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Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica

Overview of attention for article published in BMC Genomics, August 2015
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Title
Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica
Published in
BMC Genomics, August 2015
DOI 10.1186/s12864-015-1758-z
Pubmed ID
Authors

Konstantia Gkarmiri, Roger D. Finlay, Sadhna Alström, Elizabeth Thomas, Marc A. Cubeta, Nils Högberg

Abstract

Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq. Approximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10 % of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log2 fold-change > 3 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation. This RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 101 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Japan 1 <1%
Canada 1 <1%
Unknown 99 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 27 27%
Student > Master 17 17%
Researcher 13 13%
Student > Doctoral Student 9 9%
Student > Bachelor 8 8%
Other 11 11%
Unknown 16 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 54 53%
Biochemistry, Genetics and Molecular Biology 18 18%
Environmental Science 3 3%
Computer Science 2 2%
Engineering 2 2%
Other 7 7%
Unknown 15 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 25 August 2015.
All research outputs
#10,647,130
of 16,638,522 outputs
Outputs from BMC Genomics
#5,614
of 9,107 outputs
Outputs of similar age
#131,747
of 241,614 outputs
Outputs of similar age from BMC Genomics
#1
of 1 outputs
Altmetric has tracked 16,638,522 research outputs across all sources so far. This one is in the 23rd percentile – i.e., 23% of other outputs scored the same or lower than it.
So far Altmetric has tracked 9,107 research outputs from this source. They receive a mean Attention Score of 4.3. This one is in the 30th percentile – i.e., 30% of its peers scored the same or lower than it.
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