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Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

Overview of attention for article published in Frontiers in Microbiology, June 2017
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  • Good Attention Score compared to outputs of the same age (67th percentile)
  • Above-average Attention Score compared to outputs of the same age and source (56th percentile)

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Title
Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium
Published in
Frontiers in Microbiology, June 2017
DOI 10.3389/fmicb.2017.01204
Pubmed ID
Authors

Henrique Machado, Lone Gram

Abstract

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 61 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 61 100%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 10 16%
Student > Ph. D. Student 10 16%
Student > Master 10 16%
Researcher 7 11%
Student > Doctoral Student 6 10%
Other 7 11%
Unknown 11 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 26 43%
Biochemistry, Genetics and Molecular Biology 10 16%
Unspecified 5 8%
Immunology and Microbiology 5 8%
Environmental Science 2 3%
Other 3 5%
Unknown 10 16%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 06 February 2019.
All research outputs
#6,469,459
of 23,106,390 outputs
Outputs from Frontiers in Microbiology
#6,548
of 25,291 outputs
Outputs of similar age
#103,198
of 315,541 outputs
Outputs of similar age from Frontiers in Microbiology
#231
of 531 outputs
Altmetric has tracked 23,106,390 research outputs across all sources so far. This one has received more attention than most of these and is in the 71st percentile.
So far Altmetric has tracked 25,291 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.4. This one has gotten more attention than average, scoring higher than 73% 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 315,541 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 67% of its contemporaries.
We're also able to compare this research output to 531 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 56% of its contemporaries.