Abstract
Burkholderia glumae causes rice (Oryza sativa) bacterial panicle blight, which is an increasingly economically important disease worldwide. As the first B. glumae strain isolated from patients with chronic infections, AU6208 has been reported as an opportunistic clinic pathogen. However, our understanding of the molecular mechanism underlying human pathogenesis by B. glumae remains rudimentary. In this study, we report the complete genome sequence of the human-isolated B. glumae strain AU6208 and compare this to the genome of the rice-pathogenic B. glumae type strain LMG 2196T. Analysis of the average nucleotide identity demonstrated 99.4% similarity between the human- and plant-pathogenic strains. However, the phenotypic results from this study suggest a history of niche adaptation and divergence. In particular, we found 44 genes were predicted to be horizontally transferred into AU6208, and most of these genes were upregulated in conditions that mimic clinical conditions. In these, the gene pair sbnAB encodes key enzymes in antibiotic biosynthesis. These results suggest that horizontal gene transfer in AU6208 may be responsible for selective advantages in its pathogenicity in humans. Our analysis of the AU6208 genome and comparison with that of LMG 2196T reveal the evolutionary signatures of B. glumae in the process of switching niches from plants to humans.
Highlights
Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Department of Plant Pathology & Ecology, the Connecticut Agricultural Experiment Station, State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, These authors contributed
The size of the B. glumae AU6208 whole genome is 6.06 Mbp and the genome contains 5008 predicted coding sequences (CDSs), which are located on two chromosome
257 genes were found to be unique in AU6208 compared to LMG 2196T (Table S1)
Summary
To better understand the unique features of the human-pathogenic strain AU6208, we first sequenced its entire genome and analyzed general features of the full-length sequenced genome and assembly information (Table 1 and Figure 1). 257 genes were found to be unique in AU6208 compared to LMG 2196T (Table S1). Most of these genes are annotated as hypothetical protein. The whole genome of B. glumae AU6208 contained 147 and 4 genes related to virulence and antibiotic resistance, respectively (Tables S2 and S3). The number of virulence- and antibiotic-resistance-related genes in LMG 2196T is virtually identical to that of AU6208, except that AU6208 contains two additional virulence-related genes encoding pmlR/bspR1 and BCAL3235 (Tables S2 and S3), which play important roles in capsule polysaccharide biosynthesis in Burkholderia cecocepacia [14]. The purple dots represent the synteny genes between the two strains, while the blue dots represent the rearrangement genes. The lines connected1by dots represent the high synteny regions (purple lines) or rearrangement (reverse arrangement) regions (blue lines)
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