Over the past half year, Professor Ronald de Vries and co-workers have published 10 papers with a strong bioinformatics component in the field of Fungal Physiology. The results are highly relevant for both our fundamental understanding of this process as well as for the improvement of biotechnology applications based on plant biomass.

The research includes genome analysis, construction of genome-based metabolic models, transcriptome studies, and proteome studies to understand the response of fungi to different plant biomass substrates. All studies are based on significant amounts of experimental data to support the bioinformatic analysis and contribute to a major research focus of the De Vries group: understanding the degradation of plant biomass and metabolic conversion of the released monomers by fungi.

List of publications

• Genomic and genetic insights into a cosmopolitan fungus, Paecilomyces variotii (Eurotiales). The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet.
• A community-driven reconstruction of the Aspergillus niger metabolic network.
• Duplications and losses of genes encoding known elements of the stress defense system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance.
• Dichomitus squalens partially tailors its molecular responses to the composition of solid wood.
• Enzymatic adaptation of Podospora anserina to different plant biomass provides leads to optimized commercial enzyme cocktails.
• The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi.
• Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli.
• Investigation of inter- and intra-species variation through genome sequencing of Aspergillus section Nigri.
• In silico analysis of putative sugar transporter genes in Aspergillus niger using phylogeny and comparative transcriptomics.

Professor Ronald de Vries is the Fungal Physiology group leader at the Westerdijk Fungal Biodiversity Institute. He is also Professor in Fungal Molecular Physiology at Utrecht University and visiting Professor at the University of Helsinki (Finland).