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Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform

Overview of attention for article published in Frontiers in Plant Science, January 2016
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  • High Attention Score compared to outputs of the same age and source (86th percentile)

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Title
Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform
Published in
Frontiers in Plant Science, January 2016
DOI 10.3389/fpls.2015.01199
Pubmed ID
Authors

Aparupa Bose Mazumdar, Sharmila Chattopadhyay

Abstract

Phyllanthus amarus Schum. and Thonn., a widely distributed annual medicinal herb has a long history of use in the traditional system of medicine for over 2000 years. However, the lack of genomic data for P. amarus, a non-model organism hinders research at the molecular level. In the present study, high-throughput sequencing technology has been employed to enhance better understanding of this herb and provide comprehensive genomic information for future work. Here P. amarus leaf transcriptome was sequenced using the Illumina Miseq platform. We assembled 85,927 non-redundant (nr) "unitranscript" sequences with an average length of 1548 bp, from 18,060,997 raw reads. Sequence similarity analyses and annotation of these unitranscripts were performed against databases like green plants nr protein database, Gene Ontology (GO), Clusters of Orthologous Groups (COG), PlnTFDB, KEGG databases. As a result, 69,394 GO terms, 583 enzyme codes (EC), 134 KEGG maps, and 59 Transcription Factor (TF) families were generated. Functional and comparative analyses of assembled unitranscripts were also performed with the most closely related species like Populus trichocarpa and Ricinus communis using TRAPID. KEGG analysis showed that a number of assembled unitranscripts were involved in secondary metabolites, mainly phenylpropanoid, flavonoid, terpenoids, alkaloids, and lignan biosynthetic pathways that have significant medicinal attributes. Further, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values of the identified secondary metabolite pathway genes were determined and Reverse Transcription PCR (RT-PCR) of a few of these genes were performed to validate the de novo assembled leaf transcriptome dataset. In addition 65,273 simple sequence repeats (SSRs) were also identified. To the best of our knowledge, this is the first transcriptomic dataset of P. amarus till date. Our study provides the largest genetic resource that will lead to drug development and pave the way in deciphering various secondary metabolite biosynthetic pathways in P. amarus, especially those conferring the medicinal attributes of this potent herb.

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X Demographics

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 43 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 2%
Unknown 42 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 30%
Researcher 4 9%
Student > Postgraduate 3 7%
Student > Bachelor 3 7%
Student > Doctoral Student 2 5%
Other 8 19%
Unknown 10 23%
Readers by discipline Count As %
Agricultural and Biological Sciences 12 28%
Biochemistry, Genetics and Molecular Biology 10 23%
Environmental Science 2 5%
Pharmacology, Toxicology and Pharmaceutical Science 1 2%
Veterinary Science and Veterinary Medicine 1 2%
Other 2 5%
Unknown 15 35%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 10 February 2016.
All research outputs
#7,118,510
of 25,371,288 outputs
Outputs from Frontiers in Plant Science
#3,940
of 24,593 outputs
Outputs of similar age
#107,040
of 405,473 outputs
Outputs of similar age from Frontiers in Plant Science
#60
of 465 outputs
Altmetric has tracked 25,371,288 research outputs across all sources so far. This one has received more attention than most of these and is in the 71st percentile.
So far Altmetric has tracked 24,593 research outputs from this source. They receive a mean Attention Score of 3.9. This one has done well, scoring higher than 83% 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 405,473 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 73% of its contemporaries.
We're also able to compare this research output to 465 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 86% of its contemporaries.