New pathogen resource launched
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.
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.
Credit: Rothamsted Research
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. For more information visit: www.phytopathdb.org.
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. For more information visit: www.ebi.ac.uk.
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. For more information visit: www.embl.org.
About Rothamsted Research
Rothamsted is the longest running agricultural research station in the world, providing cutting-edge science and innovation for over 160 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. For more information visit: www.rothamsted.ac.uk.
BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by Government, and with an annual budget of around £445M, we support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.