Genome analysis and pathogenicity of a new potential biothreat, Pantoea allii, to onion production in Canada

Onion is a root vegetable that is commonly consumed all over the world. It is easily grown in different types of soil. In 2004, a new species of Pantoea, Pantoea allii Brady et al. 2011, isolated from onions in South Africa and USA, was found to cause pathogenic infections to onions. There is currently no evidence of the presence of P. allii in Canada. Given that onion is an important export/import crop, the introduction of this new pathogen into Canada could have severe economic consequences. Thus, it is important to proactively study this ‘new’ pathogen, especially at the genome level, to generate new knowledge that can be used to develop diagnostic tools. Illumina MiSeq sequencing technology was used to generate paired-end reads and de novo assemblies were performed using CLC Genomics Workbench and ABySS platforms. In addition, the pathogenicity of P. allii DOAB 206 on commercially available Canadian bulb and green onions was investigated. The genome data based on the number of
contigs, N50 and total sum of nucleotides, concluded that ABySS is the better platform. The size of thedraft genome is about 5.2 Mb with 4880 protein-encoding sequences. In silico DNA-DNA hybridizationof the draft genome sequence of P. allii with the closest phylogenetic relative, Pantoea ananatis revealed a 35.7-36.5% similarity. Pathogenicity tests showed that this pathogen can infect Canadian bulb and green onions. Precautionary measures are required to prevent infected onion imports from introducing P. allii into Canada.