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Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes

Overview of attention for article published in BMC Biology, August 2014
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (61st percentile)

Mentioned by

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3 tweeters

Citations

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101 Dimensions

Readers on

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125 Mendeley
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1 CiteULike
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Title
Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes
Published in
BMC Biology, August 2014
DOI 10.1186/s12915-014-0066-4
Pubmed ID
Authors

Pere Puigbò, Alexander E Lobkovsky, David M Kristensen, Yuri I Wolf, Eugene V Koonin

Abstract

BackgroundGenomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer (HGT) and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of events across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species.ResultsWe performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically 7 and 20 times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction that is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about 10 fold more gene families than the typical genome in the group although some groups appear to have vast, ¿open¿ supergenomes.ConclusionsReconstruction of evolution in groups of closely related bacteria and archaea reveals extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

Twitter Demographics

The data shown below were collected from the profiles of 3 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 125 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 2%
United Kingdom 3 2%
Spain 2 2%
Netherlands 2 2%
Czechia 1 <1%
Sweden 1 <1%
Canada 1 <1%
Australia 1 <1%
Germany 1 <1%
Other 0 0%
Unknown 110 88%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 41 33%
Researcher 28 22%
Student > Bachelor 11 9%
Student > Master 10 8%
Student > Postgraduate 7 6%
Other 17 14%
Unknown 11 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 65 52%
Biochemistry, Genetics and Molecular Biology 21 17%
Computer Science 6 5%
Environmental Science 4 3%
Immunology and Microbiology 4 3%
Other 10 8%
Unknown 15 12%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 03 November 2014.
All research outputs
#1,919,887
of 4,507,652 outputs
Outputs from BMC Biology
#467
of 653 outputs
Outputs of similar age
#44,190
of 118,301 outputs
Outputs of similar age from BMC Biology
#25
of 38 outputs
Altmetric has tracked 4,507,652 research outputs across all sources so far. This one has received more attention than most of these and is in the 56th percentile.
So far Altmetric has tracked 653 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 11.2. 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 118,301 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 61% of its contemporaries.
We're also able to compare this research output to 38 others from the same source and published within six weeks on either side of this one. This one is in the 28th percentile – i.e., 28% of its contemporaries scored the same or lower than it.