Functional genomics of fungal morphogenesis

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fun with fungi

Project group "Functional genomics of fungal morphogenesis" (principal investigator: Minou Nowrousian) at the Department of General and Molecular Botany at the Ruhr-Universität Bochum.
Filamentous fungi grow in form of hyphae (elongated, branched cell filaments). They can aggregate to form complex structures, e.g. fruiting bodies in which spores are formed. We are interested in the genetic basis of these differentiation processes. To analyze how fruiting body formation is regulated at the molecular level, we use mutant strains that are blocked at early stages of development and compare gene expression in the mutants to that of the wild type using microarray analyses, a combination of laser microdissection and RNA-seq, and quantitative real time PCR. Additionally, we compare gene expression in several fungal species to identify expression patterns that are evolutionary conserved (comparative functional genomics). Genes with similar regulation will help to define a core group of genes involved in fungal fruiting body development. More details about these projects can be found on the projects page or in several publications.

Latest results from the comparative functional genomics project:

The mitochondrial genome of Pyronema confluens was sequenced recently, in addition to the previously sequenced nuclear genome. P. confluens is a member of the early-diverging Pezizomycete lineage of filamentous ascomycetes, and no mitochondrial genome had been sequenced from this lineage. With more than 191 kb, the mitochondrial genome of P. confluens is among the largest within the fungi, indicating that a trend towards mitochondrial genome expansion was already present in the ancestor of filamentous ascomycetes.

In a joint effort at the Department of General and Molecular Botany, we have used available RNA-seq data of the filamentous ascomycetes Pyronema confluens and Sordaria macrospora as well as the Taphrinomycete Schizosaccharomyces pombe to conduct an analysis of RNA editing during sexual development. We found A-to-I RNA editing during sexual development in the two filamentous ascomycetes, but not in the yeast S. pombe. Furthermore, we found that A-to-I editing increased during later stages of sexual development, and that it was not detectable in S. macrospora mutants that were blocked relatively early in fruiting body development.

In a collaboration organized by the labs of Gregory Jedd and Jason Stajich, the genome of the Taphrinomycete Neolecta irregularis was sequenced. In contrast to many relatives that grow as yeasts, N. irregularis makes complex multicellular structure in the form of fruiting bodies. A search for genes conserved in N. irregularis and the Pezizomycotina (filamentous ascomycetes), but absent or divergent in budding or fission yeasts uncovered a group of more than 1000 genes enriched for functions related to endomembrane systems. These genes might be interesting candidates for future functional studies to determine their role in fungal multicellular development. Furthermore, with respect to the evolution of RNA editing during fungal sexual differentiation, it will be interesting to study transcriptomics data from different stages of N. irregularis development.

Publications:

Nowrousian M (2016) Complete mitochondrial genome sequence of the Pezizomycete Pyronema confluens. Genome Announc 4: e00355-16 Paper at Genome Announcements

Teichert I, Dahlmann T, Kück U, Nowrousian M (2017) RNA editing during sexual development occurs in distantly related filamentous ascomycetes. Genome Biol Evol 9: 855-868 Paper at Genome Biology and Evolution

Nguyen TA, Cissé OH, Wong JY, Zheng P, Hewitt D, Nowrousian M, Stajich JE, Jedd G (2017) Innovation and constraint leading to complex multicellularity in the Ascomycota. Nat Commun 8:14444, doi: 10.1038/ncomms14444 Paper at Nature Communications