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Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms

Overview of attention for article published in Plant Biotechnology Journal, June 2013
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Title
Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms
Published in
Plant Biotechnology Journal, June 2013
DOI 10.1111/pbi.12081
Pubmed ID
Authors

Tyson Koepke, Scott Schaeffer, Artemus Harper, Federico Dicenta, Mark Edwards, Robert J. Henry, Birger L. Møller, Lee Meisel, Nnadozie Oraguzie, Herman Silva, Raquel Sánchez‐Pérez, Amit Dhingra

Abstract

Prunus is an economically important genus with a wide range of physiological and biological variability. Using the peach genome as a reference, sequencing reads from four almond accessions and one sweet cherry cultivar were used for comparative analysis of these three Prunus species. Reference mapping enabled the identification of many biological relevant polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall scaffold coverage, we identified many potentially interesting regions including hundreds of small scaffolds with no coverage from any individual. Non-sense mutations account for about 70 000 of the 13 million identified single nucleotide polymorphisms (SNPs). Blast2GO analyses on these non-sense SNPs revealed several interesting results. First, non-sense SNPs were not evenly distributed across all gene ontology terms. Specifically, in comparison with peach, sweet cherry is found to have non-sense SNPs in two 1-aminocyclopropane-1-carboxylate synthase (ACS) genes and two 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the nonclimacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were identified by comparing sweet and bitter almond sequences. To the best of our knowledge, this is the first report in plants of non-sense SNP abundance in a genus being linked to specific GO terms.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 42 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Chile 1 2%
Netherlands 1 2%
Saudi Arabia 1 2%
Unknown 39 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 21%
Researcher 8 19%
Other 4 10%
Professor > Associate Professor 4 10%
Student > Bachelor 2 5%
Other 7 17%
Unknown 8 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 25 60%
Biochemistry, Genetics and Molecular Biology 5 12%
Business, Management and Accounting 1 2%
Pharmacology, Toxicology and Pharmaceutical Science 1 2%
Computer Science 1 2%
Other 1 2%
Unknown 8 19%
Attention Score in Context

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 16 June 2013.
All research outputs
#21,981,335
of 24,525,936 outputs
Outputs from Plant Biotechnology Journal
#2,025
of 2,151 outputs
Outputs of similar age
#177,514
of 201,191 outputs
Outputs of similar age from Plant Biotechnology Journal
#8
of 9 outputs
Altmetric has tracked 24,525,936 research outputs across all sources so far. This one is in the 1st percentile – i.e., 1% of other outputs scored the same or lower than it.
So far Altmetric has tracked 2,151 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 11.5. This one is in the 1st percentile – i.e., 1% 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 201,191 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 9 others from the same source and published within six weeks on either side of this one.