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Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence.

Urban M, Irvine AG, Cuzick A, Hammond-Kosack KE - Front Plant Sci (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology and Crop Science, Rothamsted Research Harpenden, UK.

ABSTRACT
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.

No MeSH data available.


Ensembl genome browser view for Fusarium graminearum. The website at http://fungi.ensembl.org/Fusarium_graminearum was searched for the gene id FGSG_05906 encoding the secreted lipase gene Fgfgl1. The PHI-base phenotype of the mutant is displayed and color coded in orange as “reduced virulence.”
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Figure 1: Ensembl genome browser view for Fusarium graminearum. The website at http://fungi.ensembl.org/Fusarium_graminearum was searched for the gene id FGSG_05906 encoding the secreted lipase gene Fgfgl1. The PHI-base phenotype of the mutant is displayed and color coded in orange as “reduced virulence.”

Mentions: 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.


Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence.

Urban M, Irvine AG, Cuzick A, Hammond-Kosack KE - Front Plant Sci (2015)

Ensembl genome browser view for Fusarium graminearum. The website at http://fungi.ensembl.org/Fusarium_graminearum was searched for the gene id FGSG_05906 encoding the secreted lipase gene Fgfgl1. The PHI-base phenotype of the mutant is displayed and color coded in orange as “reduced virulence.”
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526803&req=5

Figure 1: Ensembl genome browser view for Fusarium graminearum. The website at http://fungi.ensembl.org/Fusarium_graminearum was searched for the gene id FGSG_05906 encoding the secreted lipase gene Fgfgl1. The PHI-base phenotype of the mutant is displayed and color coded in orange as “reduced virulence.”
Mentions: 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.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology and Crop Science, Rothamsted Research Harpenden, UK.

ABSTRACT
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.

No MeSH data available.