Welcome to the MIPS Fungal Genomics Group

The group focuses on the analysis of fungal genomes. Starting on yeast and Neurospora crassa the current focus is on plant pathogenic fungi and model systems. Further more we provide comprehensive analysis of nearly all publically available fungal genomes.

The basis to explore the species specific properties are correct gene calls. Our main interest is to improve the gene sets of our core projects and in future of any of the analyzed genomes by applying comparative gene calling procedures.  Group details

Maintained Resources

FGDB - MIPS Fusarium graminearum Genome DataBase

MUMDB – MIPS Ustilago maydis DataBase

MSRDB – MIPS Sporisorium reiianum DataBase

MUHDB – MIPS Ustilago hordei DataBase

MNCDB - MIPS Neurospora crassa DataBase

CYGD - The MIPS Comprehensive Yeast Genome DataBase

We process most of the publicly available fungal genome sequences with automatic gene modelling (in case the sequencing project does not provide valuable sets) and automatic protein analysis. The PEDANT system provides a convenient interface to these data.

PEDANT  analysis of fungal genomes

Fusarium graminearum

The filamentous fungus Fusarium graminearum is the causal agent of head blight (scab) of wheat and barley, a plant disease of great economic impact on agriculture throughout the world. The 36 Mb genome of F. graminearum (Gibberella zeae) was sequenced by the Broad Institute, Cambridge, MA. Initially this project was funded by the Austrian Federal Ministry for Education, Science and Culture, which has established the national genome programme GEN-AU (GENome Research in AUstria: http://www.gen-au.at/). The Fusarium graminearum Genome Database – FGDB - aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous ascomycete (Güldener et al. 2006). The resource was essential in the identification and analysis of the regions of genome innovation (Cuomo et al. 2007).

Currently the project is funded by the Austrian FWF-SFB ‚Fusarium metabolites and detoxification reactions: determinants of pathogen virulence and plant resistance‘ headed by Prof. G. Adam, BOKU, Vienna. To outline the fungal pathogen factors and the often involved gene clusters we extend the gene structure validation onto several related Fusarium genomes. Subsequent comparative analysis reconfirmed the known clusters and locate so far unknown pathogenicity related factors and clusters. FGDB

Ustilago maydis

Ustilago maydis, the causal agent of corn smut disease, has been used for over 100 years as a model system for studying genetics and pathogen-host interactions. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants.

The 19,7 Mb genome of U.maydis was sequenced by the Broad Institute, Cambridge, MA. A project was initiated by the Department of Organismic Interactions (Regine Kahmann´s group) at the Max Planck Institute for Terrestrial Microbiology in collaboration with MIPS to analyze and annotate the entire genome.

The MIPS Ustilago maydis Genome Database (MUMDB) was set up providing a user friendly comparative database. The database aims to present information about the molecular structure and functional network of the entirely sequenced basidiomycete. Manual validation of all gene calls was accomplished in a 2 year effort. This work could be improved by comparative gene calling of some related species (unpublished, ongoing work).

The manually validated set of gene calls was the pre-requisite for the exploration of 12 clusters of genes encoding small, secreted proteins with unknown function (Kämper et al. 2006). A significant fraction of these genes exists in small gene families. Most of the genes contained in these clusters are co-regulated and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from complete lack of symptoms to hypervirulence. Despite years of research concerning the mechanism of pathogenicity in U. maydis, no "true" virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate novel mechanisms of pathogenicity operating in the biotrophic fungi. MUMDB

Sporisorium reilianum

Sporisorium reilianum causes head smut of maize and sorghum and is closely related to the corm smut pathogen Ustilago maydis. While U. maydis is still the best analyzed smut species to date, molecular tools developed for U. maydis are easily applicable for use in S. reilianum. S. reilianum emerges as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, host specificity and species-specific disease etiology.

