24BBR: Integrated bioinformatics resources for fungal and oomycetes pathogens of plants

The spread of fungal and oomycete species presents significant challenges for current and future efforts in global food security, and threatens important non-food plant species in the UK ecosystem. Monoculture farming, changing climate and international trade are driving phytopathogen expansion into new geographical regions and new hosts. Discovery and translational research is increasingly reliant on genomic and other large-scale technologies, for example to identify genes implicated in invasion, pathogenesis, and plant responses/immunity. Genomes, population diversity data, and genomic-scale gene/protein expression datasets are now available in archival repositories for many phytopathogens, but, these static repositories do not support robust updating, querying and data-mining, making them difficult to exploit even by groups with extensive bioinformatics expertise. Our teams are responsible for the development and dissemination of two major international genome database resources: Ensembl and VEuPathDB (the Eukaryotic Pathogen, Vector and Host Knowledgebase) – both recognized as Global Core Biodata and Core Elixir Data resources, reflecting their international importance. Ensembl subsites relevant to plant health include Ensembl Fungi, Ensembl Protists (including oomycetes) and Ensembl Plants. Key features include a powerful, customisable genome browser supporting community tracks, phylogenetic gene trees displaying ortholog and paralog relationships across taxa, and visualisation of synteny, driven by whole genome alignments. Ensembl also provides production-grade genome annotation and transcriptome analysis, used in-house and integrated into the VEuPathDB pipeline to maximise efficiency and consistency, and minimise duplication of effort. VEuPathDB includes subsites focussed on infectious disease pathogens, including human and animal diseases prioritised by past/current funders, but also including plant pathogens with extensive functional data. The FungiDB component supports hundreds of species, including scores of important plant pathogens (Blumeria, Botrytis, Colletotrichum, Fusarium, Magnaporthe, Melampsora, Phytophthora, Puccinia, Ustilago, Zymoseptoria, etc) as well as taxa important in the food production and biotech sectors. In addition to gene/genome browsers, this knowledgebase provides powerful web-based tools and APIs for data integration and exploration, enabling users to ask their own questions in silico, seeking (for example) plant pathogen effectors based on protein motifs, gene/protein expression timing, signatures of selection and epigenetic marks, gene set enrichment, and leveraging orthology for cross-species functional inference based on phenotypic information. The HostDB component supports simultaneous interrogation of combined host-pathogen datasets. These proven, cost-effective resources have coordinated efforts for years, but have not previously benefited from dedicated funding to focus on phytopathogens. We propose to: Load or update 80+ genomes from archival repositories, using Ensembl annotation pipelines to build new or improve gene annotations, and the Apollo interface to capture expert knowledge from the community. Generate orthology mappings across taxa, protein domain annotations for all genomes, and further develop/deploy fungal-specific annotation tools focused on virulence factors, biosynthetic gene clusters and, protein structure-driven discovery of new or updated functions. Process/load 200+ functional genomic datasets and 30-40 plant response to infection datasets, enabling user-driven queries to identify genes of interest (e.g. for specific plant diseases), including support for analysis and visualisation of host-pathogen interactions (e.g. co-expression networks). Building on a history of successful collaboration and community engagement, outreach efforts will obtain community input on dataset prioritisation, and promote/explain effective use of informatics tools to advance research. FAIR data access is a priority; all datasets, tools and code will be fully open source and freely available through multiple routes (web browser, API, downloads) in support of plant health research.