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De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia

Overview of attention for article published in BMC Genomics, September 2016
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  • Good Attention Score compared to outputs of the same age (70th percentile)
  • Good Attention Score compared to outputs of the same age and source (73rd percentile)

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9 tweeters

Citations

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20 Dimensions

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37 Mendeley
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Title
De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia
Published in
BMC Genomics, September 2016
DOI 10.1186/s12864-016-3083-6
Pubmed ID
Authors

Marina Mora-Ortiz, Martin T. Swain, Martin J. Vickers, Matthew J. Hegarty, Rhys Kelly, Lydia M. J. Smith, Leif Skøt

Abstract

Sainfoin (Onobrychis viciifolia) is a highly nutritious tannin-containing forage legume. In the diet of ruminants sainfoin can have anti-parasitic effects and reduce methane emissions under in vitro conditions. Many of these benefits have been attributed to condensed tannins or proanthocyanidins in sainfoin. A combination of increased use of industrially produced nitrogen fertilizer, issues with establishment and productivity in the first year and more reliable alternatives, such as red clover led to a decline in the use of sainfoin since the middle of the last century. In recent years there has been a resurgence of interest in sainfoin due to its potential beneficial nutraceutical and environmental attributes. However, genomic resources are scarce, thus hampering progress in genetic analysis and improvement. To address this we have used next generation RNA sequencing technology to obtain the first transcriptome of sainfoin. We used the library to identify gene-based simple sequence repeats (SSRs) and potential single nucleotide polymorphisms (SNPs). One genotype from each of five sainfoin accessions was sequenced. Paired-end (PE) sequences were generated from cDNA libraries of RNA extracted from 7 day old seedlings. A combined assembly of 92,772 transcripts was produced de novo using the Trinity programme. About 18,000 transcripts were annotated with at least one GO (gene ontology) term. A total of 63 transcripts were annotated as involved in the tannin biosynthesis pathway. We identified 3786 potential SSRs. SNPs were identified by mapping the reads of the individual assemblies against the combined assembly. After stringent filtering a total of 77,000 putative SNPs were identified. A phylogenetic analysis of single copy number genes showed that sainfoin was most closely related to red clover and Medicago truncatula, while Lotus japonicus, bean and soybean are more distant relatives. This work describes the first transcriptome assembly in sainfoin. The 92 K transcripts provide a rich source of SNP and SSR polymorphisms for future use in genetic studies of this crop. Annotation of genes involved in the condensed tannin biosynthesis pathway has provided the basis for further studies of the genetic control of this important trait in sainfoin.

Twitter Demographics

The data shown below were collected from the profiles of 9 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 37 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 5%
Unknown 35 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 24%
Student > Doctoral Student 5 14%
Researcher 5 14%
Student > Master 3 8%
Student > Postgraduate 3 8%
Other 5 14%
Unknown 7 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 21 57%
Biochemistry, Genetics and Molecular Biology 5 14%
Computer Science 2 5%
Unspecified 1 3%
Engineering 1 3%
Other 0 0%
Unknown 7 19%

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 28 September 2016.
All research outputs
#4,173,566
of 15,918,484 outputs
Outputs from BMC Genomics
#2,045
of 8,858 outputs
Outputs of similar age
#78,525
of 270,822 outputs
Outputs of similar age from BMC Genomics
#4
of 19 outputs
Altmetric has tracked 15,918,484 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 8,858 research outputs from this source. They receive a mean Attention Score of 4.3. This one has done well, scoring higher than 76% 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 270,822 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 70% of its contemporaries.
We're also able to compare this research output to 19 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 73% of its contemporaries.