title: Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
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 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. salzberg@umd.edu
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Daniel D
authors.initials: DD
authors.lastname: Sommer
authors.forename: Michael C
authors.initials: MC
authors.lastname: Schatz
authors.forename: Adam M
authors.initials: AM
authors.lastname: Phillippy
authors.forename: Pablo D
authors.initials: PD
authors.lastname: Rabinowicz
authors.forename: Seiji
authors.initials: S
authors.lastname: Tsuge
authors.forename: Ayako
authors.initials: A
authors.lastname: Furutani
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Ochiai
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Delcher
authors.forename: David
authors.initials: D
authors.lastname: Kelley
authors.forename: Ramana
authors.initials: R
authors.lastname: Madupu
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.forename: Diana
authors.initials: D
authors.lastname: Radune
authors.forename: Martin
authors.initials: M
authors.lastname: Shumway
authors.forename: Cole
authors.initials: C
authors.lastname: Trapnell
authors.forename: Gudlur
authors.initials: G
authors.lastname: Aparna
authors.forename: Gopaljee
authors.initials: G
authors.lastname: Jha
authors.forename: Alok
authors.initials: A
authors.lastname: Pandey
authors.forename: Prabhu B
authors.initials: PB
authors.lastname: Patil
authors.forename: Hiromichi
authors.initials: H
authors.lastname: Ishihara
authors.forename: Damien F
authors.initials: DF
authors.lastname: Meyer
authors.forename: Boris
authors.initials: B
authors.lastname: Szurek
authors.forename: Valerie
authors.initials: V
authors.lastname: Verdier
authors.forename: Ralf
authors.initials: R
authors.lastname: Koebnik
authors.forename: J Maxwell
authors.initials: JM
authors.lastname: Dow
authors.forename: Robert P
authors.initials: RP
authors.lastname: Ryan
authors.forename: Hisae
authors.initials: H
authors.lastname: Hirata
authors.forename: Shinji
authors.initials: S
authors.lastname: Tsuyumu
authors.forename: Sang
authors.initials: S
authors.lastname: Won Lee
authors.forename: Young-Su
authors.initials: YS
authors.lastname: Seo
authors.forename: Malinee
authors.initials: M
authors.lastname: Sriariyanum
authors.forename: Pamela C
authors.initials: PC
authors.lastname: Ronald
authors.forename: Ramesh V
authors.initials: RV
authors.lastname: Sonti
authors.forename: Marie-Anne
authors.initials: MA
authors.lastname: Van Sluys
authors.forename: Jan E
authors.initials: JE
authors.lastname: Leach
authors.forename: Frank F
authors.initials: FF
authors.lastname: White
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Bogdanove
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D015321:Gene Rearrangement; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D018895:Microsatellite Repeats; D012275:Oryza / Q000382:microbiology*; D015203:Reproducibility of Results; D013997:Time Factors; D014974:Xanthomonas / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D004251:DNA Transposable Elements