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

doi:10.1186/1471-2180-8-99

BMC Microbiology

Volume 8

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Lin Y
Jung KH
Chou HH
Bogdanove A
Ronald P

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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

Young-Su Seo¹^* , Malinee Sriariyanun¹^* , Li Wang²^,6 , Janice Pfeiff³ , Jirapa Phetsom¹ , Ye Lin⁴ , Ki-Hong Jung¹ , Hui Hsien Chou⁴^,5 , Adam Bogdanove² and Pamela Ronald¹

¹Department of Plant Pathology, University of California, Davis, CA 95616, USA

²Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA

³ArrayCore Facility, School of Veterinary Medicine, Molecular Biosciences, University of California, Davis, CA 95616, USA

⁴Department of Computer Science, Iowa State University, Ames, IA 50011, USA

⁵Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA

⁶Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA

author email corresponding author email* Contributed equally

BMC Microbiology 2008, 8:99doi:10.1186/1471-2180-8-99


Published:	18 June 2008

Additional 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.

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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).

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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.

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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.

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Additional file 5:

Xanthomonas oryzae pv. oryzae KACC10331 primary annotation retrieved from the public Comprehensive Microbial Resource version 2.3 on December 22, 2005.

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Additional file 6:

Xanthomonas oryzae pv. oryzicola BLS256 primary annotation retrieved from the public Comprehensive Microbial Resource version 2.3 on December 22, 2005.

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