News › New pathogen resource launched

Infection of wheat crops at anthesis (flowering) with the fungal pathogen Fusarium graminearum (Gibberella zeae) causes reductions to grain quality, losses of grain yield and frequently leads to contamination of the harvested grain with various mycotoxins which are harmful to human and animal health. Fusarium graminearum was one of the first phytopathogenic fungi for which full genomic sequence information became available in the mid-2000s.

10 January 2012

A new resource to help researchers find ways to combat agricultural pathogens, called PhytoPath, is launched today. PhytoPath, which was developed with funding from BBSRC, integrates genome-scale data of important plant pathogen species with literature-curated information about the phenotypes of host infection. This resource could make it easier for researchers to understand the origins of crop diseases and devise new strategies to control them.

PhytoPath uses the Ensembl Genomes browser to provide access to complete genome assembly and gene models of agriculturally important fungal and oomycete plant pathogens. It links genes to experimentally verified functional information on disease progression in the host using data from PHI-base, a curated resource that describes interactions between pathogens and their hosts as well as the intervention targets of commercially used anti-infective chemistries.

PhytoPath helps researchers make the most of the vast quantities of data produced in sequencing experiments, for example genomes, gene expression and sequence variation, by integrating them with curated information about infectious phenotypes. PhytoPath also provides several analysis tools to help researchers compare predicted gene repertoires of pathogens with similar (or dissimilar) lifestyles.

Just as the 1000 Genomes Project is critical for understanding variation in human populations, studies of population-scale variation are increasingly critical to the molecular dissection of plant disease.

PhytoPath contains the genomes of many devastating pathogens, including Phytophthora infestans, which brought on the Irish potato famine of the mid-19th Century and has re-emerged as an important biotic threat to global food security. Also included are the genomes of several cereal fungal pathogens that regularly lower global grain production by between 15 and 30%: Magnaporthe oryzae (rice and wheat blast), Puccinia graminis and P. triticina (the rusts), Blumeria graminis (powdery mildew), the wheat leaf-infecting pathogen Septoria tricitici (Mycosphaerella graminicola) and Fusarium graminearum (Gibberella zeae), a fungus which produces mycotoxins that are harmful to human and animal health.

PhytoPath also provides enhanced searching of the PHI-base resource as well as the fungi and protists in Ensembl Genomes. To keep pace with the growing body of information in the scientific literature, a new community curation initiative will be launched in 2012.

PhytoPath is a collaboration between the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) and Rothamsted Research in the UK. PHI-base has been given National Capability status by BBSRC for its part in helping the UK deliver world-leading environmental research.

Contacts

› Kim Hammond-Kosack, Jacek Grzebyta, Martin Urban and Mansoor Saqi

Notes to Editors

About EMBL-EBI

The European Bioinformatics Institute (EBI) is part of the European Molecular Biology Laboratory (EMBL) and is located on the Wellcome Trust Genome Campus in Hinxton near Cambridge, UK. The EBI grew out of EMBL's pioneering work in providing public biological databases to the research community. It hosts some of the world's most important collections of biological data, including DNA sequences (ENA), protein sequences (UniProt), animal genomes (Ensembl), 3D structures (the Protein Databank in Europe), data from gene expression experiments (ArrayExpress), protein-protein interactions (IntAct) and pathway information (Reactome). EMBL-EBI hosts several research groups and its scientists continually develop new tools for the biocomputing community.

About EMBL

The European Molecular Biology Laboratory is a basic research institute funded by public research monies from 20 member states (Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom) and associate member state Australia. Research at EMBL is conducted by approximately 85 independent groups covering the spectrum of molecular biology. The Laboratory has five units: the main Laboratory in Heidelberg, and outstations in Grenoble, Hamburg, Hinxton and Monterotondo (near Rome). The cornerstones of EMBL's mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; to develop new instruments and methods in the life sciences and to actively engage in technology transfer activities. Around 190 students are enrolled in EMBL's International PhD programme. Additionally, the Laboratory offers a platform for dialogue with the general public through science communication activities such as lecture series, visitor programmes and the dissemination of scientific achievements.

Rothamsted Research Press Office

For further information, please contact Darren Hughes, Head of Communications, on +44 (0) 1582 763 133 ext 2673, email darren.hughes@rothamsted.ac.uk

Rothamsted is the longest running agricultural research station in the world, providing cutting-edge science and innovation for nearly 170 years. Our mission is to deliver the knowledge and new practices to increase crop productivity and quality and to develop environmentally sustainable solutions for food and energy production. Our strength lies in our integrated, multidisciplinary approach to research in plant and soil science.

Rothamsted Research receives strategic funding from the Biotechnology and Biological Sciences Research Council (BBSRC) . It is the longest running agricultural research station in the world, developing environmentally sustainable solutions for food and energy production through science and innovation for nearly 170 years.

About BBSRC

BBSRC is the UK funding agency for research in the life sciences and the largest single public funder of agriculture and food-related research.

Sponsored by Government, BBSRC's budget for 2011-12 is around £445M which it is investing in a wide range of research that makes a significant contribution to the quality of life in the UK and beyond and supports a number of important industrial stakeholders, including the agriculture, food, chemical, healthcare and pharmaceutical sectors.

BBSRC provides institute strategic research grants to the following:

The Babraham Institute, Institute for Animal Health, Institute for Biological, Environmental and Rural Sciences (Aberystwyth University), Institute of Food Research, John Innes Centre, The Genome Analysis Centre, The Roslin Institute (University of Edinburgh) and Rothamsted Research.

The Institutes conduct long-term, mission-oriented research using specialist facilities. They have strong interactions with industry, Government departments and other end-users of their research.

For more information see: www.bbsrc.ac.uk