PhytoPath: an integrative resource for plant pathogen genomics.

Area of Science:

• Plant pathology
• Genomics
• Bioinformatics

Background:

• Plant pathogens cause significant agricultural losses.
• Genomic and phenotypic data are crucial for understanding pathogen virulence.
• Existing resources often lack integrated, user-friendly analysis tools.

Purpose of the Study:

• To develop PhytoPath, a comprehensive resource for plant pathogen genomic and phenotypic data.
• To integrate data from PHI-base (Pathogen Host Interactions database) with Ensembl tools.
• To facilitate the identification and analysis of genes involved in pathogenicity.

Main Methods:

• Integration of genomic sequences and annotations for fungi, protists (oomycetes), and bacteria.
• Incorporation of curated pathogenicity gene data from PHI-base.
• Utilized Ensembl tools for data visualization and analysis.
• Implemented a BioMart-based query tool for cross-species gene identification.
• Supported community annotation via WebApollo.

Main Results:

• PhytoPath provides data for 135 genomic sequences from 87 plant pathogen species.
• Includes 1364 curated genes linked to pathogenicity and chemical intervention targets.
• Enables visualization of genes in genomic context and facilitates data querying.
• Supports collaborative gene model annotation.

Conclusions:

• PhytoPath serves as a valuable, integrated resource for plant pathogen research.
• Enhances the analysis of pathogenicity mechanisms and potential control targets.
• Promotes community engagement in improving reference annotations for key species.