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.

Recently added

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Mycosphaerella musicola is a fungal plant pathogen, which is the causal agent of Yellow Sigatoka leaf spot disease on banana plants.

(Text from Wikipedia, the free encyclopaedia.)

Browse this genome on Ensembl Genomes.

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Black sigatoka is a leaf-spot disease of banana plants caused by the ascomycete fungus Mycosphaerella fijiensis (Morelet). Also known as black leaf streak, it was discovered in 1963 and named for its similarities with the yellow sigatoka, which is caused by Mycosphaerella musicola (Mulder), which was itself named after the Sigatoka Valley in Fiji, where an outbreak of this disease reached epidemic proportions from 1912 to 1923. Plants with leaves damaged by the disease may have up to 50% lower yield of fruit and control can take up to 50 sprays a year.

(Text from Wikipedia, the free encyclopaedia.)

Browse this genome on Ensembl Genomes.

This release

The current release of PhytoPath is built from the 32th release (October 2016) of Ensembl Genomes and version 4.1 of PHI-base and was released on November 2016. 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 254 genomic sequences (from 83 fungi, 15 protists and 16 bacteria).

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.