De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural, functional and regulatory genes with special reference to secondary metabolism

Sangwan, Rajender Singh; Tripathi, Sandhya; Singh, Jyoti; Narnoliya, Lokesh Kumar; Sangwan, Neelam S.

doi:10.1016/j.gene.2013.04.057

Cited by 101 publications

(72 citation statements)

References 47 publications

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“…; Sangwan et al . ) and other plant biotechnology applications. This wealth of genomic data, in turn, enables more comprehensive transcriptomic studies using custom microarrays and high‐throughput mRNA sequencing (RNA‐Seq), which are generating a vast volume of expression data.…”

Section: Introductionmentioning

confidence: 99%

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Lohse

Nagel

Herter

et al. 2013

Plant Cell & Environment

546

439

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Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan-to-GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/ Mercator.

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Section: Introductionmentioning

confidence: 99%

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Lohse

Nagel

Herter

et al. 2013

Plant Cell & Environment

546

439

View full text Add to dashboard Cite

show abstract

“…RNA-seq is a comprehensive and efficient way to qualitatively and quantitatively characterize transcriptomes, and discover new exons and splicing variants (Shi et al 2011; Chikara et al 2014). Significant number of medicinal plant species need to be profiled and analyzed for their transcriptomic data to help us (1) understand system biology of their metabolic pathways with reference to the metabolome, (2) compare them across the genes related to biogeneration of the same group of secondary metabolites and with the sets of genes with similar catalytic properties (gene families and super families), (3) elucidate metabolic pathways and their regulation, and (4) understand functional genomics of individual enzymatic step of significance/interest in the species (Sangwan et al 2013). …”

Section: Introductionmentioning

confidence: 99%

Next-generation sequencing of representational difference analysis products for identification of genes involved in diosgenin biosynthesis in fenugreek (Trigonella foenum-graecum)

Ciura

Szeliga

Grzesik

et al. 2017

Planta

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Main conclusion Representational difference analysis of cDNA was performed and differential products were sequenced and annotated. Candidate genes involved in biosynthesis of diosgenin in fenugreek were identified. Detailed mechanism of diosgenin synthesis was proposed.Fenugreek (Trigonella foenum-graecum L.) is a valuable medicinal and crop plant. It belongs to Fabaceae family and has a unique potential to synthesize valuable steroidal saponins, e.g., diosgenin. Elicitation (methyl jasmonate) and precursor feeding (cholesterol and squalene) were used to enhance the content of sterols and steroidal sapogenins in in vitro grown plants for representational difference analysis of cDNA (cDNA-RDA). To identify candidate genes involved in diosgenin biosynthesis, differential, factor-specific libraries were subject to the nextgeneration sequencing. Approximately 9.9 million reads were obtained, trimmed, and assembled into 31,491 unigenes with an average length of 291 bp. Then, functional annotation and gene ontogeny enrichment analysis was performed by aligning all-unigenes with public databases.

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“…7a). The TFs belonging to bHLH, MYB, AP2/ERF, and WRKY families execute key roles in regulation of biosynthesis of terpenes, which is the largest secondary metabolite family [45–49]. Some of the TF genes have been characterized for regulating biosynthesis of terpene secondary metabolites in different plants e.g.…”

Section: Resultsmentioning

confidence: 99%

De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

et al. 2017

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BackgroundRose-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.Results 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.ConclusionBeing 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3437-0) contains supplementary material, which is available to authorized users.

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De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural, functional and regulatory genes with special reference to secondary metabolism

Cited by 101 publications

References 47 publications

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Next-generation sequencing of representational difference analysis products for identification of genes involved in diosgenin biosynthesis in fenugreek (Trigonella foenum-graecum)

De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

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