PhytoPath: an integrative resource for plant pathogen genomics

A - Papers appearing in refereed journals

Pedro, H., Maheswari, U., Urban, M., Irvine, A. G., Cuzick, A., Mcdowall, M. D., Staines, D. M., Kulesha, E., Hammond-Kosack, K. E. and Kersey, P. J. 2016. PhytoPath: an integrative resource for plant pathogen genomics. Nucleic Acids Research. 44 (D1), pp. D688-D693.

AuthorsPedro, H., Maheswari, U., Urban, M., Irvine, A. G., Cuzick, A., Mcdowall, M. D., Staines, D. M., Kulesha, E., Hammond-Kosack, K. E. and Kersey, P. J.
Abstract

PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species.

Year of Publication2016
JournalNucleic Acids Research
Journal citation44 (D1), pp. D688-D693
Digital Object Identifier (DOI)doi:10.1093/nar/gkv1052
PubMed ID26476449
PubMed Central IDPMC4702788
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeWheat
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 [2014-2017]
PhytoPath: an Integrated resource for comparative phytopathogen genomics [2011-2014]
Publisher's version
Output statusPublished
Publication dates
Online17 Oct 2015
Publication process dates
Accepted01 Oct 2015
PublisherOxford University Press (OUP) Oxford
Oxford University Press (OUP)
Copyright licenseCC BY
ISSN0305-1048

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