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Sweet orange genes regulated by TAL effectors of Xanthomonas citri (Xc) or Xanthomonas aurantifolii pathotype C

ABSTRACT: Microarray analyses of sweet orange epicotyls transiently transfected with the pthA2, pthA4 or pthC1 gene, relative to epicotyls transfected with the uid gene (GUS) This experiment was used to identify sweet oragne genes regulated by TAL effectors

ORGANISM(S): Citrus sinensis

PROVIDER: GSE51368 | GEO | 2014/01/10

SECONDARY ACCESSION(S): PRJNA222844

REPOSITORIES: GEO

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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.

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Sweet orange genes regulated by TAL effectors of Xanthomonas citri (Xc) or Xanthomonas aurantifolii pathotype C

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