PhytoPath was a joint scientific project between the

European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Well ...

and

Rothamsted Research Rothamsted Research, previously known as the Rothamsted Experimental Station and then the Institute of Arable Crops Research, is one of the oldest agricultural research institutions in the world, having been founded in 1843. It is located at Harp ...

, running from January 2012 to May 30, 2017. 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, 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 Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other v ...

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 Pathogen-Host Interactions database (PHI-base) is a biological database that contains curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database is maintained by researchers at Rotham ...

. 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

* * * {{reflist, refs= {{cite journal , last1=Pedro , first1=Helder , last2=Maheswari , first2=Uma , last3=Urban , first3=Martin , last4=Irvine , first4=Alistair George , last5=Cuzick , first5=Alayne , last6=McDowall , first6=Mark D. , last7=Staines , first7=Daniel M. , last8=Kulesha , first8=Eugene , last9=Hammond-Kosack , first9=Kim Elizabeth , last10=Kersey , first10=Paul Julian , title=PhytoPath: an integrative resource for plant pathogen genomics , journal=

Nucleic Acids Research ''Nucleic Acids Research'' is an open-access peer-reviewed scientific journal published since 1974 by the Oxford University Press. The journal covers research on nucleic acids, such as DNA and RNA, and related work. According to the ''Journal Cit ...

, publisher=

Oxford University Press Oxford University Press (OUP) is the university press of the University of Oxford. It is the largest university press in the world, and its printing history dates back to the 1480s. Having been officially granted the legal right to print books ...

(OUP) , volume=44 , issue=D1 , date=2015-10-17 , issn=0305-1048 , doi=10.1093/nar/gkv1052 , pages=D688–D693 , pmid=26476449 , pmc=4702788 {{cite web , title=PhytoPath, an infrastructure for hundreds of plant pathogen genomes , website=

, date=2014-05-31 , url=http://repository.rothamsted.ac.uk/project/80w1q/phytopath-an-infrastructure-for-hundreds-of-plant-pathogen-genomes-2014-2017 , access-date=2021-03-19

External links

PhytoPathPathogen-Host Interaction databaseEnsembl
Biological databases Genetic engineering in the United Kingdom Rothamsted Experimental Station Science and technology in Cambridgeshire Science and technology in Hertfordshire South Cambridgeshire District Wellcome Trust