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Pectobacterium atrosepticum

ABSTRACT: Causative agent for blackleg and soft rot disease in potatoes

PROVIDER: PRJNA35215 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ALIV01.dat.gz	Other
	ALIV01.fasta.gz	Fasta.gz
	ALIV01.master.dat	Other
	AODV01.dat.gz	Other

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Pectobacterium atrosepticum SCRI1043

Project description:Causative agent of soft rot and blackleg of potato

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Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots

Project description:Pectobacterium atrosepticum (Pba) is a gram-negative bacterium which causes blackleg and tuber soft rot on potato. To investigate the molecular processes and responses involved in Pba-host (potato) and Pba-non-host (radish) interactions, under laboratory conditions, we used total RNA-sequencing to measure the gene expression patterns from all three species. Samples from infected and non-infected plant roots were collected after fourteen days of inoculation with Pba SCRI_1039 and subjected to total RNA-sequencing on an Illumina sequencing platform.

2024-01-17 | E-MTAB-13434 | biostudies-arrayexpress

Pectobacterium parmentieri WPP163

Project description:Causal agent of soft rot disease in plants

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Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum

Project description:Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within the adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress response. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 63 sRNAs were differentially expressed with 57 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST (e-value < 0.001) showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. A large number of these sRNAs is starvation-induced, suggesting their role in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens.

2016-01-26 | GSE68547 | GEO

Dickeya chrysanthemi Ech1591

Project description:Causal agent of onion soft rot

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Streptomyces scabiei

Project description:Causative disease of scab disease of potatoes

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Transcriptome analysis of Pectobacterium atrosepticum

Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of Pectobacterium upon treatment of polyphenol compound.

2022-10-05 | GSE196675 | GEO

Genome Sequence of Pectobacterium atrosepticum Strain 21A.

Project description:We report the annotated genome sequence of the enterobacterial plant pathogen Pectobacterium atrosepticum strain 21A, isolated in Belarus from potato stem with blackleg symptoms.

| S-EPMC4172277 | biostudies-literature

Novel N4-Like Bacteriophages of Pectobacterium atrosepticum.

Project description:Pectobacterium atrosepticum is an economically important phytopathogen that is responsible for potato blackleg and soft rot, and for which current control strategies are limited. In this study, stem samples of potato crops exhibiting blackleg were taken from three farms in Co. Cork, Ireland, and they were found to be infected with P. atrosepticum. Three closely related bacteriophages (phages) that are specific to this phytopathogen were isolated and characterized, namely vB_PatP_CB1, vB_PatP_CB3, and vB_PatP_CB4 (abbreviated as CB1, CB3, and CB4). Both CB1 and CB3 were determined to infect 12 strains and CB4 10 strains of the 19 strains of P. atrosepticum tested. Morphology, latent periods, burst sizes, and their stability at various temperatures and pHs were also examined. Genome sequencing of the three phages revealed that they shared a minimum nucleotide identity of 93% with each other. Their genomes exhibited an Enquartavirinae genome organization, possessing several conserved proteins that were associated with phages of this group, like the type species Escherichia virus N4. Tandem electrospray ionization-mass spectrometry (ESI-MS/MS) allowed for the identification of ten structural proteins that form the virion of CB1, six that are conserved in phage N4. Biocontrol experiments demonstrated that the phages suppress soft rot formation upon co-inoculation with P. atrosepticum on whole tubers. The results of this study indicate that CB1 related phages could be good candidates for phage-based control.

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Project description:The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant losses in crop yields worldwide. While genetic resistance has been used to mitigate the disease, little information about the genes and gene regulatory networks underlying blackleg resistance is currently available. High-throughput RNA sequencing and rigorous bioinformatics approaches revealed dynamic changes in the host transcriptome and identified plant defense pathways specific to the host-pathogen incompatible LepR1-AvrLepR1 interaction.

2016-04-01 | GSE77723 | GEO

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