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 Seo^1* , Malinee Sriariyanun^1* , Li Wang^2,6 , Janice Pfeiff³ , Jirapa Phetsom¹ , Ye Lin⁴ , Ki-Hong Jung¹ , Hui Hsien Chou^4,5 , Adam Bogdanove² and Pamela Ronald¹

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

author email corresponding author email* Contributed equally

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

Published:	18 June 2008

Abstract

Background

Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) are bacterial pathogens of the worldwide staple and grass model, rice. Xoo and Xoc are closely related but Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice in many parts of the world, and Xoc colonizes the mesophyll parenchyma to cause bacterial leaf streak, a disease of emerging importance. Both pathogens depend on hrp genes for type III secretion to infect their host. We constructed a 50–70 mer oligonucleotide microarray based on available genome data for Xoo and Xoc and compared gene expression in Xoo strains PXO99^A and Xoc strain BLS256 grown in the rich medium PSB vs. XOM2, a minimal medium previously reported to induce hrp genes in Xoo strain T7174.

Results

Three biological replicates of the microarray experiment to compare global gene expression in representative strains of Xoo and Xoc grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of Xoo and 39 genes of Xoc were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for Xoo and Xoc selected for validation. The differentially expressed genes represent 17 functional categories.

Conclusion

We describe here the construction and validation of a two-genome microarray for the two pathovars of X. oryzae. Microarray analysis revealed that using representative strains, a greater number of Xoo genes than Xoc genes are differentially expressed in XOM2 relative to PSB, and that these include hrp genes and other genes important in interactions with rice. An exception was the rax genes, which are required for production of the host resistance elicitor AvrXa21, and which were expressed constitutively in both pathovars.