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

Salzberg Steven L., Sommer Daniel D., Schatz Michael C., Phillipy Adam M., Rabinowicz Pablo D., Tsuge Seiji, Furutani Ayako, Ochiai Hirokazu, Delcher Arthur L., Kelley David, Madapu Ramana, Puiu Daniela, Radune Diana, Shumway Martin, Trapnell Cole, Aparna Gudlur, Jha Gopaljee, Pandey Alok, Patil Prabhu B., Hishihara Hiromichi, Szurek Boris, Meyer Damien. 2008. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics, 9 (204), 16 p.

Résumé : 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 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. 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.

Mots-clés Agrovoc : Xanthomonas oryzae, génome, variation génétique, séquence nucléotidique, Oryza sativa

Classification Agris : H20 - Maladies des plantes

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

• Salzberg Steven L., University of Maryland (USA)
• Sommer Daniel D., University of Maryland (USA)
• Schatz Michael C., University of Maryland (USA)
• Phillipy Adam M., University of Maryland (USA)
• Rabinowicz Pablo D., University of Maryland (USA)
• Tsuge Seiji, Kyoto University (JPN)
• Furutani Ayako, Kyoto University (JPN)
• Ochiai Hirokazu, National Institute of Agrobiological Resources (JPN)
• Delcher Arthur L., University of Maryland (USA)
• Kelley David, University of Maryland (USA)
• Madapu Ramana, University of Maryland (USA)
• Puiu Daniela, University of Maryland (USA)
• Radune Diana, University of Maryland (USA)
• Shumway Martin, University of Maryland (USA)
• Trapnell Cole, University of Maryland (USA)
• Aparna Gudlur, CSIR (IND)
• Jha Gopaljee, CSIR (IND)
• Pandey Alok, CSIR (IND)
• Patil Prabhu B., CSIR (IND)
• Hishihara Hiromichi, Colorado State University (USA)
• Szurek Boris, IRD (FRA)
• Meyer Damien, CIRAD-BIOS-UPR Contrôle des maladies (GLP) ORCID: 0000-0003-2735-176X

Source : Cirad - Agritrop (https://agritrop.cirad.fr/549419/)

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