Doctoral Degrees (Botany and Zoology)
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Browsing Doctoral Degrees (Botany and Zoology) by Author "Aylward, Janneke"
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- ItemComparative genomics of Knoxdaviesia species in the Core Cape Subregion(Stellenbosch : Stellenbosch University, 2017-03) Aylward, Janneke; Dreyer, L. L.; Roets, Francois; Steenkamp, Emma T.; Wingfield, Brenda D.; Wingfield, Michael J.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Knoxdaviesia capensis and K. proteae are saprotrophic fungi that inhabit the seed cones (infructescences) of Protea plants in the Core Cape Subregion (CCR) of South Africa. Arthropods, implicated in the pollination of Protea species, disperse these native fungi from infructescences to young flower heads (inflorescences). Knoxdaviesia proteae is a specialist restricted to one Protea species, while the generalist K. capensis occupies a range of Protea species. Within young flower heads, Knoxdaviesia species grow vegetatively, but switch to sexual reproduction once flower heads mature into enclosed infructescences. Nectar becomes depleted and infructescences are colonised by numerous other organisms, including the arthropod vectors of the fungi. The aim of this dissertation was to study the ecology of K. capensis and K. proteae by making use of their genome sequences. Knoxdaviesia belongs to the family Gondwanamycetaceae, for which no genomes were available at the start of this study. Using Illumina technology, we determined the genome sequences of both CCR Knoxdaviesia species and applied them to investigate reproduction, substrate use and tolerance to competition. Population genetic studies on K. capensis and K. proteae have revealed massive diversity, suggesting an outcrossing reproductive strategy. To determine the genetic basis for this diversity, we used the genomes to identify and characterise their mating type (MAT) loci. Each species contained only a single MAT idiomorph per isolate, indicating that they require an individual of the opposite mating type for sexual reproduction. The MAT loci of the two Knoxdaviesia species were almost identical, reflecting their phylogenetic relatedness. The features of the Knoxdaviesia MAT1-2-7 gene also suggested a historic recombination event between the MAT1-1 and MAT1-2 idiomorphs. The carbon resources that Knoxdaviesia species utilise were investigated with phenome assays and compared to the carbon usage profile of a Protea pathogen, Ceratocystis albifundus. Knoxdaviesia capensis, the generalist, utilised the widest range of substrates, whereas the pathogen utilised the least. The Knoxdaviesia species were able to grow on all monosaccharides that occur in Protea nectar. The predicted proteins in the Knoxdaviesia and C. albifundus genomes suggested that cell wall degradation is important to the nutrition of Knoxdaviesia species in infructescences, whereas the pathogen prefers plant storage polysaccharides. Overall, carbon metabolism in three ecologically different, but related fungi reflected their ecological adaptations. Knoxdaviesia species appear to be effective competitors in infructescences. Few secondary metabolite biosynthesis clusters were, however, detected from the K. capensis and K. proteae genomes. This may suggest that it is the antimicrobial products of Streptomyces bacteria that rid infructescences of fungal competitors. The few secondary metabolite clusters of the Knoxdaviesia species likely produce compounds that enable them to tolerate these bacteria and arthropod and nematode predation. Proteins involved in cell defence were also detected among the predicted secreted proteins of K. capensis and K. proteae. Knoxdaviesia proteae appears to have some non-functional secondary metabolite clusters and secretes less cell defence proteins than K. capensis, suggesting that its specialisation on a single host has resulted in the loss of some functions.