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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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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

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Mendeley readers

The data shown below were compiled from readership statistics for 41 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 41 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 10 24%
Researcher 7 17%
Student > Doctoral Student 5 12%
Student > Master 4 10%
Student > Bachelor 2 5%
Other 7 17%
Unknown 6 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 13 32%
Biochemistry, Genetics and Molecular Biology 10 24%
Immunology and Microbiology 3 7%
Unspecified 1 2%
Veterinary Science and Veterinary Medicine 1 2%
Other 7 17%
Unknown 6 15%

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 18 June 2016.
All research outputs
#13,721,098
of 20,585,116 outputs
Outputs from PLOS ONE
#115,332
of 177,676 outputs
Outputs of similar age
#173,135
of 299,765 outputs
Outputs of similar age from PLOS ONE
#3,344
of 5,398 outputs
Altmetric has tracked 20,585,116 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 177,676 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 14.4. This one is in the 26th percentile – i.e., 26% 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 299,765 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 33rd percentile – i.e., 33% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 5,398 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.