Powdery Mildews Genome Project Description
Data Release Statement
The Erysiphe pisi and Golovinomyces orontii genomes have been sequenced at the Max Planck Institute for Plant Breeding Research, Cologne with funds from the Max Planck Society. We intend to publish the complete annotated genomes in a peer-reviewed journal as soon as possible. The permission of the principal investigators Ralph Panstruga or Paul Schulze-Lefert must be obtained before publishing any genome-scale analyses based on unpublished sequences, genes or other features presented on this web site. In any publications, users of this resource are requested to acknowledge the Max Planck Institute for Plant Breeding Research and to cite the database as follows:
Max Planck Institute for Plant Breeding Research Powdery Mildew Genome Project http://www.mpipz.mpg.de/powdery_mildew_project_description
Questions concerning this project or use of the data should be sent to Emiel Ver Loren van Themaat or Ralph Panstruga / Paul Schulze-Lefert.
The powdery mildew-plant pathosystem
Owing to their obligate biotrophic lifestyle, powdery mildews rely on living plant tissue for growth and reproduction. At present, powdery mildews can neither be kept in axenic culture nor modified genetically. The molecular basis of this extreme lifestyle remains unknown. However, recent comparative analysis of the genomes of powdery mildews and the genomes of other distantly related phytopathogens that acquired the same way of life by convergent evolution, suggests that obligate biotrophy tends to be associated with genome size inflation and substantial irreversible gene losses.
The asexual life cycle of powdery mildew fungi commences with the landing of a conidiospore on the leaf surface. Following germination and the formation of an appressorium, host cell penetration and the formation of a highly specialized invasive infection structure, the haustorium, represent key events in the establishment of a compatible plant-powdery mildew interaction. The formation of a functional haustorium is the prerequisite for the expansion of hyphae that ultimately make up an multi-branched epiphytic mycelium. The generation of asexual spore carriers, condiophores, which harbour the next generation of conidia, completes the asexual powdery mildew life cycle.
It is thought that haustoria serve a dual role as feeding organs for nutrient uptake and for the targeted delivery of small secreted proteins (effectors) for host cell manipulation. Knowledge about powdery mildew effectors is scarce to date, but it is presumed that a substantial proportion of them function in the suppression of plant defence and the prevention of host cell death. Many powdery mildew effector candidates harbour an N-terminal tripeptide motif that may play a role in the uptake of these proteins into plant cells.
The genome sequencing project
The aim of this project is to produce genome assemblies for E. pisi and G. orontii, which will provide a valuable resource for:
- Obtaining insights into the molecular basis of the obligate biotrophic lifestyle
- studying mechanisms of fungal pathogenicity
- identification of secreted effector proteins required for host manipulation
- comparative genomic analysis of the evolutionary and functional relationships between powdery mildew species
The genome of the barley pathogen, Blumeria graminis f.sp. hordei, has already been sequenced by the BluGen consortium and a high quality draft assembly has been released:
BluGen link
This provides the opportunity to compare the genomes of three closely-related species that differ in their host specificity. It will also enable the identification of genes undergoing rapid evolution (diversifying selection), which are likely to be involved in interactions with the host plant, e.g. those encoding effector proteins. Overall, we envisage that B. graminis f.sp. hordei will provide a model for the powdery mildew disease on monocot hosts, while G. orontii will become the model of choice for studying powdery mildew infection of dicot plants.
The E. pisi and G. orontii isolates selected for sequencing are anonymous isolates collected by members of the MPIPZ.
Strategy used for whole-genome sequencing
For sequencing the estimated 150 Mbp genome of the two powdery mildew species, we have used exclusively next-generation sequencing technologies. Sequencing was conducted by the MPI for Molecular Genetics (Berlin, Germany). The following raw sequence data have been generated:
| E. pisi | |
| Roche 454 GS20 shot-gun reads | 2556571 |
| Roche 454 FLX shot-gun reads | 3999718 |
| Roche 454 Titanium paired-end reads (3 kb inserts) | 902525 |
| G. orontii | |
| Roche 454 GS20 shot-gun reads | 1912516 |
| Roche 454 FLX shot-gun reads | 27159552 |
The assemblies are publically available through NCBI (GenBank project IDs 50315 (E. pisi) and 50317 G. orontii)).
