Sequencing the genome of the powdery mildew fungus Blumeria graminis
Lead Research Organisation:
Imperial College London
Department Name: Life Sciences
Abstract
This proposal aims at obtaining 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 at obtaining 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.
Publications
Spanu PD
(2010)
Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism.
in Science (New York, N.Y.)
Spanu PD
(2017)
Cereal immunity against powdery mildews targets RNase-Like Proteins associated with Haustoria (RALPH) effectors evolved from a common ancestral gene.
in The New phytologist
Spanu PD
(2012)
The genomics of obligate (and nonobligate) biotrophs.
in Annual review of phytopathology
Wicker T
(2013)
The wheat powdery mildew genome shows the unique evolution of an obligate biotroph.
in Nature genetics
Yu SC
(2019)
Yeast transformation efficiency is enhanced by TORC1- and eisosome-dependent signaling.
in MicrobiologyOpen
Yu SC
(2016)
Nutrient supplements boost yeast transformation efficiency.
in Scientific reports
Description | A. Full sequencing and high definition annotation of the Blumeria graminis f sp hordei genome. Main paper published in Science (2010) B. Creation and coordination of an effective international consortium (BluGen) which initially contributed to genome annotation and is now continuing working through regular workshops post-project in Feb 2012 (funded by New Phytologist) and July 2012 (as a satellite meeting of the IS MPMI congress in Kyoto). Next planned ones are in Copenhagen (August 2013) and Kew, London (September 2014) C. Web base-resource for access to the genome data and annotation (http://www.blugen.org/). This is regularly accessed from world-wide researchers to support work in powdery mildew genomics, biology and comparative genomics in other fields |
Exploitation Route | They already have.The immediate and the wider community has made extensive use of the data generated. |
Sectors | Agriculture, Food and Drink |
URL | http://www.blugen.org/ |
Title | Blumeria genome |
Description | Reference sequence for the powdery mildew fungi |
Type Of Material | Database/Collection of data |
Provided To Others? | No |
Impact | No actual impacts realised to date |