GEO DataSets

(Submitter supplied) Convergent microbial biocatalysis has emerged as a promising approach for the conversion of lignin side-streams into value-added chemicals in recent decades. However, the current knowledge of metabolic pathways directing the bioconversion of lignin-related aromatics is still limited to a few microbial species and unavailable for some of these compounds. Thus, the aim of this study was to identify the genes involved in the bioconversion of aromatic compounds in Xanthomonas citri subsp. more...

Organism:

Xanthomonas citri subsp. citri 306

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34065

38 Samples

Download data: XLSX

(Submitter supplied) To investigate the bacterial functions involved in seed contamination during their formation, we sequenced bacterial mRNA at 24, 35 and 42 days after pollination (DAP). Gene expression was compared between the different stages.

Organism:

Xanthomonas citri pv. fuscans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33255

17 Samples

Download data: SF

(Submitter supplied) To gain insight on the role of ROS pathway on the modulation of the cooperative behavior of a potentiall pathogenic leaf commensal Xanthomonas L148, in planta bacterial transcriptome landscape was profiled.

Organism:

Xanthomonas sp. Leaf148

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33208

16 Samples

Download data: CSV

(Submitter supplied) CRISPR-Cas systems store fragments of invader DNA as spacers to recognize and clear those same invaders in the future. Spacers can also be acquired from the host’s genomic DNA, leading to lethal self-targeting. While self-targeting can be circumvented through different mechanisms, natural examples remain poorly explored. Here, we investigate extensive self-targeting by two CRISPR-Cas systems encoding an astonishing 24 self-targeting spacers in the plant pathogen Xanthomonas albilineans. more...

Organism:

Xanthomonas albilineans

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL33333

4 Samples

Download data: BED, TXT

(Submitter supplied) RNAseq analysis of Xanthomonas citri pv. glycines 12-2 wild-type, phoB and phoU mutants under phosphate limited condition

Organism:

Xanthomonas citri pv. glycines

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31233

9 Samples

Download data: TXT

(Submitter supplied) To gain an understanding of the regulatory role of PilG and PilH in Xcc a set of global gene expression profiles,we performed transcriptome analysis.Transcriptome analyses that showed PilG and PilH regulating many genes involved chemotaxis and flagellar biosynthesis.Taken this data together it is clear the impact of PilG and PilH on the expression of specific genes at the transcriptional level accounts for the phenotypes seen in the ΔpilG and ΔpilH strains.

Organism:

Xanthomonas campestris pv. campestris str. 8004

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25598

6 Samples

Download data: XLSX

(Submitter supplied) Xanthomonas oryzae pv. oryzae (Xoo) causes the bacterial leaf blight of rice, which leads to as much as 50% yield losses. To understand the landscape of virulence mechanisms, we constructed in planta transcriptional profiling of Xoo KACC10331 using RNA-seq. Three in planta transcriptome of Xoo KACC10331 derived from infected rice leafs were compared to three in vitro data from rich media. To obtain differentially expressed genes, we used the DEGseq package with MA-plot-based method in the R statistical environment and identified 2,094 transcripts that were significantly altered.

Organism:

Xanthomonas oryzae pv. oryzae KACC 10331

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22653

6 Samples

Download data: TXT

(Submitter supplied) We performed a transcriptomic analysis of the necrotrophic bacteria Xanthomonas campestris pv. campestris exposed to two different isothiocyanates (allyl-isothiocyanate and indol-3-carbinol), searching for mechanisms of adaptation and detoxification of these chemicals.

Organism:

Xanthomonas campestris pv. campestris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24162

6 Samples

Download data: TXT

(Submitter supplied) The aim of the study was to understand the differences in the transcriptome of Xanthomonas oryzae pv. oryzae BXO43 vs it's XopQ mutatnt that is virulence deficient. Our study indicates a key role of XopQ in regulating biofilm to planktonic lifestyle switch in Xoo.

Organism:

Xanthomonas oryzae pv. oryzae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30323

6 Samples

Download data: TXT

(Submitter supplied) Arsenic (As) is highly toxic element to all forms of life and is a major environmental contaminant. Understanding acquisition, detoxification, and adaptation mechanisms in bacteria that are associated with host in arsenic-rich conditions can provide novel insights into dynamics of host-microbe-microenvironment interactions. In the present study, we have investigated an arsenic resistance mechanism acquired during the evolution of a particular lineage in the population of Xanthomonas oryzae pv. more...

Organism:

Xanthomonas oryzae pv. oryzae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29508

8 Samples

Download data: TXT

(Submitter supplied) Xyloglucans are highly substituted polysaccharides found in the primary cell walls of all vascular plants, acting as a first barrier against pathogens. Herein, we revealed that the diverse and economically relevant Xanthomonas phytopathogens are endowed with an enzymatic system targeting xyloglucans. Furthermore, we demonstrate that the products generated by this system elicit the expression of multiple virulence factors including the type III secretion system, a membrane-embedded machinery to deliver effector proteins into the host cells. Together, these findings illuminate the intricate enzymatic apparatus employed by Xanthomonas to break down xyloglucans and connect this system to the pathogenesis through activating the expression of key virulence factors. 

