Xanthomonas oryzae pv. oryzicola BLS256
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA16740 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR9418250.fastq.gz | Fastqsanger.gz | |||
| SRR9418251.fastq.gz | Fastqsanger.gz | |||
| SRR9418245.fastq.gz | Fastqsanger.gz | |||
| SRR9418246.fastq.gz | Fastqsanger.gz |
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Project description:We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease.
2016-07-07 | GSE75131 | GEO
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
Project description:We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease. Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354 with three biological replicates compared to three replicates of mock inoculated O. sativa as the control.
2016-07-07 | E-GEOD-75131 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2008-02-08 | GSE9658 | GEO
Project description:Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) lead to the devastating rice bacterial diseases and have a very close genetic relationship. There are tissue-specificity differences between Xoo and Xoc, i.e., Xoo only proliferating in xylem vessels and Xoc spreading in intercellular space of mesophyll cell. But there is little known about the determinants of tissue-specificity between Xoo and Xoc. Here we show that Xoc can spread in the intercellular spaces of mesophyll cells to form streak lesions. But Xoo is restricted to growth in the intercellular spaces of mesophyll cells on the inoculation sites. In vivo, Xoc largely breaks the surface and inner structures of cell wall in mesophyll cells in comparison with Xoo. In vitro, Xoc strongly damages the cellulose filter paper in comparison with Xoo. These results suggest that the stronger cell wall-degradation ability of Xoc than that of Xoo may be directly determining the tissue-specificity.
| S-EPMC7157550 | biostudies-literature
Project description:Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR) phenotype, but the molecular mechanism(s) underlying this type of non-host resistance remain largely unknown. Results A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc mediated by Rxo1 using a pair of transgenic and non-transgenic rice lines. Our results indicated that Rxo1 appeared to function in the very early step of the interaction between rice and Xoc, and could specifically activate large numbers of genes involved in signaling pathways leading to HR and some basal defensive pathways such as SA and ET pathways. In the former case, Rxo1 appeared to differ from the typical host R genes in that it could lead to HR without activating NDR1. In the latter cases, Rxo1 was able to induce a unique group of WRKY TF genes and a large set of genes encoding PPR and RRM proteins that share the same G-box in their promoter regions with possible functions in post-transcriptional regulation. In conclusion, Rxo1, like most host R genes, was able to trigger HR against Xoc in the heterologous rice plants by activating multiple defensive pathways related to HR, providing useful information on the evolution of plant resistance genes. Maize non-host resistance gene Rxo1 could trigger the pathogen-specific HR in heterologous rice, and ultimately leading to a localized programmed cell death which exhibits the characteristics consistent with those mediated by host resistance genes, but a number of genes encoding pentatricopeptide repeat and RNA recognition motif protein were found specifically up-regulated in the Rxo1 mediated disease resistance. These results add to our understanding the evolution of plant resistance genes.
2009-12-11 | GSE19239 | GEO
Project description:We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with 10 geographically diverse strains of Xanthomonas oryzae pv. oryzicola, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease.
2015-05-01 | GSE67588 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE9640: Transcriptome Profiling of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola on two different medias GSE9643: Transcriptome Profiling of Xanthomonas oryzae pv. oryzae knockout mutants at different hybridization conditions and PMTs Keywords: SuperSeries Refer to individual Series
2010-05-26 | E-GEOD-9658 | biostudies-arrayexpress
Project description:DNA N6-methyladenine (6mA) modifications expand the information capacity of DNA and have long been known to exist in bacterial genomes. Xanthomonas oryzae pv. Oryzicola (Xoc) is the causative agent of bacterial leaf streak, an emerging and destructive disease in rice worldwide. However, the genome-wide distribution patterns and potential functions of 6mA in Xoc are largely unknown. In this study, we analyzed the levels and global distribution patterns of 6mA modification in genomic DNA of seven Xoc strains (BLS256, BLS279, CFBP2286, CFBP7331, CFBP7341, L8 and RS105). The 6mA modification was found to be widely distributed across the seven Xoc genomes, accounting for percent of 3.80, 3.10, 3.70, 4.20, 3.40, 2.10, and 3.10 of the total adenines in BLS256, BLS279, CFBP2286, CFBP7331, CFBP7341, L8, and RS105, respectively. Notably, more than 82% of 6mA sites were located within gene bodies in all seven strains. Two specific motifs for 6 mA modification, ARGT and AVCG, were prevalent in all seven strains. Comparison of putative DNA methylation motifs from the seven strains reveals that Xoc have a specific DNA methylation system. Furthermore, the 6 mA modification of rpfC dramatically decreased during Xoc infection indicates the important role for Xoc adaption to environment.
| S-EPMC6215013 | biostudies-literature
Project description: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.
2019-03-29 | GSE126994 | GEO