PhytoPath

Database

Content
Description	The PhytoPath project collects and integrates genome-scale data from important fungal, oomycete and bacterial plant pathogens with literature-curated information on mutant phenotypes. Data are displayed using the Ensembl Genomes platform.
Data types captured	Genome-scale data, phenotypes of microbial mutants
Organisms	88 fungal, 24 bacterial and 23 protist pathogens
Contact
Research center	EMBL-EBI and Rothamsted Research
Primary citation	PMID 26476449
Release date	2012[1]
Access
Data format	FASTA, GFF3
Website	PhytoPath
Tools
Web	PhytoPath BioMart search
Miscellaneous
License	Apache 2.0 software license
Versioning	Yes
Data release frequency	quarterly
Version	PhytoPath is built from 32nd release (Aug 2016) of Ensembl Genomes and version 4.2 of PHI-base

PhytoPath was a joint scientific project between the European Bioinformatics Institute and Rothamsted Research, running from January 2012^[1] to May 30, 2017.^[2] The project aimed to enable the exploitation of the growing body of “-omics” data being generated for phytopathogens, their plant hosts and related model species. Gene mutant phenotypic information is directly displayed in genome browsers.

Background[]

PhytoPath was a bioinformatics resource launched in 2012,^[1] which integrated genome scale data from important plant pathogenic species with literature-curated information about the phenotypes of host infection available from the Pathogen-Host Interaction database (PHI-base). It provides access to complete genome assembly and gene models from priority crop and model phytopathogenic species of fungi and oomycetes through the Ensembl Genomes Browser interface. Phytopath also links directly from individual gene sequence models within the Ensembl genome browser to the peer reviewed phenotype information curated within PHI-base. The Phytopath resource aimed to provide tools for comparative analysis of fungal and oomycete genomes. Since the final update - in May 2017 - the database makes accessible 275 genomic sequences in genome browsers from 113 fungal, 25 protist, and 137 bacterial species. Support for community annotation for gene models was provided using the WebApollo online gene editor for some species.

References[]

• Flicek; et al. (2011). "Ensembl 2011". Nucleic Acids Research. 39 (Database issue): D800–6. doi:10.1093/nar/gkq1064. PMC 3013672. PMID 21045057.
• Winnenburg, R.; Urban, M.; Beacham, A.; Baldwin, T.K.; Holland, S.; Lindeberg, M.; Hansen, H.; Rawlings, C.; Hammond-Kosack, K.; Köhler, J. (2008). "PHI-base update: additions to the pathogen host interactions database". Nucleic Acids Research. 36 (Database issue): D572–6. doi:10.1093/nar/gkm858. PMC 2238852. PMID 17942425.
• Baldwin, T.K.; Winnenburg, R.; Urban, M.; Rawlings, C.; Köhler, J.; Hammond-Kosack, K.E. (2006). "The Pathogen-Host Interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity". Molecular Plant-Microbe Interactions. 19 (12): 1451–62. doi:10.1094/mpmi-19-1451. PMID 17153929.

External links[]

• PhytoPath
• Pathogen-Host Interaction database
• Ensembl Fungi
• Ensembl