→ Slides doi:10.7490/f1000research.1112714.1
- Christian Schudoma, The Genome Analysis Centre, The Sainsbury Laboratory, Norwich UK
- Yogesh Gupta, The Sainsbury Laboratory, Norwich, UK
- Pirasteh Pahlavan, Leibniz-Institut DSMZ, Braunschweig, University of Würzburg, Germany
- Agathe Jouet, , The Sainsbury Laboratory, Norwich, UK
- Dan MacLean, The Sainsbury Laboratory, Norwich, UK
- Ksenia Krasileva, The Genome Analysis Centre, The Sainsbury Laboratory, Norwich UK
The analysis of plant immunity and plant-pathogen interactions are major topics in plant disease research.
Plant immunity is conferred by so-called nucleotide-binding leucine-rich repeat (NLR) proteins. A specific group of these proteins is fused to additional (integrated) domains that can recognise pathogen effector molecules. In a recent study, 41 plant genomes were computationally screened for such NLR-ID proteins.
Analysis of the interactions between plant-pathogens and their host can provide insight into both the pathogen’s effector proteins, i.e. its attack mechanisms, and the plant’s defense mechanisms. These interactions can be investigated by tailored metagenomics approaches. Results
We present Galaxy tools/pipelines for screening of plant NLR-ID proteins (idFusion) and for complementing metagenomics analysis of plant-pathogen interactions (Ktoolu - Kraken tools and utilities). idFusion is a Galaxy implementation of the NLR-ID screening pipeline described in (Sarris et al, BMC Biology 2016). Ktoolu is a collection of tools and their Galaxy wrappers that allow to dissect sequencing datasets using the taxonomy information assigned by the Kraken metagenomics classifier as well as to visualise the results utilising the Krona tools.