Sequencing the genome of the powdery mildew fungus Blumeria graminis
Lead Research Organisation:
UNIVERSITY OF EXETER
Department Name: Biosciences
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.
Organisations
People |
ORCID iD |
| Nicholas Talbot (Principal Investigator) |
Publications
| Description | The most significant achievement of this project was the generation of the full genome sequence of the barley powdery mildew fungus Blumeria graminis f. sp. hordei. This revealed fundamental new information regarding the molecular basis of obligate biotrophy. With regard to primary metabolism, the genome provided evidence that B. graminis lacks the ability to generate glycerol from glycolytic intermediates and lacks the ability to utilize inorganic nitrogen sources (nitrate) as sole nitrogen source, reflecting its colonization of living host tissue as its sole growth medium. The genome sequence also revealed a general absence/under-representation of secondary metabolism and plant cell wall-degrading enzymes, in marked contrast to non-obligate plant pathogenic fungi. The genome provided evidence for 248 putative effector-encoding genes and considerable variation in effectors among powdery mildew species. The principal results of the project were published as a major landmark paper (Science 2010 Volume 330: 1543-6). Objective 1) Sequence the genome of Blumeria graminis f sp hordei (7x coverage). Objective fully met. Objective 2) Assemble the sequence using a combination of automated assembly (Arachne), BAC end sequences and genetically mapped molecular markers. This was carried out as specified in the original application and using the Celera CABOG assembler. ESTs generated were important in formulating robust gene models for annotation of genes in assembled genome sequence. Objective fully met. Objective 3) Annotate the sequence automatically, followed by manual annotation and curation. Use previously sequenced EST as well as the EST sequence obtained below to train gene finding programmes specific for Blumeria. A total dataset of 49,307 EST sequences was generated from existing data (including COGEME data) and new ESTs (4). These were clustered into 11,411 unisequences using the B. graminis genome sequence as a scaffold. The quality of these unisequences was ascertained by alignment against the B. graminis genome sequence. 7,769 of them showed greater than 95% sequence coverage at 98% sequence identity Objective fully met. Objective 4) Obtain a cDNA library form Blumeria haustoria and sequence 10000 ESTs (from both ends). New DNA sequencing contributed to the 49,307 ESTs used to generate the gene models. This was pivotal in successful genome assembly. Objective fully met. Objective 5) Annotate the haustorial ESTs. Functional annotation of genes was performed. The Exeter component of the project focused on carbohydrate active enzymes, primary metabolism and secondary metabolism. We performed comparisons between these sets of genes in B. graminis and the closely related fungi Botrytis cinerea and Sclerotinia sclerotiorum. This formed a major part of the genome paper. Objective fully met. Objective 6) Organise a meeting of end-users to release annotated genomic and EST sequences through COGEME. A meeting was organized and all data submitted to public databases. Objective fully met. |
| Exploitation Route | The research is of considerable utility to the agricultural biotechnology community and is actively being used by groups concerned with fungicide discovery and development The data will prove pivotal to future control strategies for this significant plant disease. Gene functional analysis is being pursued in the laboratory of the Principal Investigator, Dr Pietro Spanu using host-induced gene silencing. This will be the subject of application and industrial engagement. |
| Sectors | Agriculture, Food and Drink |
| URL | http://www.exeter.ac.uk/nicktalbot/ |
| Description | No further updates to information submitted last year |
| Sector | Agriculture, Food and Drink |
| Impact Types | Policy & public services |