Salzberg, S. L., Sommer, D. D., Schatz, M. C., Phillippy, A. M., Rabinowicz, P. D., Tsuge, S., Furutani, A., Ochiai, H., Delcher, A. L., Kelley, D., Madupu, R., Puiu, D., Radune, D., Shumway, M., Trapnell, C., Aparna, G., Jha, G., Pandey, A., Patil, P. B., Ishihara, H., Meyer, D. F., Szurek, B., Verdier, V., Koebnik, R., Maxwell, J. M., Ryan, R. P., Hirata, H., Tsuyumu, S., Won Lee, S., Ronald, P. C., Sonti, R. V., Van Sluys, M. A., Leach, J. E., White, F. F., Bogdanove, A. J. (2008) Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics, 9. ISSN 1471-2164
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Abstract
Background: 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. Results: The PXO99 A 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. PXO99 A 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. Conclusion: 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. © 2008 Salzberg et al; licensee BioMed Central Ltd.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | article bacterial blight bacterial gene bacterial strain bacterial virulence chromosome rearrangement clustered regularly interspersed short palindromic repeat gene insertion genetic variability nonhuman nucleotide sequence rice strain difference tandem repeat Xanthomonas xanthomonas oryzae bacterial genome gene duplication gene rearrangement genetics genomics horizontal gene transfer microbiology molecular evolution reproducibility time transposon Bacteria (microorganisms) Oryza sativa Xanthomonas oryzae pv. oryzae bacterial protein microsatellite DNA Bacterial Proteins Base Sequence DNA Transposable Elements Evolution, Molecular Gene Transfer, Horizontal Genome, Bacterial Microsatellite Repeats Reproducibility of Results Time Factors |
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > bacteria bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes organism description > plant organism description > plant > rice |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab |
| Depositing User: | Matt Covey |
| Date: | 2008 |
| Date Deposited: | 15 Mar 2013 16:54 |
| Last Modified: | 15 Mar 2013 16:54 |
| PMCID: | PMC2432079 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/27830 |
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