Application of High‐Throughput Sequencing in Medicinal Plant Transcriptome Studies

Hao, Da‐Cheng; Chen, Shilin; Xiao, Pei‐Gen; Liu, Ming

doi:10.1002/ddr.21041

Cited by 23 publications

(14 citation statements)

References 51 publications

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“…The arrival of Next-Generation Sequencing (NGS) technologies could overcome the limitations and allow investigators to simultaneously measure the changes and regulation at a genome-wide level under certain biological conditions for non-model plants for which the background genomic information is not available [39], [58]–[59]. In recent years,the newly developed NGS-based RNA-seq technique has been widely used for de novo transcriptome sequencing assembly, discovery of novel genes and investigation of gene expression in many non-model plants such as rice [60], peanuts [61], purple sweet potato [62], medicinal plant Polygonum cuspidatum [63] and floral plant Dendrocalamus latiflorus [64].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

et al. 2013

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Lead (Pb), one of the most toxic heavy metals, can be absorbed and accumulated by plant roots and then enter the food chain resulting in potential health risks for human beings. The radish (Raphanus sativus L.) is an important root vegetable crop with fleshy taproots as the edible parts. Little is known about the mechanism by which radishes respond to Pb stress at the molecular level. In this study, Next Generation Sequencing (NGS)–based RNA-seq technology was employed to characterize the de novo transcriptome of radish roots and identify differentially expressed genes (DEGs) during Pb stress. A total of 68,940 assembled unique transcripts including 33,337 unigenes were obtained from radish root cDNA samples. Based on the assembled de novo transcriptome, 4,614 DEGs were detected between the two libraries of untreated (CK) and Pb-treated (Pb1000) roots. Gene Ontology (GO) and pathway enrichment analysis revealed that upregulated DEGs under Pb stress are predominately involved in defense responses in cell walls and glutathione metabolism-related processes, while downregulated DEGs were mainly involved in carbohydrate metabolism-related pathways. The expression patterns of 22 selected genes were validated by quantitative real-time PCR, and the results were highly accordant with the Solexa analysis. Furthermore, many candidate genes, which were involved in defense and detoxification mechanisms including signaling protein kinases, transcription factors, metal transporters and chelate compound biosynthesis related enzymes, were successfully identified in response to heavy metal Pb. Identification of potential DEGs involved in responses to Pb stress significantly reflected alterations in major biological processes and metabolic pathways. The molecular basis of the response to Pb stress in radishes was comprehensively characterized. Useful information and new insights were provided for investigating the molecular regulation mechanism of heavy metal Pb accumulation and tolerance in root vegetable crops.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

et al. 2013

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“…However, the compounds often exist in minute quantities, in sometimes rare plants, making the identification of the genetic basis for biochemical pathways and their transfer to more tractable systems of both economic and environmental interest. Targeted genomic or transcriptomic sequencing of medicinal plant species (Hao et al, 2012; Sharma and Shrivastava, 2016) could lead to synthetic biology approaches to produce specific bioactive compounds in yeast or E. coli , as has been done with Artemisia annua , the source of artemisinin, a potent anti-malarial drug (Ro et al, 2006; Westfall et al, 2012), and the opium poppy Papaver somniferum , the source of medical opiates (Thodey et al, 2014). …”

Section: Medicinal Plantsmentioning

confidence: 99%

Field Guide to Plant Model Systems

Chang

Bowman

Meyerowitz

2016

Cell

108

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For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.

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“…Sequencing of medicinal plants transcriptome will provide direct information regarding novel genes and various underlying mechanism of biosynthetic pathways as depicted in Fig. 2 (Hao et al 2012). Unlike microarray and realtime PCR, absolute and genome-wide quantification of the transcripts is made possible by NGS (Mutz et al 2013).…”

Section: Expressive Transcriptomementioning

confidence: 99%

Renaissance in phytomedicines: promising implications of NGS technologies

Sharma

Shrivastava

2016

Planta

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Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.

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Application of High‐Throughput Sequencing in Medicinal Plant Transcriptome Studies

Cited by 23 publications

References 51 publications

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

Field Guide to Plant Model Systems

Renaissance in phytomedicines: promising implications of NGS technologies

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