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

被引：292

作者：

Salzberg, Steven L. ^{[1
]}

Sommer, Daniel D. ^{[1
]}

Schatz, Michael C. ^{[1
]}

Phillippy, Adam M. ^{[1
]}

Rabinowicz, Pablo D. ^{[2
,3
]}

Tsuge, Seiji ^{[4
]}

Furutani, Ayako ^{[4
,5
]}

Ochiai, Hirokazu ^{[5
]}

Delcher, Arthur L. ^{[1
]}

Kelley, David ^{[1
]}

Madupu, Ramana ^{[2
]}

Puiu, Daniela ^{[1
]}

Radune, Diana ^{[2
]}

Shumway, Martin ^{[2
]}

Trapnell, Cole ^{[1
,9
]}

Aparna, Gudlur ^{[6
]}

Jha, Gopaljee ^{[7
]}

Pandey, Alok ^{[6
]}

Patil, Prabhu B. ^{[6
]}

Ishihara, Hiromichi ^{[8
]}

Meyer, Damien F. ^{[9
]}

Szurek, Boris ^{[10
]}

Verdier, Valerie ^{[10
]}

Koebnik, Ralf ^{[10
]}

Dow, J. Maxwell ^{[11
]}

Ryan, Robert P. ^{[11
]}

Hirata, Hisae ^{[12
]}

Tsuyumu, Shinji ^{[11
]}

Lee, Sang Won ^{[13
]}

Ronald, Pamela C. ^{[13
]}

Sonti, Ramesh V. ^{[6
]}

Van Sluys, Marie-Anne ^{[14
]}

Leach, Jan E. ^{[7
]}

White, Frank F. ^{[15
]}

Bogdanove, Adam J. ^{[9
]}

机构：

[1] Univ Maryland, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA

[2] Inst Genom Res, Rockville, MD 20850 USA

[3] Univ Maryland, Inst Genome Sci, Baltimore, MD 21201 USA

[4] Kyoto Prefectural Univ, Plant Pathol Lab, Sakyo Ku, Kyoto 6068522, Japan

[5] Natl Inst Agrobiol Sci, Dept Genet Resources, Tsukuba, Ibaraki 3058602, Japan

[6] CSIR, Ctr Cellular & Mol Biol, Hyderabad, Andhra Pradesh, India

[7] CSIR, Inst Himalayan Bioresource Technol, Palampur, Himachal Prades, India

[8] Colorado State Univ, Dept Bioagr Sci & Pest Management, Ft Collins, CO 80523 USA

[9] Iowa State Univ, Dept Plant Pathol, Ames, IA USA

[10] Inst Rech Dev, F-34090 Montpellier, France

[11] Natl Univ Ireland Univ Coll Cork, BioSci Inst, BIOMERIT Res Ctr, Cork, Ireland

[12] Shizuoka Univ, Grad Sch Nat Sci & Technol, Suruga Ku, Shizuoka 4228017, Japan

[13] Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA

[14] IB USP, Dept Bot, Sao Paulo, SP, Brazil

[15] Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA

来源：

BMC GENOMICS | 2008年 / 9卷 / 1期

关键词：

D O I：

10.1186/1471-2164-9-204

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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 PXO99(A) 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. PXO99(A) 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 PXO99(A) lineage. PXO99(A) 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.

引用

页数：16

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