Comparative genomics of Knoxdaviesia species in the Core Cape Subregion

[摘要] 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 frominfructescences to young flower heads (inflorescences). Knoxdaviesia proteae is a specialistrestricted to one Protea species, while the generalist K. capensis occupies a range of Proteaspecies. Within young flower heads, Knoxdaviesia species grow vegetatively, but switch tosexual reproduction once flower heads mature into enclosed infructescences. Nectar becomesdepleted and infructescences are colonised by numerous other organisms, including thearthropod vectors of the fungi.The aim of this dissertation was to study the ecology of K. capensis and K. proteae bymaking use of their genome sequences. Knoxdaviesia belongs to the familyGondwanamycetaceae, for which no genomes were available at the start of this study. UsingIllumina technology, we determined the genome sequences of both CCR Knoxdaviesiaspecies and applied them to investigate reproduction, substrate use and tolerance tocompetition.Population genetic studies on K. capensis and K. proteae have revealed massive diversity,suggesting an outcrossing reproductive strategy. To determine the genetic basis for thisdiversity, 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 requirean individual of the opposite mating type for sexual reproduction. The MAT loci of the twoKnoxdaviesia species were almost identical, reflecting their phylogenetic relatedness. Thefeatures of the Knoxdaviesia MAT1-2-7 gene also suggested a historic recombination eventbetween the MAT1-1 and MAT1-2 idiomorphs.The carbon resources that Knoxdaviesia species utilise were investigated with phenomeassays and compared to the carbon usage profile of a Protea pathogen, Ceratocystisalbifundus. Knoxdaviesia capensis, the generalist, utilised the widest range of substrates,whereas the pathogen utilised the least. The Knoxdaviesia species were able to grow on allmonosaccharides that occur in Protea nectar. The predicted proteins in the Knoxdaviesia andC. albifundus genomes suggested that cell wall degradation is important to the nutrition ofKnoxdaviesia species in infructescences, whereas the pathogen prefers plant storage polysaccharides. Overall, carbon metabolism in three ecologically different, but related fungireflected their ecological adaptations.Knoxdaviesia species appear to be effective competitors in infructescences. Few secondarymetabolite biosynthesis clusters were, however, detected from the K. capensis and K. proteaegenomes. This may suggest that it is the antimicrobial products of Streptomyces bacteria thatrid infructescences of fungal competitors. The few secondary metabolite clusters of theKnoxdaviesia species likely produce compounds that enable them to tolerate these bacteriaand arthropod and nematode predation. Proteins involved in cell defence were also detectedamong the predicted secreted proteins of K. capensis and K. proteae. Knoxdaviesia proteaeappears to have some non-functional secondary metabolite clusters and secretes less celldefence proteins than K. capensis, suggesting that its specialisation on a single host hasresulted in the loss of some functions.

[发布机构] Stellenbosch University