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De novo assembly and characterization of Camelina sativatranscriptome by paired-end sequencing

Overview of attention for article published in BMC Genomics, March 2013
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Title
De novo assembly and characterization of Camelina sativatranscriptome by paired-end sequencing
Published in
BMC Genomics, March 2013
DOI 10.1186/1471-2164-14-146
Pubmed ID
Authors

Chao Liang, Xuan Liu, Siu-Ming Yiu, Boon Leong Lim

Abstract

BACKGROUND: Biofuels extracted from the seeds of Camelina sativa have recently been used successfully as environmentally friendly jet-fuel to reduce greenhouse gas emissions. Camelina sativa is genetically very close to Arabidopsis thaliana, and both are members of the Brassicaceae. Although public databases are currently available for some members of the Brassicaceae, such as A. thaliana, A. lyrata, Brassica napus, B. juncea and B. rapa, there are no public Expressed Sequence Tags (EST) or genomic data for Camelina sativa. In this study, a high-throughput, large-scale RNA sequencing (RNA-seq) of the Camelina sativa transcriptome was carried out to generate a database that will be useful for further functional analyses. RESULTS: Approximately 27 million clean "reads" filtered from raw reads by removal of adaptors, ambiguous reads and low-quality reads (2.42 gigabase pairs) were generated by Illumina paired-end RNA-seq technology. All of these clean reads were assembled de novo into 83,493 unigenes and 103,196 transcripts using SOAPdenovo and Trinity, respectively. The average length of the transcripts generated by Trinity was 697 bp (N50 = 976), which was longer than the average length of unigenes (319 bp, N50 = 346 bp). Nonetheless, the assembly generated by SOAPdenovo produced similar number of non-redundant hits (22,435) with that of Trinity (22,433) in BLASTN searches of the Arabidopsis thaliana CDS sequence database (TAIR). Four public databases, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Swiss-prot, NCBI non-redundant protein (NR), and the Cluster of Orthologous Groups (COG), were used for unigene annotation; 67,791 of 83,493 unigenes (81.2%) were finally annotated with gene descriptions or conserved protein domains that were mapped to 25,329 non-redundant protein sequences. We mapped 27,042 of 83,493 unigenes (32.4%) to 119 KEGG metabolic pathways. CONCLUSIONS: This is the first report of a transcriptome database for Camelina sativa, an environmentally important member of the Brassicaceae. We showed that C. savita is closely related to Arabidopsis spp. and more distantly related to Brassica spp. Although the majority of annotated genes had high sequence identity to those of A. thaliana, a substantial proportion of disease-resistance genes (NBS-encoding LRR genes) were instead more closely similar to the genes of other Brassicaceae; these genes included BrCN, BrCNL, BrNL, BrTN, BrTNL in B. rapa. As plant genomes are under long-term selection pressure from environmental stressors, conservation of these disease-resistance genes in C. sativa and B. rapa genomes implies that they are exposed to the threats from closely-related pathogens in their natural habitats.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 115 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 2%
Australia 2 2%
France 1 <1%
United Kingdom 1 <1%
Canada 1 <1%
Netherlands 1 <1%
Unknown 107 93%

Demographic breakdown

Readers by professional status Count As %
Researcher 29 25%
Student > Ph. D. Student 28 24%
Student > Master 15 13%
Student > Doctoral Student 6 5%
Professor 6 5%
Other 21 18%
Unknown 10 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 85 74%
Biochemistry, Genetics and Molecular Biology 11 10%
Computer Science 3 3%
Social Sciences 2 2%
Neuroscience 1 <1%
Other 1 <1%
Unknown 12 10%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 07 March 2013.
All research outputs
#9,479,913
of 12,378,406 outputs
Outputs from BMC Genomics
#5,221
of 7,251 outputs
Outputs of similar age
#94,589
of 144,168 outputs
Outputs of similar age from BMC Genomics
#123
of 185 outputs
Altmetric has tracked 12,378,406 research outputs across all sources so far. This one is in the 20th percentile – i.e., 20% 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 is in the 22nd percentile – i.e., 22% of its peers scored the same or lower than it.
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We're also able to compare this research output to 185 others from the same source and published within six weeks on either side of this one. This one is in the 29th percentile – i.e., 29% of its contemporaries scored the same or lower than it.