Plant Health Bioinformatics Network

Project Details

Description

Main research question/goal

Plant disease detection by high throughput sequencing (HTS) is a relatively new and fast developing discipline, with very variable levels of expertise in (diagnostic) phytopathology laboratories 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. In this project, we will improve collaboration and communication among laboratories regarding bioinformatics analyses and close the knowledge gap between those with little to no experience and those with lots of experience with HTS and in a phytopathology context.


Research approach

The PHBN project has ended. Our approach was fourfold: 1) Develop training materials to help unexperienced labs get started; 2) Develop complex (semi-)artificial datasets which can be used for pipeline testing and validation, including comparison of pipelines; 3) Transfer some of the knowledge built in the virology community to other disciplines in plant pathology by organizing a community effort where the labs with RNA-seq datasets generated for the detection of viruses, will use those datasets to check for sequences of other relevant organisms, such as phytoplasmas, bacteria and fungi and 4) Improve communication by sharing all obtained information on open online repositories.


Relevance/Valorisation

The developed training materials and accompanying reference datasets were considered valuable both for teams with little experience as well as for more experienced teams to test new software and to compare pipelines. The community effort to screen for non-viral sequences in existing RNA-seq datasets used for virus detection taught us that RNA-seq can potentially be used for the detection of  other pathogens as well, mainly for fungi and insects/mites. In the long term this will ideally lead to an “all-in-one” detection protocol. Finally, the fact that all developed resources are available in living open repositories will stimulate collaborations and will stimulate an “open science” attitude among researchers.


Funding provider(s)
FOD Volksgezondheid, Veiligheid van de voedselketen en Leefmilieu
AcronymPHBN
StatusFinished
Effective start/end date1/09/1928/02/22

Flemish Discipline list

  • Development of bioinformatics software, tools and databases
  • Phytopathology
  • Virology
  • Analysis of next-generation sequence data