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.
Stereum hirsutum is a fungus typically forming multiple brackets on dead wood. It is also a plant pathogen infecting peach trees. S. hirsutum is in turn parasitised by certain other species such as the fungus Tremella aurantia Substrates for S. hirsutum include dead limbs and trunks of both hardwoods and conifers.
Training Course in Bioinfomatics of Plants and Plant Pathogens
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 30th release (December 2015) of Ensembl Genomes and version 4.0 of PHI-base and was released on December 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 65 Fungi species and 16 Protist species that cause plant diseases.