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X Demographics
Mendeley readers
Attention Score in Context
| Title |
Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content
|
|---|---|
| Published in |
Plant Biotechnology Journal, April 2018
|
| DOI | 10.1111/pbi.12912 |
| Pubmed ID | |
| Authors |
Hue T.M. Tran, Thiruvarangan Ramaraj, Agnelo Furtado, Leonard Slade Lee, Robert J. Henry |
| Abstract |
Arabica coffee (Coffea arabica) has a small gene pool limiting genetic improvement. Selection for caffeine content within this gene pool would be assisted by identification of the genes controlling this important trait. Sequencing of DNA bulks from 18 genotypes with extreme high- or low-caffeine content from a population of 232 genotypes was used to identify linked polymorphisms. To obtain a reference genome, a whole genome assembly of arabica coffee (variety K7) was achieved by sequencing using short read (Illumina) and long-read (PacBio) technology. Assembly was performed using a range of assembly tools resulting in 76 409 scaffolds with a scaffold N50 of 54 544 bp and a total scaffold length of 1448 Mb. Validation of the genome assembly using different tools showed high completeness of the genome. More than 99% of transcriptome sequences mapped to the C. arabica draft genome, and 89% of BUSCOs were present. The assembled genome annotated using AUGUSTUS yielded 99 829 gene models. Using the draft arabica genome as reference in mapping and variant calling allowed the detection of 1444 nonsynonymous single nucleotide polymorphisms (SNPs) associated with caffeine content. Based on Kyoto Encyclopaedia of Genes and Genomes pathway-based analysis, 65 caffeine-associated SNPs were discovered, among which 11 SNPs were associated with genes encoding enzymes involved in the conversion of substrates, which participate in the caffeine biosynthesis pathways. This analysis demonstrated the complex genetic control of this key trait in coffee. |
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.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 1 | 50% |
| Unknown | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 1 | 50% |
| Members of the public | 1 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 111 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 111 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 17 | 15% |
| Student > Master | 15 | 14% |
| Student > Ph. D. Student | 11 | 10% |
| Student > Bachelor | 8 | 7% |
| Student > Doctoral Student | 7 | 6% |
| Other | 20 | 18% |
| Unknown | 33 | 30% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 37 | 33% |
| Biochemistry, Genetics and Molecular Biology | 22 | 20% |
| Environmental Science | 4 | 4% |
| Computer Science | 4 | 4% |
| Economics, Econometrics and Finance | 2 | 2% |
| Other | 7 | 6% |
| Unknown | 35 | 32% |
Attention Score in Context
This research output has an Altmetric Attention Score of 4. 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 November 2019.
All research outputs
#6,494,717
of 23,031,582 outputs
Outputs from Plant Biotechnology Journal
#949
of 2,041 outputs
Outputs of similar age
#114,585
of 327,968 outputs
Outputs of similar age from Plant Biotechnology Journal
#25
of 50 outputs
Altmetric has tracked 23,031,582 research outputs across all sources so far. This one has received more attention than most of these and is in the 70th percentile.
So far Altmetric has tracked 2,041 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 11.2. This one has gotten more attention than average, scoring higher than 52% 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 327,968 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 64% of its contemporaries.
We're also able to compare this research output to 50 others from the same source and published within six weeks on either side of this one. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.