title: Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts.
abstract: BACKGROUND
  In addition to human and animal diseases, bacteria of the genus Burkholderia can cause plant diseases. The representative species of rice-pathogenic Burkholderia are Burkholderia glumae, B. gladioli, and B. plantarii, which primarily cause grain rot, sheath rot, and seedling blight, respectively, resulting in severe reductions in rice production. Though Burkholderia rice pathogens cause problems in rice-growing countries, comprehensive studies of these rice-pathogenic species aiming to control Burkholderia-mediated diseases are only in the early stages.
  
  
  RESULTS
  We first sequenced the complete genome of B. plantarii ATCC 43733T. Second, we conducted comparative analysis of the newly sequenced B. plantarii ATCC 43733T genome with eleven complete or draft genomes of B. glumae and B. gladioli strains. Furthermore, we compared the genome of three rice Burkholderia pathogens with those of other Burkholderia species such as those found in environmental habitats and those known as animal/human pathogens. These B. glumae, B. gladioli, and B. plantarii strains have unique genes involved in toxoflavin or tropolone toxin production and the clustered regularly interspaced short palindromic repeats (CRISPR)-mediated bacterial immune system. Although the genome of B. plantarii ATCC 43733T has many common features with those of B. glumae and B. gladioli, this B. plantarii strain has several unique features, including quorum sensing and CRISPR/CRISPR-associated protein (Cas) systems.
  
  
  CONCLUSIONS
  The complete genome sequence of B. plantarii ATCC 43733T and publicly available genomes of B. glumae BGR1 and B. gladioli BSR3 enabled comprehensive comparative genome analyses among three rice-pathogenic Burkholderia species responsible for tissue rotting and seedling blight. Our results suggest that B. glumae has evolved rapidly, or has undergone rapid genome rearrangements or deletions, in response to the hosts. It also, clarifies the unique features of rice pathogenic Burkholderia species relative to other animal and human Burkholderia species.
authors.affiliation: Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea. yseo2011@pusan.ac.kr.
authors.forename: Young-Su
authors.initials: YS
authors.lastname: Seo
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. jyni0619@daum.net.
authors.forename: Jae Yun
authors.initials: JY
authors.lastname: Lim
authors.affiliation: Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea. jjuwoogi@pusan.ac.kr.
authors.forename: Jungwook
authors.initials: J
authors.lastname: Park
authors.affiliation: Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea. k7crescent@pusan.ac.kr.
authors.forename: Sunyoung
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea. ehyuna0210@naver.com.
authors.forename: Hyun-Hee
authors.initials: HH
authors.lastname: Lee
authors.affiliation: Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Suwon, 443-400, Republic of Korea. hcheong75@gmail.com.
authors.forename: Hoon
authors.initials: H
authors.lastname: Cheong
authors.affiliation: Yeongnam Regional Office, Animal and Plant Quarantine Agency, Busan, 600-016, Republic of Korea. supraorder@korea.kr.
authors.forename: Sang-Mok
authors.initials: SM
authors.lastname: Kim
authors.affiliation: Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-633, Republic of Korea. jsmoon@kribb.re.kr.
authors.forename: Jae Sun
authors.initials: JS
authors.lastname: Moon
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. ingyu@snu.ac.kr.
authors.forename: Ingyu
authors.initials: I
authors.lastname: Hwang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D058947:Bacterial Secretion Systems / Q000235:genetics; D001427:Bacterial Toxins / Q000096:biosynthesis; D019117:Burkholderia / Q000166:cytology / Q000235:genetics* / Q000502:physiology*; D064113:CRISPR-Cas Systems; D004777:Environment; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D058507:Host Specificity / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D012275:Oryza / Q000382:microbiology*; D053038:Quorum Sensing / Q000235:genetics
chemical_list: D058947:Bacterial Secretion Systems; D001427:Bacterial Toxins