PhytoBacExplorer: A Phylogenomic Resource for the Phytobacterial Community

Bacteria that infect plants are diverse and can be transmitted via air, water, and soil, or via vectors like insects or nematodes. For bacteria that infect humans, the medical community has benefited immensely from EnteroBase, a computational system for processing and analysis of bacterial DNA sequences. It is used by labs around the world to promptly identify the causes of outbreaks, track multi-country outbreaks, inform prompt public health decision making and subsequent recall of contaminated products in increasingly global food chains. We will use the EnteroBase platform to develop PhytoBacExplorer, a new system dedicated to plant bacteria. We will provide curation to ensure rich, consistent, and high-quality data including geographic information, host ranges, and genes underlying pathogenicity. The system will inherit many useful features from EnteroBase, including processing of raw data, identification of the shared "core" genome in a population, identification of the phylogenetic (ancestry) tree based on core genomes, and powerful interactive visualisations. Users can upload raw sequencing data for PhytoBacExplorer to process and integrate with the full data set. Users will learn whether their strains are new species or have been previously observed and can identify their likely functional characteristics. This will enable monitoring of ongoing pathogen evolution, and significantly reduce time spend on data processing tasks. Users will have input into the development of the system. The project has a budget for sequencing to cover poorly represented clades. The system will enable identification of DNA sequences unique to specific pathogens and enable faster development of more precise molecular tests. This will greatly facilitate regulatory bodies and Plant Health field officers in tracking new threats to the environment and contribute to precision agriculture.