A - Papers appearing in refereed journals
Urban, M., Irvine, A. G., Cuzick, A. and Hammond-Kosack, K. E. 2015. Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence. Frontiers in Plant Science. 6, p. 605. https://doi.org/10.3389/fpls.2015.00605
|Authors||Urban, M., Irvine, A. G., Cuzick, A. and Hammond-Kosack, K. E.|
New pathogen-host interaction mechanisms can be revealed by integrating mutant phenotype data with genetic information. PHI-base is a multi-species manually curated database combining peer-reviewed published phenotype data from plant and animal pathogens and gene/protein information in a single database.
PHI-base is a multi-species knowledge database capturing the phenotypes available on forward and reverse mutants from 231 pathogenic organisms described in the literature. Plant pathogens represent 60% of the species within PHI-base. Simple and advanced search tools, available at www.phi-base.org, allow users to query PHI-base directly. Flat file downloads enable larger comparative biology studies, systems biology approaches and a richer annotation of genomes, transcriptomes and proteome data sets. Since 2014, phenotype information from PHI-base is directly displayed in pathogen genome browsers accessible at www.phytopathdb.org (Kersey et al., 2014). PHI-base regularly interacts with the international community to provide researchers with effective query tools and new data types to study pathogen-host interactions.
Available online since 2005, PHI-base catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, protist, and bacterial pathogens which infect animal, plant, fish, insect, and/or fungal hosts (Urban et al., 2015). PHI-base is a database devoted to the identification and presentation of information on pathogenicity and effector genes and their host interactions. PHI-base was developed out of a need for a knowledge database enabling the discovery of candidate targets in medically and agronomically important species for intervention with chemistries and/or host modifications. Recent bioinformatics studies enabled by whole-database downloads of PHI-base, include comparative analyses, genome/transcript and proteome annotations, and system biology approaches (Hu et al., 2014; Zhang et al., 2014). PHI-base has been cited in 122 published articles including genetics, genomics and bioinformatics research and review articles (for an up-to-date list, see the “About” page of the PHI-base website). In 2014, the web site had more than 6000 visits and the entire content was downloaded >300 times. Phenotypic outcome data from PHI-base are also displayed directly in genome browsers as permanent tracks in public genome sequence resources such as Ensembl Fungi (Figure 1). Through a simple system of color coding and using nine high level PHI-base phenotypes (Urban et al., 2015), genomic features such as pathogenicity islands can directly be investigated.
|Keywords||gene regulatory networks; plant diseases; protein interaction mapping; genetic recombination; comparative genomics; horizontal gene transfer; phytopathogens; emerging diseases|
|Year of Publication||2015|
|Journal||Frontiers in Plant Science|
|Journal citation||6, p. 605|
|Digital Object Identifier (DOI)||https://doi.org/10.3389/fpls.2015.00605|
|PubMed Central ID||PMC4526803|
|Open access||Published as ‘gold’ (paid) open access|
|Funder||Biotechnology and Biological Sciences Research Council|
|Funder project or code||Wheat|
|Pathogen-Host Interactions Database: PHI Database [2012-2017]|
|[20:20 Wheat] Protecting yield potential of wheat|
|PhytoPath, an infrastructure for hundreds of plant pathogen genomes|
|Online||06 Aug 2015|
|Publication process dates|
|Accepted||22 Jul 2015|
|Publisher||Frontiers Media SA|
|Copyright license||CC BY|
Permalink - https://repository.rothamsted.ac.uk/item/8v0v9/using-the-pathogen-host-interactions-database-phi-base-to-investigate-plant-pathogen-genomes-and-genes-implicated-in-virulence