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Int. J. Mol. Sci. 2016, 17(2), 259; doi:10.3390/ijms17020259

Transcriptome-Based Identification of Differently Expressed Genes from Xanthomonas oryzae pv. oryzae Strains Exhibiting Different Virulence in Rice Varieties

1
National Institute of Crop Science, Rural Development Administration, Wanju-gun 55365, Korea
2
National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea
3
Department of Biomedical Chemistry, Konkuk University, Chungju 27478, Korea
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editors: Patrick C. Y. Woo and Dilantha Fernando
Received: 4 January 2016 / Revised: 30 January 2016 / Accepted: 16 February 2016 / Published: 19 February 2016
(This article belongs to the Special Issue Microbial Genomics and Metabolomics)
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Abstract

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight (BB) in rice (Oryza sativa L.). In this study, we investigated the genome-wide transcription patterns of two Xoo strains (KACC10331 and HB1009), which showed different virulence patterns against eight rice cultivars, including IRBB21 (carrying Xa21). In total, 743 genes showed a significant change (p-value < 0.001 in t-tests) in their mRNA expression levels in the HB1009 (K3a race) strain compared with the Xoo KACC10331 strain (K1 race). Among them, four remarkably enriched GO terms, DNA binding, transposition, cellular nitrogen compound metabolic process, and cellular macromolecule metabolic process, were identified in the upregulated genes. In addition, the expression of 44 genes was considerably higher (log2 fold changes > 2) in the HB1009 (K3a race) strain than in the Xoo KACC10331 (K1 race) strain. Furthermore, 13 and 12 genes involved in hypersensitive response and pathogenicity (hrp) and two-component regulatory systems (TCSs), respectively, were upregulated in the HB1009 (K3a race) strain compared with the Xoo KACC10331 (K1 race) strain, which we determined using either quantitative real-time PCR analysis or next-generation RNA sequencing. These results will be helpful to improve our understanding of Xoo and to gain a better insight into the Xoo–rice interactions. View Full-Text
Keywords: bacterial blight; differently expressed gene; transcriptome; virulence; Xanthomonas oryzae pv. oryzae bacterial blight; differently expressed gene; transcriptome; virulence; Xanthomonas oryzae pv. oryzae
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Noh, T.-H.; Song, E.-S.; Kim, H.-I.; Kang, M.-H.; Park, Y.-J. Transcriptome-Based Identification of Differently Expressed Genes from Xanthomonas oryzae pv. oryzae Strains Exhibiting Different Virulence in Rice Varieties. Int. J. Mol. Sci. 2016, 17, 259.

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