The genome and transcriptome of Pyronema confluens - a window into fungal evolution
Final Report Abstract
Fungi (Eumycota) are are one of the most species-rich groups within the eukaryotes with a huge impact on nearly all ecosystems as well as for agriculture, medicine, pharmacology and biotechnology. However, their differentiation processes are little understood, even though most symbiotic or pathogenic interactions as well as the production of pharmaceutically or biotechnologically relevant metabolites are restricted to specific stages of the fungal life cycle. Therefore, the analysis of fungal differentiation processes is essential for understanding the impact of fungi on ecology including human life as well as for the use of fungi in biotechnological applications. As part of the project, we have sequenced the genome and several transcriptomes of Pyronema confluens. This species is a member of the basal Pezizomycete group of filamentous ascomycetes, and at the beginning of the project, only one Pezizomycete genome was available, namely that of the truffle (Tuber melanosporum). The truffle genome is unusually large and repeat-rich for a filamentous ascomycete. Our results show that the P. confluens genome is more similar in size and repeat content to higher filamentous ascomycete genomes, indicating that the differing features of the truffle genome might be life style-specific adaptations. Apart from this, we found that the genomic environment of the mating-type genes that is conserved in higher filamentous ascomycetes is only partly conserved in P. confluens; thus P. confluens might reflect an "intermediate state"’ in the evolution of mating type loci. Furthermore, we found that the P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. The identification of a frq homolog in P. confluens that was shown to be rhythmically expressed under constant conditions suggests association of frq with the circadian clock in the last common ancestor of filamentous ascomycetes. In addition to the large-scale genomic/transcriptomic analyses, we focused on several candidate genes based on their expression during development in different fungi, and functionally characterized the genes asf1, chs7, and sec22. The bioinformatics techniques that were established as part of the project could also be applied in a number of scientific collaborations on the analysis of development and evolution in fungi. This included the identification of causative mutations through mutant genome sequencing, the establishing of laser microdissection/RNA-seq for S. macrospora, and genome and transcriptome projects for Lichtheimia corymbifera and Trichosporon oleaginosus. The genome and transcriptome data that were generated as part of the project are available in public databases, and can be used for future comparative genomics and transcriptomics analyses to further improve our understanding of the evolution of complex multicellular structures in fungi.
Publications
- (2012) Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development. BMC Genomics 13: 511
Teichert I, Wolff G, Kück U, Nowrousian M
(See online at https://doi.org/10.1186/1471-2164-13-511) - (2012) The histone chaperone ASF1 is essential for sexual development in the filamentous fungus Sordaria macrospora. Mol Microbiol 84: 748-765
Gesing S, Schindler D, Fränzel B, Wolters D, Nowrousian M
(See online at https://doi.org/10.1111/j.1365-2958.2012.08058.x) - (2013) Suppression subtractive hybridization and comparative expression analysis to identify developmentally regulated genes in filamentous fungi. J Basic Microbiol 53: 742-751
Gesing S, Schindler D, Nowrousian M
(See online at https://doi.org/10.1002/jobm.201200223) - (2013) The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. PLoS Genet 9: e1003820
Traeger S, Altegoer F, Freitag M, Gabaldon T, Kempken F, Kumar A, Marcet-Houben M, Pöggeler S, Stajich JE, Nowrousian M
(See online at https://doi.org/10.1371/journal.pgen.1003820) - (2014) New insights into the roles of NADPH oxidases in sexual development and ascospore germination in Sordaria macrospora. Genetics 196: 729-744
Dirschnabel DE, Nowrousian M, Cano-Domínguez N, Aguirre J, Teichert I, Kück U
(See online at https://doi.org/10.1534/genetics.113.159368) - (2015) Analysis of circadian rhythms in the basal filamentous ascomycete Pyronema confluens. G3 (Bethesda)
Traeger S, Nowrousian M
(See online at https://doi.org/10.1534/g3.115.020461) - (2015) Functional analysis of developmentally regulated genes chs7 and sec22 in the ascomycete Sordaria macrospora. G3 (Bethesda) 5: 1233-1245
Traeger S, Nowrousian M
(See online at https://doi.org/10.1534/g3.115.017681) - (2015) Genomics and transcriptomics of the oilaccumulating basidiomycete yeast Trichosporon oleaginosus: insights into substrate utilization and alternative evolutionary trajectories of fungal mating systems. mBio 6: e00918-15
Kourist R, Bracharz F, Lorenzen J, Kracht O, Chovatia M, Daum C, Deshpande S, Lipzen A, Nolan M, Ohm RA, Grigoriev IV, Sun S, Heitman J, Brück T, Nowrousian M
(See online at https://doi.org/10.1128/mBio.00918-15)