Organism:

Xanthomonas citri pv. citri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29238

10 Samples

Download data: XLS

(Submitter supplied) Host-pathogen interactions, in particular during the early stage of infection, are important for the fate of boththe invading pathogen and host. In pathogens, these interactions activate diverse pahogenic signals to cause disease in the host and evade the inevitably activated immune responses of the infected host. In this study, we used in vitro assay system and RNA-seq to analyze the time-resolved genome-wide gene expressions of Xoo evoked by the interactions with rice leaf extracts. more...

Organism:

Xanthomonas oryzae pv. oryzae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28880

6 Samples

Download data: CSV

(Submitter supplied) The zig-zag model of host-pathogen interaction describes the relative strength of defense response across a spectrum of pathogen-induced plant phenotypes. A stronger defense response results in increased resistance. Here, we investigate the strength of pathogen virulence during disease and place these findings in the context of the zig-zag model. Xanthomonas vasicola pv. holcicola (Xvh) causes sorghum bacterial leaf streak. more...

Organism:

Xanthomonas vasicola; Sorghum bicolor

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27913 GPL27914 GPL27912

21 Samples

Download data: TXT

(Submitter supplied) In this study, using a novel dual RNA-seq approach we monitored the global transcriptional changes in real time of Xanthomonas oryzae pv. oryzicola and rice during infection. Our transcriptome maps of Xoc strains infecting rice provide mechanistic insights into the bacterias adaptive responses to the host niche, with modulation of central metabolism being an important signature. The study also uncovers that infected rice responds by substantial alteration of the cell wall, stress and structural proteins.

Organism:

Xanthomonas oryzae pv. oryzicola; Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL26222 GPL13160

5 Samples

Download data: TXT

(Submitter supplied) ChIP-seq database identifies genes with promoter regions bound by VgrR in X. campestris pv. campestris grown under osmostress conditions

Organism:

Xanthomonas campestris pv. campestris str. 8004

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25598

2 Samples

Download data: WIG

(Submitter supplied) By analyzing the transcriptome of WT/ΔpcrR/ΔpcrK strains in the presence of 2iP and comparing gene expression level between them, we report genes with different expression levels between WT and ΔpcrR/ΔpcrK strains in the presence of plant cytokinin 2iP.

Organism:

Xanthomonas campestris pv. campestris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24162

3 Samples

Download data: TXT

(Submitter supplied) It is well known that bacteria often exist in naturally formed multispecies biofilms. Within these biofilms, interspecies interactions seem to play an important role in ecological processes. Little is known about the effects of interspecies interactions on gene expression in these multispecies biofilms. This study presents a comparative gene expression analysis of the Xanthomonas retroflexus transcriptome when grown in a single-species biofilm and in dual- and four-species consortia with Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus. more...

Organism:

Stenotrophomonas rhizophila; Paenibacillus amylolyticus; Microbacterium oxydans; Xanthomonas retroflexus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

17 Samples

Download data: FASTA, TXT

(Submitter supplied) In this study, simultaneous gene expression, of both the host and pathogen, in the incompatible interaction between rice immune line H471 and Xoo race PXO99A with strong virulence, and in compatible ones between H471’s parents and PXO99A, were analyzed in the same infected leaf blades at 1 day and 3 days post-inoculation (dpi) using the RNA-Seq technique.This study provides the first insights into the differantial gene expression profiles of both organisms interacting simultaneously in the incompatible and compatible interactions between Xanthomonas oryzae pv. more...

Organism:

Oryza sativa; Xanthomonas oryzae pv. oryzae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18696

6 Samples

Download data: TXT

(Submitter supplied) Host-pathogen interactions, in particular during the early stages of infection, are important for the fate of both the invading pathogen and host. In pathogens, these interactions activate diverse pathogenic signals to cause disease in the host and evade the inevitably activated immune responses of the infected host. In this study, we used in vitro assay system and RNA-seq to analyze the time-resolved genome-wide gene expressions of Xanthomonas oryzae pv. more...

Organism:

Xanthomonas oryzae pv. oryzae KACC 10331

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19216

14 Samples

Download data: TXT

(Submitter supplied) An attempt has been made to investigate gene expression patterns of three Xoo strains in XOM2, PXO99 (P6) and PXO86 (P2) from Phillipines, and GD1358 (C5) from China, which exhibited different virulence in 30 rice varieties, with putative virulence factors using deep sequencing. In total, 4759 transcripts were identified in this study, and 1151 and 3076 genes were differentially expressed when P6 compared with P2 and P6 compared with C5, respectively. more...

Organism:

Xanthomonas oryzae pv. oryzae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16609

3 Samples

Download data: XLS