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

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The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall deconstruction. It causes white rot of hardwood.

Browse this genome in Ensembl Genomes

Scan from Naše škodljive rastline (1892)

Covered smut of barley is caused by the fungus Ustilago hordei. The disease is found worldwide and it is more extensively distributed than either loose smut or false loose smut.

(Text from Wikipedia)

Browse this genome in Ensembl Genomes

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 27th release (June 2015) of Ensembl Genomes and version 3.6 of PHI-base and was released on June 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 16 new Fungi and 2 Phytophthora plant pathogens. It also add more strains to the following species: Blumeria graminis, Botrytis cinerea, Fusarium oxysporum and Phytophthora parasitica