↓ Skip to main content

Global transcriptome analysis of Huperzia serrata and identification of critical genes involved in the biosynthesis of huperzine A

Overview of attention for article published in BMC Genomics, March 2017
Altmetric Badge

About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (87th percentile)
  • High Attention Score compared to outputs of the same age and source (90th percentile)

Mentioned by

news
2 news outlets
twitter
2 X users

Citations

dimensions_citation
29 Dimensions

Readers on

mendeley
43 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
Global transcriptome analysis of Huperzia serrata and identification of critical genes involved in the biosynthesis of huperzine A
Published in
BMC Genomics, March 2017
DOI 10.1186/s12864-017-3615-8
Pubmed ID
Authors

Mengquan Yang, Wenjing You, Shiwen Wu, Zhen Fan, Baofu Xu, Mulan Zhu, Xuan Li, Youli Xiao

Abstract

Huperzia serrata (H. serrata) is an economically important traditional Chinese herb with the notably medicinal value. As a representative member of the Lycopodiaceae family, the H. serrata produces various types of effectively bioactive lycopodium alkaloids, especially the huperzine A (HupA) which is a promising drug for Alzheimer's disease. Despite their medicinal importance, the public genomic and transcriptomic resources are very limited and the biosynthesis of HupA is largely unknown. Previous studies on comparison of 454-ESTs from H. serrata and Phlegmariurus carinatus predicted putative genes involved in lycopodium alkaloid biosynthesis, such as lysine decarboxylase like (LDC-like) protein and some CYP450s. However, these gene annotations were not carried out with further biochemical characterizations. To understand the biosynthesis of HupA and its regulation in H. serrata, a global transcriptome analysis on H. Serrata tissues was performed. In this study, we used the Illumina Highseq4000 platform to generate a substantial RNA sequencing dataset of H. serrata. A total of 40.1 Gb clean data was generated from four different tissues: root, stem, leaf, and sporangia and assembled into 181,141 unigenes. The total length, average length, N50 and GC content of unigenes were 219,520,611 bp, 1,211 bp, 2,488 bp and 42.51%, respectively. Among them, 105,516 unigenes (58.25%) were annotated by seven public databases (NR, NT, Swiss-Prot, KEGG, COG, Interpro, GO), and 54 GO terms and 3,391 transcription factors (TFs) were functionally classified, respectively. KEGG pathway analysis revealed that 72,230 unigenes were classified into 21 functional pathways. Three types of candidate enzymes, LDC, CAO and PKS, responsible for the biosynthesis of precursors of HupA were all identified in the transcripts. Four hundred and fifty-seven CYP450 genes in H. serrata were also analyzed and compared with tissue-specific gene expression. Moreover, two key classes of CYP450 genes BBE and SLS, with 23 members in total, for modification of the lycopodium alkaloid scaffold in the late two stages of biosynthesis of HupA were further evaluated. This study is the first report of global transcriptome analysis on all tissues of H. serrata, and critical genes involved in the biosynthesis of precursors and scaffold modifications of HupA were discovered and predicted. The transcriptome data from this work not only could provide an important resource for further investigating on metabolic pathways in H. serrata, but also shed light on synthetic biology study of HupA.

X Demographics

X Demographics

The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
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 %
Serbia 1 2%
Unknown 42 98%

Demographic breakdown

Readers by professional status Count As %
Researcher 11 26%
Student > Ph. D. Student 6 14%
Student > Doctoral Student 3 7%
Student > Postgraduate 2 5%
Professor > Associate Professor 2 5%
Other 6 14%
Unknown 13 30%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 11 26%
Agricultural and Biological Sciences 6 14%
Medicine and Dentistry 4 9%
Pharmacology, Toxicology and Pharmaceutical Science 3 7%
Chemistry 2 5%
Other 3 7%
Unknown 14 33%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 17. 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 28 April 2017.
All research outputs
#1,856,616
of 22,961,203 outputs
Outputs from BMC Genomics
#482
of 10,686 outputs
Outputs of similar age
#38,276
of 309,336 outputs
Outputs of similar age from BMC Genomics
#20
of 203 outputs
Altmetric has tracked 22,961,203 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 91st percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 10,686 research outputs from this source. They receive a mean Attention Score of 4.7. This one has done particularly well, scoring higher than 95% 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 309,336 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 87% of its contemporaries.
We're also able to compare this research output to 203 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 90% of its contemporaries.