Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
Steven Salzberg
(1)
,
Daniel Sommer
(1)
,
Michael Schatz
(1)
,
Adam Phillippy
(1)
,
Pablo Rabinowicz
(2, 3)
,
Seiji Tsuge
(4)
,
Ayako Furutani
(4, 5)
,
Hirokazu Ochiai
(5)
,
Arthur Delcher
(1)
,
David Kelley
(1)
,
Ramana Madupu
(2)
,
Daniela Puiu
(1)
,
Diana Radune
(2)
,
Martin Shumway
(2)
,
Cole Trapnell
(1)
,
Gudlur Aparna
(6)
,
Gopaljee Jha
(6)
,
Alok Pandey
(6)
,
Prabhu Patil
(6)
,
Hiromichi Ishihara
(7)
,
Damien Meyer
(8)
,
Boris Szurek
(9)
,
Valerie Verdier
(9)
,
Ralf Koebnik
(9)
,
J Maxwell Dow
(10)
,
Robert Ryan
(10)
,
Hisae Hirata
(11)
,
Shinji Tsuyumu
(10)
,
Sang Won Lee
(12)
,
Pamela Ronald
(12)
,
Ramesh Sonti
(6)
,
Marie-Anne van Sluys
(13, 7)
,
Jan Leach
(7)
,
Frank White
(14)
,
Adam Bogdanove
(8)
1
University of Maryland [College Park]
2 TIGR - The Institute for Genomic Research
3 University of Maryland [Baltimore]
4 KPU - Kyoto Prefectural University
5 NIAS - National Institute of Agrobiological Sciences
6 CSIR - Council of Scientific and Industrial Research
7 CSU - Colorado State University [Fort Collins]
8 ISU - Iowa State University
9 IRD - Institut de Recherche pour le Développement
10 BIOMERIT Research Centre
11 University of Shizuoka
12 UC Davis - University of California [Davis]
13 Departamento de Botânica, Universidade de São Paulo
14 Kansas State University
2 TIGR - The Institute for Genomic Research
3 University of Maryland [Baltimore]
4 KPU - Kyoto Prefectural University
5 NIAS - National Institute of Agrobiological Sciences
6 CSIR - Council of Scientific and Industrial Research
7 CSU - Colorado State University [Fort Collins]
8 ISU - Iowa State University
9 IRD - Institut de Recherche pour le Développement
10 BIOMERIT Research Centre
11 University of Shizuoka
12 UC Davis - University of California [Davis]
13 Departamento de Botânica, Universidade de São Paulo
14 Kansas State University
Damien Meyer
- Fonction : Auteur
- PersonId : 801147
- ORCID : 0000-0003-2735-176X
- IdRef : 095235485
Boris Szurek
- Fonction : Auteur
- PersonId : 758529
- ORCID : 0000-0002-1808-7082
- IdRef : 175775605
Jan Leach
- Fonction : Auteur
- PersonId : 792991
- ORCID : 0000-0001-7252-4397
Adam Bogdanove
- Fonction : Auteur
- PersonId : 801153
- ORCID : 0000-0003-1683-4117
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.