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The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh

Overview of attention for article published in BMC Genomics, October 2015
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (62nd percentile)
  • Above-average Attention Score compared to outputs of the same age and source (57th percentile)

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4 tweeters

Citations

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15 Dimensions

Readers on

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46 Mendeley
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1 CiteULike
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Title
The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh
Published in
BMC Genomics, October 2015
DOI 10.1186/s12864-015-2096-x
Pubmed ID
Authors

James Boocock, David Chagné, Tony R. Merriman, Michael A. Black

Abstract

Copy number variation (CNV) is a common feature of eukaryotic genomes, and a growing body of evidence suggests that genes affected by CNV are enriched in processes that are associated with environmental responses. Here we use next generation sequence (NGS) data to detect copy-number variable regions (CNVRs) within the Malus x domestica genome, as well as to examine their distribution and impact. CNVRs were detected using NGS data derived from 30 accessions of M. x domestica analyzed using the read-depth method, as implemented in the CNVrd2 software. To improve the reliability of our results, we developed a quality control and analysis procedure that involved checking for organelle DNA, not repeat masking, and the determination of CNVR identity using a permutation testing procedure. Overall, we identified 876 CNVRs, which spanned 3.5 % of the apple genome. To verify that detected CNVRs were not artifacts, we analyzed the B- allele-frequencies (BAF) within a single nucleotide polymorphism (SNP) array dataset derived from a screening of 185 individual apple accessions and found the CNVRs were enriched for SNPs having aberrant BAFs (P < 1e-13, Fisher's Exact test). Putative CNVRs overlapped 845 gene models and were enriched for resistance (R) gene models (P < 1e-22, Fisher's exact test). Of note was a cluster of resistance gene models on chromosome 2 near a region containing multiple major gene loci conferring resistance to apple scab. We present the first analysis and catalogue of CNVRs in the M. x domestica genome. The enrichment of the CNVRs with R gene models and their overlap with gene loci of agricultural significance draw attention to a form of unexplored genetic variation in apple. This research will underpin further investigation of the role that CNV plays within the apple genome.

Twitter Demographics

The data shown below were collected from the profiles of 4 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 46 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 2%
France 1 2%
Unknown 44 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 12 26%
Researcher 9 20%
Student > Master 6 13%
Student > Bachelor 5 11%
Professor > Associate Professor 2 4%
Other 3 7%
Unknown 9 20%
Readers by discipline Count As %
Agricultural and Biological Sciences 22 48%
Biochemistry, Genetics and Molecular Biology 8 17%
Engineering 2 4%
Nursing and Health Professions 1 2%
Medicine and Dentistry 1 2%
Other 1 2%
Unknown 11 24%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 01 April 2019.
All research outputs
#7,526,775
of 14,574,683 outputs
Outputs from BMC Genomics
#3,447
of 8,480 outputs
Outputs of similar age
#104,989
of 284,791 outputs
Outputs of similar age from BMC Genomics
#399
of 997 outputs
Altmetric has tracked 14,574,683 research outputs across all sources so far. This one is in the 47th percentile – i.e., 47% of other outputs scored the same or lower than it.
So far Altmetric has tracked 8,480 research outputs from this source. They receive a mean Attention Score of 4.2. This one has gotten more attention than average, scoring higher than 57% 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 284,791 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 62% of its contemporaries.
We're also able to compare this research output to 997 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 57% of its contemporaries.