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.
Pythium iwayamai have been isolated mainly from monocotyledon plants. It grows well at lower temperatures and is pathogenic on monocot grasses under snow cover. Pythium iwayamai causes snow-rot disease of cereal plants including wheat and barley.
Pythium vexans is a plant pathogen and it causes canker, damping-off and rot disease in many economically important crops including rubber trees, potato and sugar cane. It belongs to the group oomycetes which was originally classified among thefungi, due to its morphological and functional similarities. They are now classifed as protists based on modern insights on phylogentic relationship with photosynthetic organisms such as brown algae and diatoms.
The current release of PhytoPath is built from the twentieth second (March 2014) of Ensembl Genomes and version 3.4 of PHI-base and was released on March 2014. 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 oomycetes Pythium aphanidermatum, Pythium vexans, Pythium arrhenomanes, Pythium irregulare and Pythium iwayamai.