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Phylogenetic study and multiplex PCR-based detection of Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli using gyrB and rpoD sequences

¹ Laboratory of Plant Pathology and Biotechnology, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502, Japan
² National Agricultural Research Center for Tohoku Region, Fukushima 960-2156, Japan
³ Research Institute of Molecular Genetics, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502, Japan
⁴ Laboratory of Plant Pathology, Kyushu University, Fukuoka 812-8581, Japan
⁵ Department of Microbiology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
⁶ Laboratorium voor Microbiologie, Universiteit Gent, B-9000 Gent, Belgium
⁷ National Institute for Agro-Environmental Science, Tsukuba, Ibaraki 305-8604, Japan

Correspondence
Yasufumi Hikichi
yhikichi{at}cc.kochi-u.ac.jp

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.

The GenBank/EMBL/DDBJ accession numbers for the gyrB and rpoD gene sequences determined in this study are given in Table 1.