Bacterial plant pathogens in PhytoPath

Twelve bacterial plant pathogens are now available on PhytoPath. You can see the list of species at the Pathogens page.

Update PHI-base annotations on Ensembl Genomes

The new release (September 2013) of PhytoPath contains data from Ensembl Genomes (release 20) and an updated set of annotations from PHI-base. It has 1462 annotations for twelve fungal and oomycetes species.

These data can be seen in the genome browser under the "Ontology" section in the left panel on the gene and transcript tabs. Displayed information includes the experimental conditions, host and resulting phenotype.  Bulk data download of genes with known pathogenic phenotypes can be queried using BioMart.

Here are some examples:

  • A gene from Phytophthora infestans labeled as 'effector' acording to PHI-base annotation and the corresponding associated data. 
  • The BioMart results when querying for all the genes in Gibberella zeae where the phenotype of the mutant is reduced virulence in wheat.
Inclusion of PHI-base annotation data

Since release 14 of Ensembl Genomes, genes for a subset of the PhytoPath species have been annotated with external references to PHI-base.

When browsing the genome using the location view, these genes are color coded accordingly to the phenotype of the mutant, or if the gene is a chemical target. The list of genes that have PHI-base references can also be retrieved using the  Biomart data mining tool for fungi and protists. You can see this feature in action when looking at the Guanine nucleotide-binding protein genes in Ustilago Maydis.

 

Variation data in PhytoPath

Repeat induced point mutation (RIP) mechanism in Fungal genome , combined with the study of pathogenicity makes it a interesting candidate for variation studies. F. graminearum is a causative agent of epidermic plant disease called scab or Fusarium Head Blight (FHB) in Wheat and Barley. The Fusarium comparative project of Broad Institute resulted in sequencing of two strains of Fusarium graminearum, PH-1 (NRRL 31084) and GZ3639 (NRRL 29169). The comparative study resulted in identification of 10,495 single-nucleotide polymorphisms (SNPs) between the two strains.

Mapping of the SNPs over the chromosome shown very localized distribution of SNPs in the repeat rich telomere and regions rich with pathogenicity related genes (Cuomo CA et. al). This data is now integrated in the Gibberella zeae database.

Reference: "The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization". Cuomo CA et al. Science. 2007 Sep 7;317(5843):1400-2.  Pubmed : 17823352