Welcome to PhytoPath
PhytoPath is a new bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection. Using the Ensembl Genomes browser, it provides access to complete genome assembly and gene models of priority crop and model-fungal, oomycete and bacterial phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource.
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Visualise your data
The PhytoPath project utilises the Ensembl genome browser to provide access to genomes which allows the visualisation of user custom tracks. Data in BED, GFF/GTF among other formats is supported by the Ensembl Genomes framework. You can learn how to add custom tracks in the help section of Ensembl.
Blumeria graminis is an ascomycete fungus responsible for powdery mildew in a variety of grasses, including economically important cereals such as barley and wheat, causing falls in yields of up to 40%. Its genome exhibits considerable variability, allowing the evolution of strains that are able to infect previously resistant crop varieties, or that exhibit fungicide resistant.
Microbotryum violaceum is a heterobasidiomycete fungal pathogen that causes anther smut in flowering plants including carnations and pinks. Whilst not a significant agricultural pathogen, it is used as a model for studying many aspects of pathogenicity including host-pathogen interactions.
The current release of PhytoPath is built from the twentieth (September 2013) of Ensembl Genomes and version 3.4 of PHI-base and was released on September 2013. For all species, available data includes genome sequence and gene models, functional annotation, and protein-based comparative analysis with other fungal/oomycete species (provided by Ensembl Genomes), together with expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions (provided by PHI-base). In addition, the following specific data sets are also available:
- RNA-Seq alignments for Puccinia triticina
- Variation data for Gibberella zeae, Puccinia graminis and Fusarium oxysporum.
- EST aligments for all the species except Puccinia graminis f. sp. tritici, Phytophthora ramorum, Botryotinia fuckeliana, Sclerotinia sclerotiorum, Hyaloperonospora arabidopsidis and Albugo laibachii.
- DNA alignments in the Phytophthora, Pucciniales and Pyrenophora and Hypocreales clades.
The last Ensembl Genomes release includes the pathogenic species Blumeria graminis and Microbotryum violaceum.