Project description:TITLE: Transcriptional profiling of Rgene-mediated responses in rice PROJECT DESCRIPTION: The dominant gene Xa7 and the recessive gene xa5 of rice confer resistance to several races of the bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo). To reveal the modes of action and the defense responses these genes initiate, we decided to obtain the global transcriptional profiles of the rice cultivars IRBB7, IRBB5 (which harbor Xa7 and xa5, respectively) and IR24 undergoing early infection by the Xoo Race 2 strain PXO86. Both IRBB7 and IRBB5 are resistant to PXO86 (which carry the corresponding avirulence genes avrXa7 and avrxa5), whereas IR24 is susceptible. We inoculated by vacuum infiltration the three rice cultivars ten days after seed germination (or 2 weeks after sowing) and collected inoculated tissue at 5 different timepoints within the first day after inoculation. The transcriptional profiles obtained will provide valuable insight into the similarities and differences between incompatible interactions mediated by a dominant and a recessive Rgene, in comparison to a compatible interaction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David O Nino-Liu. The equivalent experiment is OS4 at PLEXdb.]
Project description: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.
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
Project description:OsEDS1 is a key regulator of SA-mediated immunity in plants. The OsEDS1 knockout mutant (Oseds1) was characterized and shown to have increased susceptibility to Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), suggesting the positive role of OsEDS1 in regulating rice disease resistance. To identify differentially regulated downstream of Oseds1, we performed transcriptome deep sequencing (RNA-seq) of wild type (ZH11) and Oseds1 inoculated with Xanthomonas oryzae pv. Oryzae (PXO99A).
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.
Project description:Gene expression profiles in rice leaves near the inoculated site of Xanthomonas oryzae and its typeIII secretion mutant were examined.
