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 and oomycete phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource.
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.
Last added genomes
Pyrenophora triciti-repentis is the causal agent of 'tan spot', a major disease in most of common wheat varieties. It can be identified by looking at the leaves for dark oval shaped necrotic tissue with a yellow border. The Pyrenophora tritici-repentis Pt-1C-FP (Race 1) genome was generated and assembled by Broad Institute of MIT and released in March 2007 consisting of a whole-genome shotgun assembly with a size of 37.84 Mb. The assembly and protein coding gene annotation of the Pyrenophora tritici-repentis genome was imported from the annotation submitted to EMBL-Bank as the WGS project AAXI00000000.
Sporisorium reilianum is the causal agent of maize head smut. This disease, that starts the infection process by invading the roots during the early seedling stage, is responsible for important crop losses. The Sporisorium reilianum (strain SRZ2) genome was generated and assembled at 454 Life Sciences and released in December 2010 using the Genome Sequencer 20 (Roche) and the Genome Sequencer FLX (Roche). 99.75% of the genome assembly was organised into 23 chromosomes using Optical Mapping. The protein coding gene annotation of the Sporisorium reilianum genome (generated by the Munich Information Center for Protein Sequences) was imported from the annotation submitted to EMBL-Bank as the assembly project GCA_000230245.
This release
The current release of PhytoPath is built from the seventeenth release (February 2013) of Ensembl Genomes and version 3.3 of PHI-base and was released on February 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 and Puccinia graminis
- 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 5 new fungal plant pathogen: Melampsora larici-populina, Glomerella graminicola, Sporisorium reilianum, Pyrenophora teres and Pyrenophora tritici-repentis.
Featured Gene
The FKS1 gene encodes a membrane protein in yeast. Mutations in this gene leads to sensibility to known anti fungal drugs. FKS1 is part of the glucan synthase complex which is responsible for synthesizing 1,3-beta-glucan chains, the major structural polymer in many fungi and oomycetes. This gene has homologues in every plant pathogen in PhytoPath. This gene can be searched in Ensembl Fungi and gene trees can be visualized in the comparative analysis section. The gene tree for FKS1 in Fusarium oxysporum can be seen here.
