Open Access Highly Accessed Research article

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

Steven L Salzberg1*, Daniel D Sommer1, Michael C Schatz1, Adam M Phillippy1, Pablo D Rabinowicz23, Seiji Tsuge4, Ayako Furutani45, Hirokazu Ochiai5, Arthur L Delcher1, David Kelley1, Ramana Madupu26, Daniela Puiu1, Diana Radune26, Martin Shumway27, Cole Trapnell1, Gudlur Aparna8, Gopaljee Jha9, Alok Pandey8, Prabhu B Patil8, Hiromichi Ishihara10, Damien F Meyer11, Boris Szurek12, Valerie Verdier12, Ralf Koebnik12, J Maxwell Dow13, Robert P Ryan13, Hisae Hirata14, Shinji Tsuyumu13, Sang Won Lee15, Pamela C Ronald15, Ramesh V Sonti8, Marie-Anne Van Sluys169, Jan E Leach9, Frank F White17 and Adam J Bogdanove11

Author Affiliations

1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA

2 The Institute for Genomic Research, Rockville, MD 20850, USA

3 Institute for Genome Sciences, University of Maryland, Baltimore, MD 21201, USA

4 Laboratory of Plant Pathology, Kyoto Prefectural University, Sakyo, Kyoto 606-8522, Japan

5 Department of Genetic Resources, National Institute of Agrobiological Sciences, Kannondai, Tsukuba 305-8602, Japan

6 Current address: J. Craig Venter Institute, Rockville, MD 20850, USA

7 Current address: National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA

8 Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India

9 Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, India

10 Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA

11 Department of Plant Pathology, Iowa State University, Ames, IA, USA

12 Institut de la Recherche pour le Developpement, 911 Av. Agropolis, Montpellier, 34090, France

13 BIOMERIT Research Centre, BioSciences Institute, University College Cork, Cork, Ireland

14 Graduate School of Natural Science & Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8017, Japan

15 Department of Plant Pathology, UC Davis, Davis, CA 95616, USA

16 Departamento de Botânica, IB-USP, Sao Paulo, SP, Brazil

17 Department of Plant Pathology, Kansas State University, Manhattan, KS, USA

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BMC Genomics 2008, 9:204  doi:10.1186/1471-2164-9-204

Published: 1 May 2008



Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another.


The PXO99A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus.


Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world.