。此外，在6.8%的表达转录本中总共鉴定出6040个简单序列重复（SSR）基序。SSR的最高频率是三核苷酸（50%）。此外，通过基于标准PCR的方法对随机选择的推定基因的转录组组装进行了验证。通过对选定转录本的实时PCR分析验证了组装重叠群的电子表达谱。
作为玫瑰天竺葵转录组分析的首份报告，本研究中反映的数据集、线索和方向将为研究和理解其生物学的分子方面、特殊代谢途径、代谢工程、遗传多样性以及分子育种奠定基础。
