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.

Recently added

Stripe Rust, caused by Puccinia striiformis, on wheat.

Yellow rust of wheat (Puccinia striiformis f.sp. tritici), also known as stripe rust, is one of the three wheat rust diseases principally found in wheat grown in cooler environments. Such locations are generally associated with northern latitudes or cooler seasons.

(Text and image from Wikipedia)

Browse this genome on Ensembl Genomes.

Geotrichum candidum reproduces by segmentation of hyphae into arthrospores.

Geotrichum candidum is a plant pathogenic fungus that causes sour rot of citrus fruits, tomatoes, carrot and some vegetables.

The fungus can also cause a disease of the lung or other organs in humans known as geotrichosis.

This species also used widely in the production of certain dairy products including rind cheeses such as Camembert, Saint-Nectaire, Reblochon and others. The fungus can also be also found in a Scandinavian yogurt-like product known as viili where it is responsible for the product's velvety texture.

(Text from Wikipedia, the free encyclopaedia.)

Browse this genome on Ensembl Genomes.

Training Course in Bioinfomatics of Plants and Plant Pathogens

A training course on the Bioinformatics of Plants and Plant Pathogens will be held at EBI from 23rd-25th May, 2016. Please click here for more details and to register.

This release

The current release of PhytoPath is built from the 31th release (April 2016) of Ensembl Genomes and version 4.1 of PHI-base and was released on April 2016. 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, Colletrotrichum graminicola, Verticillium dahliae JR2, Zymoseptoria tritici, Phytophthora sojae, Albugo laibachi and Pythium ultimum.
  • Variation data forPhytophthora infestans, Verticillium dahliae JR2, Zymoseptoria tritici, Fusarium graminearum, Puccinia graminis Ug99, Puccinia graminis CRL 75-36-700-3 and Fusarium oxysporum.
  • DNA alignments in the Protists, Pucciniales, Glomerellales, Sacharomycetales and Hypocreales clades.

The last Ensembl Genomes release contains 73 Fungi species and 16 Protist species that cause plant diseases.

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.

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.