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.
Register now for EBI training course in Agricultural-Omics.
A course on bioinformatics for the agricultural sciences will be held at the EMBL-EBI on February 17-21, 2014. You can find more information regarding this course from the course page at EBI.
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.
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.
Blumeria graminis is an ascomycete fungus responsible for powdery mildew in a variety of grasses, including economically important cereals such as barley and wheat, causing falls in yields of up to 40%. Its genome exhibits considerable variability, allowing the evolution of strains that are able to infect previously resistant crop varieties, or that exhibit fungicide resistant.
The current release of PhytoPath is built from the twentieth first (December 2013) of Ensembl Genomes and version 3.4 of PHI-base and was released on December 2013. 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 for Gibberella zeae, Puccinia graminis and Fusarium oxysporum.
- EST aligments for all the species except Puccinia graminis f. sp. tritici, Phytophthora ramorum, Botryotinia fuckeliana, Sclerotinia sclerotiorum, Hyaloperonospora arabidopsidis and Albugo laibachii.
- DNA alignments in the Phytophthora, Pucciniales and Pyrenophora and Hypocreales clades.
The last Ensembl Genomes release includes the pathogenic species Verticillium dahliae and new DNA alignments for the Sordariomycetidae and Ustilaginaceae clades.