Computational Biology

Introduction

The arrival of next generation sequencing techniques has opened up a wide range of new research areas to study plant microbe interactions. The genomes of phytopathogenic and beneficial fungi can now be cost-effectively sequenced and gene expression profiles can be determined on a genome-wide scale for both the host plant and the pathogen or endophyte. Assembly, functional annotation and comparative analysis of the genomes of plant associated fungi will provide important novel resources to study the fungal side of plant–parasite and plant-endophyte interactions and to obtain insights into genomic (co-)evolution of interacting organisms. We focus on applying and developing computational tools to provide these resources. Our research includes collaborations with groups within the Department as well as tight communication with the local central computing facility SUSAN and the Max Planck Genome Centre Cologne (GCC). In addition to our main topics we act as a consultancy for any bioinformatics related question.

*Figure 1) Screenshot of the Colletotrichum higginsianum. Genome browser.*

*Figure 1) Screenshot of the Colletotrichum higginsianum. Genome browser.*

Fungal genomes

We are interested in fungal plant-pathogens and plant-endopytes. Among the plant-pathogens we mostly focus on fungi with a biotrophic or hemi-biotrophic lifestyle, i.e. fungi that do not kill the plant (immediately) but form organs, which take up nutrients from a living plant cell, like the powdery mildews (Blumeria graminis) and Colletotrichum higginsianum. Additionally we are trying to uncover the molecular signatures underlying endophytism and the origin of pathogenicity in Colletotrichum by comparing endophytic and pathogenic Colletotrichum species. To address these topics we are sequencing whole genomes using 454 (Roche) and Illumina technologies. The bioinformatics related topics include genome assembly, functional annotation and comparative analysis. Web-services are implemented to provide public access to the data (at present for the powdery mildews and Colletotrichum higginsianum).

*Figure 2) Picture of the model plant Arabidopsis thaliana (a). Gene expression profiles of Arabidopsis thaliana plants with different immune responses (b).*

*Figure 2) Picture of the model plant Arabidopsis thaliana (a). Gene expression profiles of Arabidopsis thaliana plants with different immune responses (b).*

Regulatory mechanisms

To study regulatory processes during infection, genome-wide gene expression profiles are being examined for the host plant and the fungal pathogen. The model plant Arabidopsis thaliana is primarily used to study immune response systems in plants. On the pathogen side biotrophic fungi are used to study attack mechanisms. Examples of high throughput methodologies used include microarrays, RNA-seq and ChIP-seq. Analyses of these data need solid statistical and computational approaches.

*Figure 3) Wooden usb stick*

*Figure 3) Wooden usb stick*

Bioinformatics support

Many graduate students and post-docs in the department perform high throughput experiments yielding large data sets. In order to facilitate the analysis related to bioinformatics, ´consultations´ can be requested and short workshops and courses on topics like the analysis of sequencing data and statistical data analysis using R were developed for graduate students and post-docs from the whole institute.