PhytoPath, an infrastructure for hundreds of plant pathogen genomes

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We will maintain the resource (PhytoPath) for high throughput molecular biology data from important phytopathogens and pathogenic phenotypes based on the Ensembl software infrastructure for genome analysis and display and PHI-base, the leading resource describing phenotypes of pathogenic infection. Information will be stored in a relational database and made available through a number of public interfaces, including a genome browser, a query optimised data warehouse, and bulk data download. Services will be operated as an integrated part of the EBI's suite of public services, and integrated with other services offering access to genome-scale data from other species (e.g. the plant hosts of pathogen-mediated disease). Species and data will be selected for incorporation according to the current research priorities of the community. Data types of interest to PhytoPath include genome sequence, variation information, functional and regulatory assays, RNA-seq, transcriptomic and proteomic data. In this funding cycle, PhytoPath will include a new tool for the community-curation of existing gene models, to supplement the tool developed in the current funding round for the community curaton of host-pathogen interactions. PHI-base will be developed to include information on the primary host targets of pathogen effector(s) and their cellular location and provide a sequence search function, and the WikiPathways tool will be included within the user interface. We will develop methods for population-scale variation analysis, and comparative genomic analysis between pathogenic and related non-pathogenic species, and include the results in each release of the database. The activities of PhytoPath are overseen by a management board comprising key members of the UK phytopathogen research community.

The driving rationale for the project, as well as its greatest potential for societal impact, is in sustainably increasing the yields of crop plants, through assisting the development of strategies for pesticide development and plant breeding. Crucially, this depends on an understanding of gene function (effectors and their targets, and other downstream biological functions dependent on these), which determine the range of possible pesticide targets, the total genetic reservoir available to plant breeders, and possible side effects (in terms of the impact on plant growth, development and overall health). Massively reduced sequencing costs have led to a sharp (and continuing) increase in the number of sequenced phytopathogens. The power of such technologies, however, is critically limited by the quality of reference information (determined by individual scientific studies, and used to infer information about less well studied systems) and by the need to describe the role of given functional elements in the life of the organism. PhytoPath seeks to address this through providing a system for the management of genome-scale data interfaced with a repository of information about pathogenic phenotypes. Potential beneficiaries thus include not only academic researchers working in this field, but also companies developing pesticides, or attempting to breed new varieties of pathogen-resistant plants. More generally, farmers and the wider global population will benefit from improved strategies for disease control, although they are not expected to be among the direct users of the result.
The PIs at both institutions will engage with society, the media and policy makers to make the case for the importance of research into plant pathogens in the context of rising global concern about food and energy security, and of the potential benefits of genomics in addressing these concerns. But the main thrust of impact activities will be aimed at raising (academic and commercial) user awareness of the resource.
Impact will be achieved through attendance at relevant conferences, publication in the database issue of Nucleic Acids Research and other suitable journals, and through the use of our Scientific Advisory Board to gain feedback from critical members of the community about needs and use cases. Furthermore, we are directly seeking support for frequent visits to important BBSRC-funded UK laboratories for direct discussions with the staff employed there. Such visits will also involve offering informatics support for the submission of data to PhytoPath; and members of such laboratories will be additionally invited to visit EBI for short working visits where this will facilitate progress. We will additionally hold 2 training courses for members of the community, following on from the successful course already held in September 2012. Rothamsted Research (RRes) has an extremely strong track record in crop science; and in the study of plant pathogens; and is at the heart of a leading network of academic and commercial groups operating in these domains. Their BBSRC funded 20:20 wheat ISPG has the ambitious objective of raising potential wheat yields to 20 tonnes per hectare through 20 years of research. Work package 2 in 20:20 wheat - 'Protecting the yield potential of wheat' has several collaborative activities with both academic and / or industrial partners that will directly benefit from the growing data and species available in PhytoPath. The EBI is Europe's leading bioinformatics service centre and is ideally placed to exploit synergies between the activities of PhytoPath and other informatics activities; and is coordinating the ELIXIR project. The EBI also has a long established industry programme which helps guide future developments in accordance with commercial needs. Jointly, the two organisations are well placed to meet the needs of the user base in an efficient and sustainable manner.