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.

New feature: Advanced Search

The Advanced Search lets you build complex queries to find genes across all the PhytoPath species. You can search for genes with specific pathogenic phenotypes, gene ontology annotation or protein domains, and download your results for further analysis.

PhytoPath needs you!

Are there important fungal or oomycetes plant pathogen genomes or data sets that you would like to see in PhytoPath? Please let us know, and we will try to prioritise these data.

Recently added

Glomerella graminicola

Glomerella graminicola (anamorph Colletotrichum graminicola) is the major cause of 'stalk rot of cereals' or 'anthracnose' in maize. Some varieties of engineered maize seem more susceptible to infection resulting in increasing economic concerns. The Glomerella graminicola (strain M1.001) genome was generated and assembled by Broad Institute of MIT and released in September 2010 consisting of a whole-genome shotgun assembly with a size of 51.6 Mb. The assembly and protein coding gene annotation of the Glomerella graminicola genome was imported from the annotation submitted to EMBL-Bank as the WGS project ACOD00000000. Funding for the assembly and annotation was provided by the National Institute of Food and Agriculture (NIFA) through the NSF/USDA Microbial Genome Sequencing Program.

Browse this genome in the Ensembl Genomes website.


Picture of leave infected with Blumeria graminis

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.

Browse this genome in the Ensembl Genomes website.

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.

This release

The current release of PhytoPath is built from the twentieth third (August 2014) of Ensembl Genomes and version 3.6 of PHI-base and was released on September 2014. 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 forPhytophthora infestans, Gibberella zeae, Puccinia graminis and Fusarium oxysporum.
  • 8 EST aligments.
  • DNA alignments in the Phytophthora, Pucciniales and Pyrenophora and Hypocreales clades.

The last Ensembl Genomes release includes 7 new Fungi and 3 Phytophthora plant pathogens.