Plant health bioinformatics network

Project coordinator: Annelies Haegeman, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Belgium

Plant disease detection by high throughput sequencing (HTS) is a relatively new and fast developing discipline, with very variable levels of expertise in phytopathology and diagnostics labs across Europe. Especially the accompanying bioinformatics analyses are a large hurdle to take for many plant pathology labs, and a lack of standards / best practices complicates this even more. Since many applications and research goals across plant pathology labs in Europe and beyond are very similar, it makes sense to build a community network across bioinformaticians and/or plant pathologists to exchange knowledge and hence avoid developing similar bioinformatics pipelines. In this project, we want to improve collaboration and communication between different labs regarding bioinformatics analyses and decrease the knowledge gap between labs with little to no experience and the labs with lots of experience with HTS in a plant diagnostic context. The main goals of the project are 4-fold: 1) Develop training materials to help unexperienced labs get started, 2) Develop complex artificial datasets for pipeline testing and validation, including comparing pipelines between labs, 3) Transfer some of the knowledge built in the virology community to other disciplines in plant pathology, 4) Improve communication by sharing pipelines and workflows as well as outreach to stakeholders. This proposal fits the following goals defined in the topic: 1) improve validation of bioinformatics pipelines by developing artificial reference datasets; 2) reach out to less skilled labs by providing training materials and 3) improve communication between diagnosticians and bioinformaticians by demonstrating the potential or RNA-seq data not only for virus detection, but also for other pathogens. This should stimulate other fields in plant pathology to learn from the built-up expertise within the virology community.