Research article
A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes
-
* Corresponding author: Pamela Ronald pcronald@ucdavis.edu
- † Equal contributors
1 Department of Plant Pathology, University of California, Davis, CA 95616, USA
2 Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA
3 ArrayCore Facility, School of Veterinary Medicine, Molecular Biosciences, University of California, Davis, CA 95616, USA
4 Department of Computer Science, Iowa State University, Ames, IA 50011, USA
5 Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
6 Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
BMC Microbiology 2008, 8:99 doi:10.1186/1471-2180-8-99
Published: 18 June 2008Additional files
Additional file 1:
Error rate for Xo microarray hybridized with labeled cDNA derived from Xoo or Xoc RNA using a heterologous gene (hph) and empty spots.
Format: DOC Size: 31KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 2:
Xoo and Xoc genes differentially expressed in XOM2 relative to PSB by microarray analysis using a false discovery rate of 5% and a fold-change minimum of 1.75 (log2ratio 0.8).
Format: DOC Size: 384KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 3:
Validation of microarray results using semi-quantitative RT-PCR. 16s rDNA (16sDNA) was used as a control. The log2 ratios are shown for the expression of 16 select genes in Xoo (A) and Xoc (B) cultured in XOM2 (X) vs. PSB (P), calculated based on densitometry of products separated by agarose gel electrophoresis and visualized by ethidium bromide staining.
Format: TIFF Size: 15MB Download file
Additional file 4:
Validation of microarray results using quantitative RT-PCR. Relative transcript levels of five Xoo (A) and two Xoc (B) genes in PSB vs. XOM2 culture were quantified with reference to corresponding standard curves and plotted as ng PCR product. The primers used are noted below each plot.
Format: PNG Size: KB Download file
Additional file 5:
Xanthomonas oryzae pv. oryzae KACC10331 primary annotation retrieved from the public Comprehensive Microbial Resource version 2.3 on December 22, 2005.
Format: XLS Size: 4.8MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 6:
Xanthomonas oryzae pv. oryzicola BLS256 primary annotation retrieved from the public Comprehensive Microbial Resource version 2.3 on December 22, 2005.
Format: XLS Size: 5MB Download file
This file can be viewed with: Microsoft Excel Viewer