Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Time-resolved genome-wide pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) via RNA-Seq

ABSTRACT: 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. RNA-seq analysis was carried out with samples of 3 different time points within 2 hours

ORGANISM(S): Xanthomonas oryzae pv. oryzae

PROVIDER: GSE154542 | GEO | 2020/09/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Time-resolved genome-wide pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) via RNA-Seq

Project description: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. oryzae (Xoo) evoked by the interactions with rice leaf extracts. RNA-seq analysis was carried out with samples of 7 different time points within 1 h. The RNA-seq data were verified by qRT-PCR. The in vitro system successfully initiated the pathogenic signals in Xoo cell culture. Many pathogenicity-related genes were expressed within 15 min. The hrpG gene was transcribed at maximum level within 10 min, and hrpX gene expression reached maximum level in 15 min. Chemotaxis and flagellar biosynthesis-related genes and cyclic-di-GMP synthesizing genes having GGDEF motif, were down-regulated until 10 min and after then up-regulated. Genes related to iron uptake and two component systems of phoB-phoR, phoP-phoQ, and pmrA-pmrB were up-regulated before 5 min. Data of multiple time points enabled non-linear regression fit of the time-resolved expression data, with which we newly developed the continuous time-resolved heat map to help the comparison of gene expression profiles. Essentiality of the transcriptionally up-regulated genes was also analyzed by the pathogenicity assay using the Xoo knockout strains, which showed not necessarily all the up-regulated genes were required for pathogenicity. the time-dependent, 0, 5, 10, 15, 30, 45, and 60 min, transcriptome analysis of genome-wide Xanthomonas oryzae pv. oryzae genes from the pathogenic interactions with RLX via RNA-Seq

2015-09-22 | E-GEOD-61607 | biostudies-arrayexpress

Time-resolved genome-wide pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) via RNA-Seq

2015-09-22 | GSE61607 | GEO

Gene expression changes induced in Rice (Oryza sativa) leaves by lipopolysaccharide (LPS) extracted from Xanthomonas oryzae pv. oryzae (Xoo) strain BXO43

Project description:Lipopolysaccharide is a Microbe Associated Molecular Pattern (MAMP) that is known to induce defense responses in plants. We have shown that treatment of rice leaves with Xoo LPS induces callose deposition, reactive oxygen production and enhances resistance against subsequent infection by the pathogen. We have performed transcriptional profiling of rice leaves that are treated with Xoo LPS to identify differentially expressed genes.

2015-06-30 | GSE61832 | GEO

Gene expression changes induced in Rice (Oryza sativa) leaves by lipopolysaccharide (LPS) extracted from Xanthomonas oryzae pv. oryzae (Xoo) strain BXO43

2015-06-30 | E-GEOD-61832 | biostudies-arrayexpress

Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice [datatset 1]

Project description:we emphatically monitored the responsive changes of genes targeted by rice miRNAs miRNAs at 0, 8, 24 hours across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by degradome technology.These findings provide new insights into the complex roles of characteristic miRNAs in rice-Xoo interactions.

2020-03-16 | GSE141775 | GEO

Transcriptome Profiling of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola on two different medias

Project description:Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) are important bacterial pathogens of the worldwide staple and grass model, rice. Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice throughout the world. Xoc colonizes the parenchyma tissue to cause bacterial leaf steak, a disease of emerging importance. We have designed oligonucleotide probes (50-70-mers) represented 2,858 Xoo genes and 1,816 Xoc genes annotated by The Institute for Genomic Research (TIGR). To validate the Xo arrays, self-hybridization samples and tests of the non-specific hybridization using randomly spotted oligonucleotides corresponding to the hygromycin phosphotransferase gene (hph), and blank spot and of the correlation coefficient between biological replicates as well as between duplicate spots revealed that the data generated from our oligo array were highly reliable and consistent. To demonstrate application of Xo array, we performed expression profiling experiments on arrays hybridized with RNA of Xoo and Xoc grown in the two different nutrient-condition media. Several sets of genes involved in bacterial movement, chemotaxis, and hrp genes differentially express in response to different treatment. Due to comprehensive views of microarray study, extended biological events of plant-bacteria interaction was described. This publicly available microarray for Xanthomonas oryzae (Xo) is an enabling resource for a large and international community of scientists to better understand not only Xo biology but also many other Xanthomonas species that cause significant losses on crops. Keywords: Media condition response

2008-02-08 | GSE9640 | GEO

Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice [datatset 2]

Project description:we emphatically monitored the responsive changes of rice miRNAs at 0, 8, 24 hours across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by small RNA sequencing, and the genes targeted by miRNAs were also detected via degradome technology. These findings provide new insights into the complex roles of characteristic miRNAs and their targets in rice-Xoo interactions.

2020-03-16 | GSE141995 | GEO

Genomic analysis of bacteriophage Xoo-sp13 infecting Xanthomonas oryzae pv. oryzae.

Project description:Xanthomonas oryzae pv. oryzae is a bacterial pathogen that gives rise to diseases in rice all over the world. A bacteriophage infecting this bacterium was isolated from rice fields in China. Here, we report the complete genome sequence of this phage, which has a linear dsDNA genome of 309,023 bp and a G + C content of 42.43%. It contains 401 open reading frames and encodes 28 tRNAs. It belongs to the family Myoviridae and has a broad host range, making it a possible candidate for phage therapy.

| S-EPMC7970823 | biostudies-literature

Transcriptome analysis of rice ABA deficient mutant Osaba1-1 and wild-type before and 72h after Xanthomonas oryzae pv. oryzae (Xoo) infection

Project description:ABA deficient mutant Osaba1-1 exhibits great resistance to Xanthomonas oryzae pv. oryzae (Xoo) infection. To investigate gene expression profile changes at whole genome level between Osaba1-1 and wild-type (Nipponbare) rice during Xoo infection, we employed microarray expression profiling as a discovery platform.

2015-05-15 | GSE63337 | GEO

Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1

Project description:African Xanthomonas oryzae pv. oryzae strains seem most closely related to and share several genetic features with pathovar oryzicola despite causing symptoms of bacterial leaf blight. The ability of most Xanthomonas plant pathogenic bacteria to infect their host relies on the action of a specific family of type III effectors called the TAL effectors. These microbial transcription factors are injected into the plant and manipulate the host transcriptome upon binding to the promoters of plant genes. The genes whose induction is of benefit to the pathogen are called susceptibility genes. RNA profiling experiments in rice using the Malian Xoo strain MAI1 and in silico prediction of TAL effector binding sites were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor.

2018-03-31 | GSE108504 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data