Assembly statistics
The first draft genome assemblies are based on a mixture of 454 shot-gun and paired-end sequencing data assembled using the Roche Newbler program for E. pisi and the PCAP program for G. orontii.
| E. pisi | |
Raw data:
|
1.3 Gb in total |
| Total number of contigs (>500): | 26142 |
| Total length of contigs (>500): | 41 Mb |
| N50 length of contigs >500: | 2.3 kb |
| CEGMA (fully/partially covered) | 82.7 / 91.5% |
| G. orontii | |
Raw data: (1.6 Gb in total)
|
1.6 Gb in total |
| Total number of contigs (>500): | 61834 |
| Total length of contigs (>500): | 65 Mb |
| . | . |
| N50 length of contigs >500: | 1.2 Kb |
| CEGMA (fully/partially covered) | 48.8 / 71.8% |
Out of 248 core genes expected to be found in all eukaryotic genomes [Parra et al. (2009) Nucl. Acids Res. 37, 289–297], 227 are present in the E.pisi assembly, suggesting that 91.5% of the total gene space is already covered. Further assembly with additional data is ongoing and future updates of the assembly and annotation will be made publically available through this website.
Annotation of the E. pisi and G. orontii genomes will be performed on the basis of the B. graminis f.sp. hordei genome and the annotated genome is planned for release in summer 2011.
Searching the sequence data
The Gbrowse (E. pisi, G. orontii) database displays:
- all genomic contigs from the current assembly.
- Results of BLASTX homology searches against the Blumeria graminis f.sp. hordei protein models
- sequences homologous to the CEGMA set of core eukaryotic genes [Parra et al. (2009) Nucl. Acids Res. 37, 289–297]
- expressed sequence tags (ESTs) from conidia and haustoria (G. orontii only)
The sequence data can be searched using a local BLAST (E. pisi, G. orontii) server, which links the results of homology searches to the corresponding genomic contigs.
Project team at the Max Planck Institute for Plant Breeding Research, Köln
Principal Investigators: Ralph Panstruga, Paul Schulze-Lefert and Emiel Ver Loren van Themaat, Plant-Microbe Interactions Department
Dr Kurt Stüber, MPIZ Genome Centre
Dr Richard Reinhardt, MPIZ Genome Centre
Collaborators
Dr. Pietro Spanu, Imperial College, London
Dr. Beat Keller, University of Zürich, Switzerland
Selected publications on powdery mildews
Panstruga R, Schulze-Lefert P (2002) Live and let live: insights into powdery mildew disease and resistance. Molecular Plant Pathology 3, 495-502.
Hückelhoven R (2005) Powdery mildew susceptibility and biotrophic infection strategies. Fems Microbiology Letters 245, 9-17.
Eichmann R, Hückelhoven R (2008) Accommodation of powdery mildew fungi in intact plant cells. Journal of Plant Physiology 165, 5-18.
Glawe DA (2008) The powdery mildews: A review of the world's most familiar (yet poorly known) plant pathogens. Annual Review of Phytopathology 46, 27-51.
Micali C, Göllner K, Humphry M, Consonni C, Panstruga R (2008) The powdery mildew disease of Arabidopsis: a paradigm for the interaction between plants and biotrophic fungi. The Arabidopsis Book
Bindschedler LV, Burgis TA, Mills DJS, Ho JTC, Cramer R, Spanu PD (2009) In planta proteomics and proteogenomics of the biotrophic barley fungal pathogen Blumeria graminis f. sp hordei. Molecular & Cellular Proteomics 8, 2368-2381.
Godfrey D, Zhang ZG, Saalbach G, Thordal-Christensen H (2009) A proteomics study of barley powdery mildew haustoria. Proteomics 9, 3222-3232.
Noir S, Colby T, Harzen A, Schmidt J, Panstruga R (2009) A proteomic analysis of powdery mildew (Blumeria graminis f.sp. hordei) conidiospores. Molecular Plant Pathology 10, 223-236.
Chandran D, Inada N, Hather G, Kleindt CK, Wildermuth MC (2010) Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. Proceedings of the National Academy of Sciences of the United States of America 107, 460-465.
Godfrey D, Bohlenius H, Pedersen C, Zhang ZG, Emmersen J, Thordal-Christensen H (2010) Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif. Bmc Genomics 11