PhytoPath: an integrative resource for plant pathogen genomics.

Helder Pedro,Martin Urban,Eugene Kulesha,Paul Julian Kersey,Mark D Mcdowall,Daniel M Staines,Uma Maheswari,Alayne Cuzick,Kim Elizabeth Hammond-Kosack,Alistair George Irvine

doi:10.1093/nar/gkv1052

Helder Pedro, Martin Urban + Show 8 more

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https://doi.org/10.1093/nar/gkv1052

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Abstract

PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species.

Highlights

Genes with associated PHI-base data can be identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser
The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention
PhytoPath provides access to all sequenced and annotated plant pathogen genomes that have been submitted to the International Nucleotide Sequence Database Nucleotide Consortium [1] (GenBank [2], the European Nucleotide Archive [3] (ENA) and the DNA Databank of Japan [4]), and is updated approximately four times per year; see http: //www.phytopathdb.org/pathogens eg for a complete list

Summary

Introduction

PhytoPath provides access to all sequenced and annotated plant pathogen genomes that have been submitted to the International Nucleotide Sequence Database Nucleotide Consortium [1] (GenBank [2], the European Nucleotide Archive [3] (ENA) and the DNA Databank of Japan [4]), and is updated approximately four times per year; see http: //www.phytopathdb.org/pathogens eg for a complete list. PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated.

Results

Conclusion