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Implementing modern species delimitation techniques into fungal taxonomy: Aspergillus charting the course
Sklenář, František ; Hubka, Vít (advisor) ; Haelewaters, Danny (referee) ; Janko, Karel (referee)
This thesis focuses on the implementation of modern methods and approaches for species delimitation in the genus Aspergillus, an economically important fungal genus and model organism. So far, taxonomic studies in Aspergillus regularly included multiple DNA loci (typically four), and the phylogenetic analysis itself mostly consisted of calculating a phylogenetic tree based on individual loci and the concatenated dataset, or less commonly on genealogical concordance principles. Additionally, the datasets usually contained only a limited number of strains per species. The inclusion of more sophisticated phylogenetic species delimitation methods (mostly based on Multispecies coalescent model) in Aspergillus taxonomy adds a whole new layer to the analysis that ensures much higher objectivity of taxonomic decisions. Each of the eight presented papers contains a taxonomic treatment of a particular part of the genus with phylogenetic analyses based on datasets containing DNA sequences from three to six loci or whole genome data (series Nigri). The available molecular data are analyzed by a gradually refined set of phylogenetic species delimitation methods reflecting progress made between years 2017 and 2022. The individual papers also examine some specific characteristics that suitably complement the...
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Molecular and Genomic Methods for Analyzing Hybridization in Aspergillus and other Fungi
Jirkovský, Pavel ; Sklenář, František (advisor) ; Kolařík, Miroslav (referee)
Interpecies hybridization is being studied since the first half of 20. century, when it was described based on phenotypical traits on plant model. Study of this process was historically centred around botanical studies, while its importance in mycology is just being uncovered in recent years. Introgression is a phenomenon that can occur when hybrid backcrosses with one of the parental species. Based on recent studies it is apparent that hybridization played its role in evolution of MAT locus genes of Neurospora, transfer of adaptive traits with Ophiostoma species (invasive pathogen of elm trees). Within Aspergillus family hybridization was described both on intraspecific and interspecific level. More detailed study of this process and improving of used methods could potentially help in clinical application by uncovering adaptive genes responsible for resistance towards antimycotics, higher virulence and other traits.
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Species limits within Aspergillus section Restricti inferred from multiple gene phylogenies and phenotype analysis
Sklenář, František ; Hubka, Vít (advisor) ; Janko, Karel (referee)
Section Restricti is one of the last sections of the genus Aspergillus that hasn't been revised in the modern taxonomic era. All species are osmophilic, have simple morphology and they are mainly important because of the food, feed and seed spoilage, some of them also have negative influence to the indoor air. The section consists of seven species according to the last taxonomic revision from 2008 based only on molecular data. It currently consists of six asexual and one homothalic species. 126 isolates from the section coming from four continents were studied in this thesis, including ex-type strains. Revision of the section was carried out combining molecular phylogenetic analysis and conventional taxonomic methods. Modern methods of species delimitation based on multispecies coalescent model were used for the phylogenetic reconstruction. From the conventional methods analysis of morphology (macro- and micromorphology including scanning electron microscopy) and physiology (ability of growing in osmotic gradient and several different temperatures) was performed. Apart from the seven known species, eight new undescribed species were discovered. Majority of the new species belongs to the Aspergillus penicillioides species complex. Key words: Aspergillus restrictus, osmophilic fungi, species...
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Vegetative incompatibility in filamentous ascomycetes
Glässnerová, Kateřina ; Hubka, Vít (advisor) ; Sklenář, František (referee)
Vegetative incompatibility is a process occurring during vegetative growth in filamentous fungi which can prevent fusion of hyphae between individuals. In case of hyphal fusion between two individuals with genetically incompatible combination of alleles of vegetative incompatibility genes (i.e. het or vic genes), the newly-emerged heterokaryotic cell is destroyed via programmed cell death, which can be mediated in various ways. The purpose of this mechanism can be to preserve the genetic individuality of an individual or to prevent the transmission of a deleterious cytoplasmatic elements (e.g. mycoviruses). Exploring the vegetative incompatibility genes plays an important role for example in the induction of sexual state in vitro or in the study of speciation mechanisms in fungi. On the molecular-genetic level, vegetative incompatibility has been so far described in detail only in three ascomycete species. This thesis aims to summarize our knowledge concerning the significance of vegetative incompatibility and genetical mechanisms that underlie this process. Key words: vegetative incompatibility, het genes, vic genes, mat locus, programmed cell death, Neurospora crassa, Podospora anserina, Cryphonectria parasitica
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Species limits within Aspergillus section Restricti inferred from multiple gene phylogenies and phenotype analysis
Sklenář, František ; Hubka, Vít (advisor) ; Janko, Karel (referee)
Section Restricti is one of the last sections of the genus Aspergillus that hasn't been revised in the modern taxonomic era. All species are osmophilic, have simple morphology and they are mainly important because of the food, feed and seed spoilage, some of them also have negative influence to the indoor air. The section consists of seven species according to the last taxonomic revision from 2008 based only on molecular data. It currently consists of six asexual and one homothalic species. 126 isolates from the section coming from four continents were studied in this thesis, including ex-type strains. Revision of the section was carried out combining molecular phylogenetic analysis and conventional taxonomic methods. Modern methods of species delimitation based on multispecies coalescent model were used for the phylogenetic reconstruction. From the conventional methods analysis of morphology (macro- and micromorphology including scanning electron microscopy) and physiology (ability of growing in osmotic gradient and several different temperatures) was performed. Apart from the seven known species, eight new undescribed species were discovered. Majority of the new species belongs to the Aspergillus penicillioides species complex. Key words: Aspergillus restrictus, osmophilic fungi, species...
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Mechanisms of water stress adaptations of the filamentous fungi
Sklenář, František ; Hubka, Vít (advisor) ; Nováková, Alena (referee)
Some species of the filamentous fungi can grow on the substrates with low water activity that have either low water content or high concentration of osmotically active substances. These fungi are usually called osmotolerant or xerotolerant. They occur particularly in the soil of arid areas and in hypersaline environments. Economically important species cause spoilage of stored food, seed and feed. This thesis brings the summary of physiological and morphological adaptations of fungal organisms to water stress and deals with the molecular genetic background of these adaptations. The current taxonomic classification of the fungal organisms adapted to grow at low water activity is summarized. Separate chapters are dedicated to the influence of different osmotically active substances on the phenotype of the fungi and to the possibilities of using media with osmotically active substances for taxonomic purposes.
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