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Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola

Overview of attention for article published in BMC Microbiology, October 2015
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  • Above-average Attention Score compared to outputs of the same age (60th percentile)
  • Good Attention Score compared to outputs of the same age and source (78th percentile)

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5 tweeters

Citations

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12 Dimensions

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38 Mendeley
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Title
Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola
Published in
BMC Microbiology, October 2015
DOI 10.1186/s12866-015-0562-x
Pubmed ID
Authors

Xiang-Na Niu, Zhi-Qiong Wei, Hai-Fan Zou, Gui-Gang Xie, Feng Wu, Kang-Jia Li, Wei Jiang, Ji-Liang Tang, Yong-Qiang He

Abstract

Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of rice bacterial leaf streak (BLS). To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid. The plasmid DNA was extracted from Xoc strain GX01 by alkaline lysis and digested with restriction enzymes. The cloned and subcloned DNA fragments in pUC19 were sequenced by Sanger sequencing. Sequences were assembled by using Sequencher software. Gaps were closed by primer walking and sequencing, and multi-PCRs were conducted through the whole plasmid sequence for verification. BLAST, phylogenetic analysis and dinucleotide calculation were performed for gene annotation and DNA structure analysis. Transformation, transconjugation and stress tolerance tests were carried out for plasmid function assays. The indigenous plasmid from Xoc strain GX01, designated pXOCgx01, is 53,206-bp long and has been annotated to possess 64 open reading frames (ORFs), including genes encoding type IV secretion system, heavy metal exporter, plasmid stability factors, and DNA mobile factors, i.e., the Tn3-like transposon. Bioinformatics analysis showed that pXOCgx01 has a mosaic structure containing different genome contexts with distinct genomic heterogeneities. Phylogenetic analysis indicated that the closest relative of pXOCgx01 is pXAC64 from Xanthomonas axonopodis pv. citri str. 306. It was estimated that there are four copies of pXOCgx01 per cell of Xoc GX01 by PCR assay and the calculation of whole genome shotgun sequencing data. We demonstrate that pXOCgx01 is a self-transmissible plasmid and can replicate in some Xanthomonas spp. strains, but not in Escherichia coli DH5α. It could significantly enhance the tolerance of Xanthomonas oryzae pv. oryzae PXO99(A) to the stresses of heavy metal ions. The plasmid survey indicated that nine out of 257 Xoc Chinese isolates contain plasmids. pXOCgx01 is the first report of indigenous plasmid from Xanthomonas oryzae pv. oryzicola, and the first completely sequenced plasmid from Xanthomonas oryzae species. It is a self-transmissible plasmid and has a mosaic structure, containing genes for macromolecule secretion, heavy metal exportation, and DNA mobile factors, especially the Tn3-like transposon which may provide transposition function for mobile insertion cassette and play a major role in the spread of pathogenicity determinants. The results will be helpful to elucidate the biological significance of this cryptic plasmid and the adaptive evolution of Xoc.

Twitter Demographics

The data shown below were collected from the profiles of 5 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 %
France 2 5%
Unknown 36 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 11 29%
Researcher 6 16%
Student > Master 5 13%
Student > Doctoral Student 2 5%
Student > Bachelor 2 5%
Other 2 5%
Unknown 10 26%
Readers by discipline Count As %
Agricultural and Biological Sciences 15 39%
Biochemistry, Genetics and Molecular Biology 4 11%
Engineering 2 5%
Economics, Econometrics and Finance 1 3%
Sports and Recreations 1 3%
Other 3 8%
Unknown 12 32%

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 30 June 2016.
All research outputs
#3,392,998
of 7,971,101 outputs
Outputs from BMC Microbiology
#484
of 1,339 outputs
Outputs of similar age
#90,837
of 243,593 outputs
Outputs of similar age from BMC Microbiology
#17
of 85 outputs
Altmetric has tracked 7,971,101 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 1,339 research outputs from this source. They receive a mean Attention Score of 3.0. This one has gotten more attention than average, scoring higher than 61% 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 243,593 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 60% of its contemporaries.
We're also able to compare this research output to 85 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 78% of its contemporaries.