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.
Ustilaginoidea virens, sexual stage Villosiclava virens, is a plant pathogen which causes the disease False Smut of rice which reduces both grain yield and grain quality. The disease occurs in more than 40 countries, especially in the rice producing countries of Asia. but also in the U.S. As the common name suggests, it is not a true smut (fungus), but an ascomycete. False smut does not replace all or part of the kernel with a mass of black spores, rather sori form erupting through the palea and lemma forming a ball of mycelia, the outermost layers are spore-producing. Infected rice kernels are always destroyed by the disease.
The blue stain fungus, Grosmannia clavigera, is a species of sac fungus. It spreads to Lodgepole pine, Ponderosa pine, Douglas-fir, and Whitebark pine trees from the body and a special structure in the heads of Mountain Pine Beetles. The blue stain fungus has evolved a relationship with mountain pine beetles that allow them to travel from tree to tree on a special structure in the beetle’s heads and stops the tree from producing resin to pitch out or kill the beetle, encouraging the pine beetle infestation occurring all along the Rocky Mountains from Mexico up into Canada. The beetles are able to mine and lay eggs while avoiding the tree’s defenses. The 33 Mb genome of this fungus was sequenced in 2009.
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.
The current release of PhytoPath is built from the 28th release (August 2015) of Ensembl Genomes and version 3.8 of PHI-base and was released on August 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, 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 62 Fungi species and 15 Protist species.