PhytoBacExplorer: A Phylogenomic Resource for the Phytobacterial Community

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The PhytoBacExplorer is a phylogenomic resource for integrative analyses of the most intensively studied phytobacteria and will greatly facilitate the identification and characterisation of new and emerging threats to food security. It will inform academics and practitioners about the ongoing evolution of plant pathogens under pressures of modern agriculture and global change, and serve the community as a central resource, focusing efforts on research rather than technical tasks, and enabling data sharing of consistently processed, richly annotated high-quality data checked by curators. It will build on the impactful and mature EnteroBase system with >4,200 users in the medical community, including a number of national reference laboratories. EnteroBase features include daily checks for new genome sequencing data in public repositories enabling automated growth, core genome identification, core genome-based Multi-Locus Sequence Tag analyses, and phylogenetic reconstruction and visualisation tools. The system will be enhanced by popular tools of the phytobacterial community including population genetic metrics, identification of virulence factors, metabolic pathways, Ks test, gene family co-evolution, and design of molecular probes/markers for the detection of specific pathogens. A query tool for metagenomic data sets will be added. The data will be enriched by curation including effectors, host ranges, and geographic data, and targeted sequencing of poorly represented interspecific clades. The resource will initially focus on Pseudomonas spp., Ralstonia spp., and Xanthomonadaceae covering 5 of the top 6 plant bacterial pathogens, but be designed for expansion to other classes as user demand dictates. A powerful API will enable integration with other systems and programmatic access needed for machine learning and AI applications. PhytoBacExplorer will play an important role in enabling early detection of emerging pathogens and thus upcoming threats to food security.