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Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates

Overview of attention for article published in PLOS ONE, October 2015
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (63rd percentile)
  • Above-average Attention Score compared to outputs of the same age and source (60th percentile)

Mentioned by

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2 tweeters
reddit
1 Redditor

Citations

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28 Dimensions

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38 Mendeley
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Title
Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates
Published in
PLOS ONE, October 2015
DOI 10.1371/journal.pone.0140274
Pubmed ID
Authors

Senanu M. Spring-Pearson, Joshua K. Stone, Adina Doyle, Christopher J. Allender, Richard T. Okinaka, Mark Mayo, Stacey M. Broomall, Jessica M. Hill, Mark A. Karavis, Kyle S. Hubbard, Joseph M. Insalaco, Lauren A. McNew, C. Nicole Rosenzweig, Henry S. Gibbons, Bart J. Currie, David M. Wagner, Paul Keim, Apichai Tuanyok

Abstract

The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is 'open', with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.

Twitter Demographics

The data shown below were collected from the profiles of 2 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 38 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 38 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 10 26%
Researcher 7 18%
Student > Doctoral Student 5 13%
Student > Master 4 11%
Student > Bachelor 2 5%
Other 5 13%
Unknown 5 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 13 34%
Biochemistry, Genetics and Molecular Biology 10 26%
Immunology and Microbiology 3 8%
Veterinary Science and Veterinary Medicine 1 3%
Pharmacology, Toxicology and Pharmaceutical Science 1 3%
Other 5 13%
Unknown 5 13%

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 18 June 2016.
All research outputs
#3,267,245
of 7,912,542 outputs
Outputs from PLOS ONE
#44,090
of 111,211 outputs
Outputs of similar age
#85,812
of 242,909 outputs
Outputs of similar age from PLOS ONE
#2,094
of 5,651 outputs
Altmetric has tracked 7,912,542 research outputs across all sources so far. This one has received more attention than most of these and is in the 58th percentile.
So far Altmetric has tracked 111,211 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 10.3. This one has gotten more attention than average, scoring higher than 58% 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 242,909 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 63% of its contemporaries.
We're also able to compare this research output to 5,651 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 60% of its contemporaries.