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Transcriptome analysis of leaves, roots and flowers of Panax notoginseng identifies genes involved in ginsenoside and alkaloid biosynthesis

Overview of attention for article published in BMC Genomics, April 2015
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  • Above-average Attention Score compared to outputs of the same age (63rd percentile)
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Title
Transcriptome analysis of leaves, roots and flowers of Panax notoginseng identifies genes involved in ginsenoside and alkaloid biosynthesis
Published in
BMC Genomics, April 2015
DOI 10.1186/s12864-015-1477-5
Pubmed ID
Authors

Ming-Hua Liu, Bin-Rui Yang, Wai-Fung Cheung, Kevin Yi Yang, He-Feng Zhou, Jamie Sui-Lam Kwok, Guo-Cheng Liu, Xiao-Feng Li, Silin Zhong, Simon Ming-Yuen Lee, Stephen Kwok-Wing Tsui

Abstract

Panax notoginseng (Burk.) F.H. Chen is one of the most highly valued medicinal plants in the world. The major bioactive molecules are triterpene saponins, which are also known as ginsenosides. However, its large genome size has hindered the assembly of a draft genome by whole genome sequencing. Hence, genomic and transcriptomic details about P. notoginseng, especially its biosynthetic pathways and gene expression in different parts of the plant, have remained largely unknown until now. In this study, RNA sequencing of three different P. notoginseng tissues was performed using next generation DNA sequencing. After assembling the high quality sequencing reads into 107,340 unigenes, biochemical pathways were predicted and 9,908 unigenes were assigned to 135 KEGG pathways. Among them, 270 unigenes were identified to be involved in triterpene saponin biosynthesis. In addition, 350 and 342 unigenes were predicted to encode cytochrome P450s and glycosyltransferases, respectively, based on the annotation results, some of which encode enzymes responsible for the conversion of the triterpene saponin backbone into different ginsenosides. In particular, one unigene predominately expressed in the root was annotated as CYP716A53v2, which probably participates in the formation of protopanaxatriol from protopanaxadiol in P. notoginseng. The differential expression of this gene was further confirmed by real-time PCR. We have established a global transcriptome dataset for P. notoginseng and provided additional genetic information for further genome-wide research and analyses. Candidate genes involved in ginsenoside biosynthesis, including putative cytochrome P450s and glycosyltransferases were obtained. The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P. notoginseng.

Twitter Demographics

The data shown below were collected from the profiles of 6 tweeters 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 %
Spain 1 2%
Brazil 1 2%
Unknown 48 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 15 30%
Researcher 7 14%
Student > Master 5 10%
Professor > Associate Professor 4 8%
Student > Doctoral Student 3 6%
Other 8 16%
Unknown 8 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 18 36%
Biochemistry, Genetics and Molecular Biology 12 24%
Pharmacology, Toxicology and Pharmaceutical Science 3 6%
Arts and Humanities 2 4%
Chemical Engineering 2 4%
Other 4 8%
Unknown 9 18%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 19 April 2015.
All research outputs
#6,343,104
of 12,378,406 outputs
Outputs from BMC Genomics
#2,970
of 7,251 outputs
Outputs of similar age
#71,014
of 197,377 outputs
Outputs of similar age from BMC Genomics
#100
of 199 outputs
Altmetric has tracked 12,378,406 research outputs across all sources so far. This one is in the 48th percentile – i.e., 48% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,251 research outputs from this source. They receive a mean Attention Score of 4.3. This one has gotten more attention than average, scoring higher than 58% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 197,377 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 63% of its contemporaries.
We're also able to compare this research output to 199 others from the same source and published within six weeks on either side of this one. This one is in the 49th percentile – i.e., 49% of its contemporaries scored the same or lower than it.