Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of sweet orange in response to PthA4-dependent infection

ABSTRACT: We used this microarray data to survey the differentially expressed genes in sweet orange by comparing leaf tissues challenged with wild type X. citri ssp. citri (Xcc) strain 306 and leaf tissues challenged with pthA4 gene defeciency mutant Xcc306M-NM-^TpthA4at 6 h and 48 h post inoculation.The deletion of pthA4 gene reduced the virulence of Xcc306, and eliminated pustule formation. The citrus gene expression changes after inoculation of these two isogenic strains represent PthA4-mediated molecular events in a susceptible reaction. Xcc306 wild-type strain and pthA4 gene deletion mutant Xcc306M-NM-^TpthA4 were used to inoculate fully expanded young leaves in sweet orange (Citrus sinensis) at the concentration of 5 X 108 cfu/ml using syringe with needle in a quarantine greenhouse facility at the Citrus Research and Education Center, Lake Alfred, FL. The leaves were harvested 6 hours and 48 hours after inoculation for RNA isolation. To allow stringent statistical data analysis, three biological replicates were conducted and three technical replicates were pooled for each strain. RNA extraction was performed by using RNeasy Plant Mini Kit (Qiagen, Valencia, CA). The quantity and quality of RNA were determined on a ND-8000 Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington,DE). Microarray labeling, hybridization, washing, scanning, and data analysis were performed at ICBR facility at University of Florida in Gainesville. Statistical tests were performed using BioConductor statistical software, open source software based on the R programming language. Robust Multichip Analysis (RMA) approach was used for normalizing the raw data. Differential expression analysis was carried out using a linear modeling approach and the empirical Bayes statistics as implemented in the Limma package. Differentially expressed genes with fold change higher than 3 and an adjusted P-value (FDR) less than 0.05 were considered as differentially expressed genes at a statistically significant level.

ORGANISM(S): Citrus sinensis

SUBMITTER: Jeffrey Jones

PROVIDER: E-GEOD-52700 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We used this microarray data to survey the differentially expressed genes in sweet orange by comparing leaves challenged with X. citri ssp. citri (Xcc) strain 306 with the pthA4 gene and leaves challenged with mutant Xcc306M-NM-^TpthA4 without the pthA4 gene 120 hours after inoculation. The deletion of the pthA4 gene reduced the virulence of Xcc306, and eliminated pustule formation. The gene expression changes after inoculation of these two strains represent PthA4-mediated molecular events in a susceptible reaction. Xcc306 wild-type strain and pthA4 gene deletion mutant Xcc306M-NM-^TpthA4 were used to inoculate fully expanded young leaves in sweet orange (Citrus sinensis) at the concentration of 5 X 10^8 cfu/ml using syringe with needle in a quarantine greenhouse facility at the Citrus Research and Education Center, Lake Alfred, FL. The leaves were harvested 120 hours after inoculation for RNA isolation. To allow stringent statistical data analysis, three biological replicates were conducted and three technical replicates were pooled for each strain. RNA extraction was performed by using RNeasy Plant Mini Kit (Qiagen, Valencia, CA). The quantity and quality of RNA were determined on a ND-8000 Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington,DE). Microarray labeling, hybridization, washing, scanning, and data analysis were performed at ICBR facility at University of Florida in Gainesville. Statistical tests were performed using BioConductor statistical software, open source software based on the R programming language. Robust Multichip Analysis (RMA) approach was used for normalizing the raw data. Differential expression analysis was carried out using a linear modeling approach and the empirical Bayes statistics as implemented in the Limma package. Differentially expressed genes with fold change higher than 3 and an adjusted P-value (FDR) less than 0.05 were considered as differentially expressed genes at a statistically significant level.

Project description:We have used the citrus GeneChip array (GPL5731) to survey the transcription profiles of sweet orange in response to the bacterial pathogens Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas axonopodis pv. aurantifolii (Xaa). Xac is the causal agent of the citrus canker disease on a wide range of citrus species, including sweet oranges (Citrus sinensis). On the other hand, Xaa is pathogenic to Mexican lime (Citrus aurantifolia) only, and in sweet orange it triggers a defense response. In order to identify the genes induced during the defense response (Xaa-responsive genes) or citrus canker development (Xac-responsive genes), we conducted microarrays hybridization experiments at 6 and 48 hours after bacterial infiltration (habi). The analysis revealed that genes commonly modulated by Xac and Xaa are associated with basal defenses normally triggered by pathogen-associated molecular patterns, including those involved in reactive oxygen species production and lignification. Significantly, Xac-infected leaves showed considerable changes in the transcriptional profiles of defense-, cell wall-, vesicle trafficking- and cell growth-related genes between 6 and 48 habi. This is consistent with the notion that Xac suppresses host defenses near the beginning of the infection and simultaneously changes the physiological status of the host to promote cell enlargement and division. Finally, Xaa triggered a MAP kinase signaling pathway involving WRKY and ethylene-responsive transcriptional factors known to activate downstream defense genes. Keywords: Comprehensive transcriptional analysis of the Citrus-Xanthomonas interaction Adult leaves of sweet orange were infiltrated with the bacterial suspensions or water (mock control). Two stages were selected after bacterial infiltration for RNA extraction and hybridization on Affymetrix microarrays. In total, these experiments consist of two biological replicates of six samples: water-infiltrated leaves, Xaa-infiltrated leaves and Xac-infiltrated leaves, at both 6 and 48 (habi).

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Transcription profiling of sweet orange in response to PthA4-dependent infection

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