Sequencing the genome of the powdery mildew fungus Blumeria graminis
Lead Research Organisation:
University of Oxford
Department Name: Plant Sciences
Abstract
This proposal aims to obtain an annotated genome sequence of the powdery mildew fungus Blumeria graminis f sp hordei. This fungus is an obligate biotrophic pathogen that causes one the agronomically most important diseases of barley and is a 'model' organism for the study of powdery mildew diseases in other crops. We will sequence the genome with a 7-fold coverage. The sequence will be assembled automatically. An EST library of cDNAs isolated from haustoria will also be sequenced and annotated; this will complement the existing collections and complete the coverage of all the important stages in the pathogen's life cycle. The ESTs are instrumental in training the gene finding processes that drive the annotation. The annotation of the genomic sequence will be carried out using a series of pipelines already used for other genome projects (Botrytis and tomato). The results from the semi-automated annotation will then be verified by manual curation and reviewed by specialist researchers in the sequencing consortium. The results will be placed on publicly accessible web-sites and a meeting will be convened with the world wide user community to bring train potential users, present major outcomes of the sequencing and the first annotations and discuss the results.
Technical Summary
This proposal aims to obtain an annotated genome sequence of the powdery mildew fungus Blumeria graminis f sp hordei. This fungus is an obligate biotrophic pathogen that causes one the agronomically most important diseases of barley and is a 'model' organism for the study of powdery mildew diseases in other crops. We will sequence the genome with a 7-fold coverage of the strain DH14: one of the parental strains used to create genetic maps of avirulence and fungicide resistance genes in Blumeria. The sequence will be contracted out to a specialised sequencing centre and obtained from shot-gun sequencing genomic libraries in different insert sizes (3 and 10kb) and combined with the end sequencing of a BAC library available for this strain. The sequence will be assembled automatically using the Arachne programme. An EST library of cDNAs isolated from purified haustoria will also be sequenced and annotated; this will complement the existing cDNA collections and complete the coverage of all the important stages in the pathogen's asexual life cycle. The ESTs are instrumental in training the gene finding processes that drive the annotation. The annotation of the genomic sequence will be carried out using a series of pipelines already used for other genome projects: specifically those of Botrytis cinerea (at URGI (FRANCE)) and tomato (at Imperial College). The results from the semi-automated annotation will then be verified by manual curation and reviewed by specialist researchers in the sequencing consortium. These reviews will be pooled and discussed at dedicated consortium meetings ('jamborees'). The results will be placed on publicly accessible web-sites (e.g. http://cogeme.ex.ac.uk/) and a meeting will be convened with the world wide user community to bring train potential users, present major outcomes of the sequencing and the first annotations and discuss the results.
People |
ORCID iD |
| Sarah Gurr (Principal Investigator) |
Publications
Muller T
(2007)
Synthesis of UDP-GlcNAc derivatives modified at OH-4 as potential chain-terminators of chitin biosynthesis
in Tetrahedron: Asymmetry
Lees K
(2007)
Gene microarray analysis using angular distribution decomposition.
in Journal of computational biology : a journal of computational molecular cell biology
Danac R
(2007)
Carbohydrate chain terminators: rational design of novel carbohydrate-based antifungal agents.
in Chembiochem : a European journal of chemical biology
Skamnioti P
(2007)
A novel role for catalase B in the maintenance of fungal cell-wall integrity during host invasion in the rice blast fungus Magnaporthe grisea.
in Molecular plant-microbe interactions : MPMI
Danac R
(2008)
Synthesis of UDP-glucose derivatives modified at the 3-OH as potential chain terminators of beta-glucan biosynthesis.
in Carbohydrate research
Saratovsky I
(2009)
The Structure of manganese oxide formed by the fungus Acremonium sp. strain KR21-2
in Geochimica et Cosmochimica Acta
Petkov V
(2009)
Atomic-scale structure of biogenic materials by total X-ray diffraction: a study of bacterial and fungal MnOx.
in ACS nano
Rodgers CJ
(2010)
Designer laccases: a vogue for high-potential fungal enzymes?
in Trends in biotechnology
Spanu PD
(2010)
Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism.
in Science (New York, N.Y.)
Gurr S
(2011)
The rise and rise of emerging infectious fungi challenges food security and ecosystem health
in Fungal Biology Reviews
Fisher MC
(2012)
Emerging fungal threats to animal, plant and ecosystem health.
in Nature
Dewey F
(2013)
Lateral-Flow Devices to Rapidly Determine Levels of Stable Botrytis Antigens in Table and Dessert Wines
in American Journal of Enology and Viticulture
Bebber D
(2013)
Crop pests and pathogens move polewards in a warming world
in Nature Climate Change
Grant-Downton RT
(2014)
A novel Botrytis species is associated with a newly emergent foliar disease in cultivated Hemerocallis.
in PloS one
Taylor C
(2014)
Fungal pathogenesis: Past, present and future
in Fungal Biology Reviews
Bebber D
(2014)
The global spread of crop pests and pathogens
in Global Ecology and Biogeography
Bebber,D
(2014)
Economic and physical determinants of the global distributions of crop pests and pathogens
in New Phytologist
Bebber DP
(2015)
Crop-destroying fungal and oomycete pathogens challenge food security.
in Fungal genetics and biology : FG & B
| Description | First genome sequence of an intractable and devastating crop pathogenic fungus |
| Exploitation Route | Further research |
| Sectors | Agriculture, Food and Drink |
| Description | First genome sequence published of a true obligate pathogen. Multiple citations of Science paper |
| First Year Of Impact | 2010 |
| Sector | Agriculture, Food and Drink |
| Description | Antifungals and Puricore |
| Organisation | Puricore |
| Country | United States |
| Sector | Private |
| PI Contribution | Mode of action studies |
| Collaborator Contribution | Provision of solutions and growth chambers |
| Impact | papers |
| Start Year | 2009 |