title: Phylogenetic study and multiplex PCR-based detection of Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli using gyrB and rpoD sequences.
abstract: In order to develop a detection method for the rice pathogens Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli, the phylogeny of six plant-pathogenic Burkholderia species was analysed using the combined nucleotide sequences of gyrB and rpoD. B. plantarii, B. glumae and B. gladioli formed tight monophyletic branches supported by high bootstrap probabilities. The high sequence similarity revealed a close phylogenetic relationship between B. glumae and B. plantarii. B. plantarii strains were divided into three subclusters comprising rice strains, whereas the single Vanda strain occupied a unique position in the phylogenetic tree. The gyrB and rpoD sequences of all B. glumae strains examined were highly conserved. In contrast, B. gladioli strains demonstrated a far greater sequence diversity, but this diversity did not correlate with pathovar, host plant or geographical origin of the strains. A multiplex-PCR protocol using specific primers from the gyrB sequences was designed that allowed the specific detection and identification of B. plantarii, B. glumae and B. gladioli in rice seeds infected with these pathogenic species.
authors.affiliation: Laboratory of Plant Pathology and Biotechnology, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502, Japan.
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Maeda
authors.affiliation: National Agricultural Research Center for Tohoku Region, Fukushima 960-2156, Japan.
authors.forename: Hirosuke
authors.initials: H
authors.lastname: Shinohara
authors.affiliation: Laboratory of Plant Pathology and Biotechnology, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502, Japan.
authors.forename: Akinori
authors.initials: A
authors.lastname: Kiba
authors.affiliation: Research Institute of Molecular Genetics, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502, Japan.
authors.forename: Kouhei
authors.initials: K
authors.lastname: Ohnishi
authors.affiliation: Laboratory of Plant Pathology, Kyushu University, Fukuoka 812-8581, Japan.
authors.forename: Naruto
authors.initials: N
authors.lastname: Furuya
authors.affiliation: Department of Microbiology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Kawamura
authors.affiliation: Department of Microbiology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Ezaki
authors.affiliation: Laboratorium voor Microbiologie, Universiteit Gent, B-9000 Gent, Belgium.
authors.forename: Peter
authors.initials: P
authors.lastname: Vandamme
authors.affiliation: National Institute for Agro-Environmental Science, Tsukuba, Ibaraki 305-8604, Japan.
authors.forename: Seiya
authors.initials: S
authors.lastname: Tsushima
authors.affiliation: Laboratory of Plant Pathology and Biotechnology, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502, Japan.
authors.forename: Yasufumi
authors.initials: Y
authors.lastname: Hikichi
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D019117:Burkholderia / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D027081:DNA Gyrase / Q000235:genetics*; D017931:DNA Primers; D004269:DNA, Bacterial / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D008969:Molecular Sequence Data; D012275:Oryza / Q000382:microbiology; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012639:Seeds / Q000382:microbiology; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D012808:Sigma Factor / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D004269:DNA, Bacterial; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases; D027081:DNA Gyrase