Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
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
BMC Genomics 2008, 9:204 doi:10.1186/1471-2164-9-204Published: 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.