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Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome

Overview of attention for article published in BMC Genomics, November 2015
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Title
Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome
Published in
BMC Genomics, November 2015
DOI 10.1186/s12864-015-2190-0
Pubmed ID
Authors

Brice Roux, Stéphanie Bolot, Endrick Guy, Nicolas Denancé, Martine Lautier, Marie-Françoise Jardinaud, Marion Fischer-Le Saux, Perrine Portier, Marie-Agnès Jacques, Lionel Gagnevin, Olivier Pruvost, Emmanuelle Lauber, Matthieu Arlat, Sébastien Carrère, Ralf Koebnik, Laurent D. Noël

Abstract

The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani). In this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins. This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.

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The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 117 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
France 3 3%
Germany 1 <1%
Portugal 1 <1%
Unknown 112 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 24 21%
Researcher 22 19%
Student > Master 13 11%
Student > Doctoral Student 8 7%
Student > Bachelor 8 7%
Other 15 13%
Unknown 27 23%
Readers by discipline Count As %
Agricultural and Biological Sciences 52 44%
Biochemistry, Genetics and Molecular Biology 25 21%
Unspecified 2 2%
Computer Science 2 2%
Immunology and Microbiology 2 2%
Other 5 4%
Unknown 29 25%
Attention Score in Context

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 23 November 2015.
All research outputs
#15,350,522
of 22,833,393 outputs
Outputs from BMC Genomics
#6,694
of 10,655 outputs
Outputs of similar age
#226,065
of 386,425 outputs
Outputs of similar age from BMC Genomics
#286
of 388 outputs
Altmetric has tracked 22,833,393 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 10,655 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 29th percentile – i.e., 29% 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 386,425 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 32nd percentile – i.e., 32% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 388 others from the same source and published within six weeks on either side of this one. This one is in the 20th percentile – i.e., 20% of its contemporaries scored the same or lower than it.