Sequencing of the 18,7 Mb genome of S. reilianum was initiated by the Department of Organismic Interactions (Regine Kahmann´s group) at the Max Planck Institute for Terrestrial Microbiology with special funds of the Max Planck Society. Sequencing of single stranded and paired end libraries was done by 454 Life Sciences, and an optical map (OpGen) helped in the generation of chromosomal supercontigs.

Annotation of the S. reilianum genome including a manual validation of all gene calls was done at MIPS and led to the creation of the user friendly comparative MIPS Sporisorium reilianum Genome Database (MSRDB). The database allows quick access to available information about the molecular structure of genome regions as well as functional classification of encoded open reading frames. In addition, a feature has been integrated that allows direct comparison of the S. reilianum genes to those of U. maydis.

The manually validated set of gene calls was the pre-requisite for the exploration of 43 diversity regions that differentiate the genomes of S. reilianum and U. maydis (Schirawski et al., 2010). Interestingly, the diversity regions host primarily genes predicted to encode secreted proteins. That the diversity regions contain factors involved in communication with the plant host and are thus necessary for virulence of the smuts, has been experimentally shown for 9 diversity regions. Thus, using genome comparison of closely related species greatly accelerated the search for genes directly involved in virulence and provided access to the genes determining species-specific disease etiology. MSRDB

Neurospora crassa

The German sequencing project of Neurospora crassa chromosome II and V started in 1998. Chromosome II and chromosome V were estimated to be 4.6 Mb and 9.2 Mb in length, respectively. The genome has a total length of about 42 Mb which is more than 3 times larger than the first completely sequenced eukaryotic genome of Saccharomyces cerevisiae. The entire genome sequence of Neurospora crassa was determined in collaboration with the Whitehead Institute for Biomedical Research (now Broad Institute) in Cambridge, Massachusetts, USA (Galagan et al. 2003). About 20 Mb of overlapping, non-redundant sequence data, mostly derived from chromosome II and V were submitted to MIPS generated by MWG BIOTECH AG. The Whitehead Institute made its third release of sequencing data (38 Mb total length) in February 2002 and provided a putative gene set (10,082 genes) for analysis. The sequencing project of Neurospora crassa chromosome II and V as well as the manual annotation of the complete genome was supported by the Deutsche Forschungsgemeinschaft (DFG). The project was coordinated by Dr. Ulrich Schulte at the Institute of Biochemistry, Heinrich-Heine-University, Düsseldorf. MIPS supplied the informatics support for this project (Schulte et al. 2002). MNCDB

CYGD – Yeast

A breakthrough in genome research was the determination of the first complete eukaryotic genome sequence of the well-studied budding yeast Saccharomyces cerevisiae finished in 1996. The Comprehensive Yeast Genome Database (CYGD) aims at a comprehensive presentation of information about the genomic structure of Saccharomyces cerevisiae and the integration of data from former systematic functional analysis projects like SCDEGEN and EUROFAN I&II.

The CYGD project was supported by the European Commission as part of the FP5 program started in late 1999. The project aims at creating a unique resource of knowledge about the genome of Saccharomyces cerevisiae and related organisms. A new infrastructure was developed, combining data generated by high-throughput methods in the laboratory with information extracted from publications, results from bioinformatics analysis and expert knowledge. The project generated a new quality of a genome resource, integrating distributed database components and data acquisition sources. The project was coordinated by MIPS, partners were the Biomax Informatics GmbH, Martinsried; Institut Pasteur, Paris; Universite Louis-Pasteur, Strasbourg; INRA, Thiverval-Grignon; GBF, Braunschweig; Unversitat de Valencia, Valencia; Universite Libre de Bruxelles, Brussels. CYGD

Comprehensive fungal genome analysis

Beside the main projects described above, we aim to provide a standard bioinformatics analysis for all publicly available fungal genome sequences in terms of automatic gene modelling (in case the sequencing project does not provide valuable sets) and automatic protein analysis. To achieve this, we process the genomes using a standard workflow of the Pedant3 suite which provides an intuitive user interface to the resulting data sets. PEDANT fungal genomes