Biology and pathology of the Eucalyptus foliar pathogen Teratosphaeria destructans

The Eucalyptus foliar pathogen Teratosphaeria destructans causes severe and widespread damage in South East Asian and South African plantations. This study aimed to investigate the biology and pathology of T. destructans. By conducting whole genome sequencing of this pathogen, the mating-type locus (MAT1) was characterised and the distribution of mating type idiomorphs was determined for isolates in China, Indonesia, South Africa, Thailand and Vietnam. Teratosphaeria destructans was found to have a heterothallic mating system and investigated populations harboured a single dominant mating type. Population structure was evaluated by developing and applying polymorphic microsatellite markers. Isolates grouped into three clusters, corresponding to their sampled regions. Populations had low genotypic diversity and no signs of recombination, indicating asexual reproduction. The microsatellites were subsequently exploited as a diagnostic tool to identify T. destructans as the causal organism for a disease outbreak in Malaysia. This population had the highest genotypic diversity, even distribution of mating types and evidence of recombination, contradicting previous findings. All investigated populations represented non-native introductions into their sampled areas and the origin of this pathogen remains unknown. Transcriptome analyses from a South African isolate grown on nitrogen-deficient and complete media enabled assessment of overall gene expression and pathogenicity determinants of T. destructans. The most highly expressed genes under both conditions were associated with infection. In total, 224 genes were highly upregulated and 92 highly downregulated (logFC > 1) in the nitrogen-starved environment. Pathogenicity- and virulence-associated genes were upregulated, including several effectors, CAZymes, genes detoxifying toxic compounds, kinases and phytotoxins. Genes involved in nitrogen metabolism and response to nitrosative stress were downregulated. The hypothesis that nitrogen starvation mimics a similar response to what would be expected from in planta studies was supported. In addition, pheromone, pheromone receptors and signalling pathway genes were identified in two isolates of opposite mating types. This represents the first study to investigate genes involved in signalling for a compatible sexual partner for any Mycosphaerellales species. Identified pheromone genes were upregulated in a mating-type-dependent manner, whereas the other identified genes were expressed in both isolates. The work presented in this thesis highlights the need for strict biosecurity measures for T. destructans and lays the foundation for future host-interaction studies and identification of pheromone genes in other Dothideomycete species.Thesis (PhD (Genetics))--University of Pretoria, 2021.National Research Foundation of South Africa (NRF) (Grant Number: 11824).The Department of Science and Technology (DST) - NRF Centre of Excellence in Plant Health Biotechnology (CPHB).The Department of Science and Technology (DST) - NRF Centre of Excellence in Tree Health Biotechnology (CTHB).The Tree Protection Co-operative program (TPCP).The SARChI chair in Fungal Genomics (Grant number: 98353).University of Pretoria (UP) Doctoral Research Bursary for financial support.GeneticsPhD (Genetics)Unrestricte