↓ Skip to main content

Characterization of a second secologanin synthase isoform producing both secologanin and secoxyloganin allows enhanced de novo assembly of a Catharanthus roseus transcriptome

Overview of attention for article published in BMC Genomics, August 2015
Altmetric Badge

About this Attention Score

  • Average Attention Score compared to outputs of the same age

Mentioned by

twitter
2 X users

Citations

dimensions_citation
53 Dimensions

Readers on

mendeley
102 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
Characterization of a second secologanin synthase isoform producing both secologanin and secoxyloganin allows enhanced de novo assembly of a Catharanthus roseus transcriptome
Published in
BMC Genomics, August 2015
DOI 10.1186/s12864-015-1678-y
Pubmed ID
Authors

Thomas Dugé de Bernonville, Emilien Foureau, Claire Parage, Arnaud Lanoue, Marc Clastre, Monica Arias Londono, Audrey Oudin, Benjamin Houillé, Nicolas Papon, Sébastien Besseau, Gaëlle Glévarec, Lucia Atehortùa, Nathalie Giglioli-Guivarc’h, Benoit St-Pierre, Vincenzo De Luca, Sarah E. O’Connor, Vincent Courdavault

Abstract

Transcriptome sequencing offers a great resource for the study of non-model plants such as Catharanthus roseus, which produces valuable monoterpenoid indole alkaloids (MIAs) via a complex biosynthetic pathway whose characterization is still undergoing. Transcriptome databases dedicated to this plant were recently developed by several consortia to uncover new biosynthetic genes. However, the identification of missing steps in MIA biosynthesis based on these large datasets may be limited by the erroneous assembly of close transcripts and isoforms, even with the multiple available transcriptomes. Secologanin synthases (SLS) are P450 enzymes that catalyze an unusual ring-opening reaction of loganin in the biosynthesis of the MIA precursor secologanin. We report here the identification and characterization in C. roseus of a new isoform of SLS, SLS2, sharing 97 % nucleotide sequence identity with the previously characterized SLS1. We also discovered that both isoforms further oxidize secologanin into secoxyloganin. SLS2 had however a different expression profile, being the major isoform in aerial organs that constitute the main site of MIA accumulation. Unfortunately, we were unable to find a current C. roseus transcriptome database containing simultaneously well reconstructed sequences of SLS isoforms and accurate expression levels. After a pair of close mRNA encoding tabersonine 16-hydroxylase (T16H1 and T16H2), this is the second example of improperly assembled transcripts from the MIA pathway in the public transcriptome databases. To construct a more complete transcriptome resource for C. roseus, we re-processed previously published transcriptome data by combining new single assemblies. Care was particularly taken during clustering and filtering steps to remove redundant contigs but not transcripts encoding potential isoforms by monitoring quality reconstruction of MIA genes and specific SLS and T16H isoforms. The new consensus transcriptome allowed a precise estimation of abundance of SLS and T16H isoforms, similar to qPCR measurements. The C. roseus consensus transcriptome can now be used for characterization of new genes of the MIA pathway. Furthermore, additional isoforms of genes encoding distinct MIA biosynthetic enzymes isoforms could be predicted suggesting the existence of a higher level of complexity in the synthesis of MIA, raising the question of the evolutionary events behind what seems like redundancy.

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 102 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Colombia 1 <1%
Serbia 1 <1%
Unknown 100 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 26 25%
Researcher 20 20%
Student > Master 15 15%
Student > Bachelor 9 9%
Professor 3 3%
Other 11 11%
Unknown 18 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 38 37%
Biochemistry, Genetics and Molecular Biology 35 34%
Chemistry 3 3%
Pharmacology, Toxicology and Pharmaceutical Science 2 2%
Economics, Econometrics and Finance 1 <1%
Other 1 <1%
Unknown 22 22%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 20 August 2015.
All research outputs
#14,822,669
of 22,824,164 outputs
Outputs from BMC Genomics
#6,141
of 10,654 outputs
Outputs of similar age
#147,075
of 266,176 outputs
Outputs of similar age from BMC Genomics
#170
of 252 outputs
Altmetric has tracked 22,824,164 research outputs across all sources so far. This one is in the 32nd percentile – i.e., 32% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,654 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 37th percentile – i.e., 37% of its peers scored the same or lower than it.
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 266,176 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 41st percentile – i.e., 41% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 252 others from the same source and published within six weeks on either side of this one. This one is in the 25th percentile – i.e., 25% of its contemporaries scored the same or lower than it.