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

Infection by Verticillium dahliae on sunflower

Verticillium dahliae is one of the causal agent of vascular wilt in numerous economically important plants causing wilting of all or only parts of the host. The most common hosts are trees and shrubs, including olive and maple, and vegetables, including cotton, tomatoes and potatoes and also ornamentals. This soilborn fungus persists in the soil for many years under the form of tiny and black resting bodies called microsclerotia. These germinate in the presence of the host plant roots when the external conditions are beneficial. The resulting hyphae invades the plant roots into the the vascular tissue. The stats panel relate to the VdLs.17 strain only.

You can find two strains of Verticillium dahliae in the Ensembl Genomes website: Verticillium dahliae VdLs.17  and Verticillium dahliae JR2

Fusarium graminearum picture

Gibberella zeae, also known by Fusarium graminearum is one of the causal agents of the wheat head blight disease. This devastating pathogen and other head blight causes important losses in crops worldwide. The genome sequence, assembly and protein coding genes annotation of the Gibberella zeae (PH-1) genome have been generated by the Broad Institute as part of their work on the Fusarium Comparative Sequencing Project.

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 fourth (January 2015) of Ensembl Genomes and version 3.6 of PHI-base and was released on January 2015. 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, Fusarium graminearum, Puccinia graminis and Fusarium oxysporum.
  • 8 EST aligments.
  • DNA alignments in the Phytophthora, Pucciniales, Pyrenophora, Glomerellales and Hypocreales clades.

The last Ensembl Genomes release includes one new phytopathogenic fungi strain, Verticillium dahliae JR2, an updated assembly for Fusarium graminearum and several renaming updates for fungal species.