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

Overview of attention for article published in BMC Genomics, January 2017
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Title
De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis
Published in
BMC Genomics, January 2017
DOI 10.1186/s12864-016-3437-0
Pubmed ID
Authors

Lokesh K. Narnoliya, Girija Kaushal, Sudhir P. Singh, Rajender S. Sangwan

Abstract

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.

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The data shown below were collected from the profile of 1 tweeter who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 50 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 2%
Unknown 49 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 14 28%
Researcher 8 16%
Student > Doctoral Student 5 10%
Student > Postgraduate 4 8%
Student > Master 4 8%
Other 5 10%
Unknown 10 20%
Readers by discipline Count As %
Agricultural and Biological Sciences 24 48%
Biochemistry, Genetics and Molecular Biology 13 26%
Chemical Engineering 1 2%
Nursing and Health Professions 1 2%
Chemistry 1 2%
Other 0 0%
Unknown 10 20%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 15 January 2017.
All research outputs
#7,730,428
of 8,912,948 outputs
Outputs from BMC Genomics
#5,451
of 6,194 outputs
Outputs of similar age
#269,493
of 328,688 outputs
Outputs of similar age from BMC Genomics
#151
of 189 outputs
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