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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Phaseolus vulgaris; Xanthomonas citri pv. fuscans

Type:

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

4 related Platforms

53 Samples

Download data: BW, SF, TXT

(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) Some phytopathogens are outfitted with a broad and diverse repertoire of enzymatic systems that enable the breakdown and utilization of host polysaccharides as a source of carbon, energy, and stimuli. However, the functional assignment of these enzymatic systems and the influence of their products on modulating pathogen behavior during host colonization is yet poorly comprehended. In this study, we performed RNA-seq analyses to provide a comprehensive, genome-wide view of the transcriptional response of the model phytopathogen Xanthomonas citri pv. more...

Organism:

Xanthomonas citri pv. citri

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL29238

12 Samples

Download data: XLSX

(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) To further development of our gene expression approach to establish that XooBphP acts as the major determinant of pathogenic circadian clock, we have employed whole genome microarray expression profiling as a discovery plateform to identify genes with the potential to synchronize the diurnal cycle by XooBphP to circumvent the host circadian defence response.

Organism:

Xanthomonas oryzae pv. oryzae; Xanthomonas oryzae

Type:

Expression profiling by array

Platform:

GPL27852

6 Samples

Download data: TXT

(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:

Sorghum bicolor; Xanthomonas vasicola

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) Transcriptional profiling of low-iron stimulon and XibR influenced regulon using wild-type Xcc 8004 and xibR mutant grown under iron-replete and iron-deplete conditions. Trancriptional analysis under iron-deplete condition, mimicking in planta environment, provides greater insights into expression pattern of several virulence-associated functions under low-iron. A genetic screen sggested the involvement of XibR (Xanthomonas iron binding regulator) in iron-uptake and metabolism. more...

Organism:

Xanthomonas campestris pv. campestris str. 8004; Xanthomonas campestris

Type:

Expression profiling by array

Platform:

GPL22612

8 Samples

Download data: TXT