Biology subjects

Gehrmann, T.

Publications and source records attributed to Gehrmann, T..

3 recordsLinked to original sources

bioRxiv2017

Variants in RNA-Seq data show a continued mutation rate during strain preservation of Schizophyllum commune

BackgroundTypical microorganism studies link genetic markers to physiological observations, like growth and survival. Experiments are carefully designed, comparing wildtype strains with knockout strains, and replications are conducted to capture biological variation. To maintain monoclonal strains, strain preservation systems are used to keep the number of generations between the primary stock and the experimental measurement low, to decrease the influence of spontaneous mutations on the experimental outcome. The impact of spontaneous mutations during the minimal number of growth cycles for the experimental design is, however, poorly studied.\n\nResultsWe set out to characterize the mutation landscape using a transcriptomic dataset of Schizophyllum commune, a laboratory model for mushroom formation. We designed a methodology to detect SNPs from the RNA-seq data, and found a mutation rate of 1.923 10-8 per haploid genome per base per generation, highly similar to the previously described mutation rate of S. commune in the wild. Our results imply that approximately 300 mutations are generated during growth of a colony on an agar plate, of which 5 would introduce stop codons. Knock-outs did not incur an increase of mutations and chromosomal recombination occurring at mating type loci was frequent. We found that missense and nonsense SNPs were selected against throughout the experiment. Also, most mutations show a low variant allele frequency and appear only in a small part of the population. Yet, we found 40 genes that gained a nonsense mutation affecting one of its annotated protein domains, and more than 400 genes having a missense mutation inside an annotated protein domain. Further, we found transcription factors, metabolic genes and cazymes having gained a mutation. Hence, the mutation landscape is wide-spread and has many functional annotations.\n\nConclusionsWe have shown that spontaneous mutations accumulate in typical microorganism experiments, where one usually assumes that these do not happen. As these mutations possibly confound experiments they should be minimized as much as possible, or, at least, be trackable. Therefore, we recommend labs to ensure that biological replicates originate from different parental plates, as much as possible.

genomics↗

bioRxiv2017

Patterns of conservation and diversification in the fungal polarization network

The combined actions of proteins in networks underlie all fundamental cellular functions. Deeper insights into the dynamics of network composition across species and their functional consequences are crucial to fully understand protein network evolution. Large-scale comparative studies with high phylogenetic resolution are now feasible through the recent rise in available genomic datasets of both model and non-model species. Here we focus on the polarity network, which is universally essential for cell proliferation and studied in great detail in the model organism, Saccharomyces cerevisiae. We examine 34 proteins, directly related to cell polarization, across 200 fungal strains/species to determine evolution of the composition of the network and patterns of conservation and diversification.\n\nWe observe strong protein conservation for a group of 16 core proteins: 95% of all strains/species possess at least 75% of these proteins, albeit in varying compositions. We find high levels of variation in prevalence and sequence identity in the remaining 18 proteins, resulting in distinct lineage-specific compositions of the network in the majority of strains/species. We test if the observed diversification in network composition correlates with potential underlying factors and find that lineage, lifestyle, and genetic distance co-vary with network size. Yeast, filamentous and basal unicellular fungi form distinctive groups based on these analyses, with substantial differences to their polarization network. Our study shows that evolution of the fungal polarization network is highly dynamic, even between closely related species, and that functional conservation is achieved by varying structural conservation of the fungal polarization proteins.\n\nData DepositionSequence alignments used are available upon request.

evolutionary biology↗

bioRxiv2017

Nucleus Specific Expression In The Multinucleated Mushroom-Forming Fungus Agaricus bisporus Reveals Different Nuclear Regulatory Programs

MotivationFungi are essential in nutrient recycling in nature. They also form symbiotic, commensal, parasitic and pathogenic interactions with other organisms including plants, animals and humans. Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are even different nuclear types within a cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the cultivated, mushroom forming basidiomycete Agaricus bisporus contains 2 to 25 nuclei of two nuclear types, P1 or P2, that originate from two parental strains. Using RNA-Seq data, we wish to assess the differential mRNA contribution of individual nuclear types in heterokaryotic cells and its functional impact.\n\nResultsWe studied differential expression between genes of the two nuclear types throughout mushroom development of A. bisporus in various tissue types. The two nuclear types, produced specific mRNA profiles which changed through development of the mushroom. The differential regulation occurred at a gene and multi-gene locus level, rather than the chromosomal or nuclear level. Although the P1 nuclear type dominates the mRNA production throughout development, the P2 type showed more differentially upregulated genes in important functional groups including genes involved in metabolism and genes encoding secreted proteins. Out of 5,090 karyolelle pairs, i.e. genes with different alleles in the two nuclear types, 411 were differentially expressed, of which 246 were up-regulated by the P2 type. In the vegetative mycelium, the P2 nucleus up-regulated almost three-fold more metabolic genes and cazymes than P1, suggesting phenotypic differences in growth. A total of 10% of the differential karyollele expression is associated with differential methylation states, indicating that epigenetic mechanisms may be partly responsible for nuclear specific expression.\n\nConclusionWe have identified widespread transcriptomic variation between the two nuclear types of A. bisporus. Our novel method enables studying karyollelle specific expression which likely influences the phenotype of a fungus in a polykaryotic stage. This is thus relevant for the performance of these fungi as a crop and for improving this species for breeding. Our findings could have a wider impact to better understand fungi as pathogens. This work provides the first insight into the transcriptomic variation introduced by genomic nuclear separation.

microbiology↗