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. 2015 Jan;43(Database issue):D645-55.
doi: 10.1093/nar/gku1165. Epub 2014 Nov 20.

The Pathogen-Host Interactions Database (PHI-base): Additions and Future Developments

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Free PMC article

The Pathogen-Host Interactions Database (PHI-base): Additions and Future Developments

Martin Urban et al. Nucleic Acids Res. .
Free PMC article

Abstract

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s).

Figures

Figure 1.
Figure 1.
Growth of the number of published articles screened by keyword search for PHI-base and the number of phenotypically curated genes. This figure was generated from literature records retrieved at PubMed and Web of Science using the search terms ‘(fung*or yeast) and (gene or factor) and (pathogenicity or virulen* or avirulence gene*)’. Key events in the history of functional gene analysis of pathogen-host interactions include: a, identification of the first avirulence gene (4); b, >1500 genome sequencing projects listed in the GOLD database (5); c, genome-wide functional analysis of pathogenicity genes in the rice blast fungus Magnaporthe oryzae; d, the first host-induced gene silencing (HIGS) study involving an obligate biotrophic species (6); e, genome-wide functional analysis of all transcription factors and protein kinases predicted in the cereal infecting fungus Fusarium graminearum (7,8).
Figure 2.
Figure 2.
GO terms assigned to PHI-base accessions in Version 3.6 mapped to a biological process.
Figure 3.
Figure 3.
Inspection of gene function using the Ensembl genome browser. (A) Displayed is a small chromosomal region in Magnaporthe oryzae showing two genes involved in pathogenicity (as annotated in PHI-base) in their genomic context (viewable in the Ensembl browser, in the transcript display). A colour code indicates the annotated role of each gene, green ‘loss of pathogenicity’ and orange ‘reduced virulence’. (B) By selecting each colour-coded MGG transcript ID, information is revealed on the associated gene deletion study curated in the PHI-base database.

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