Genetics - Theses
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ItemThe genetic and morphological characterisation of the zebrafish intestinal mutant setebos(University of Melbourne, 2010)Colorectal cancer (CRC) arises by mutation of tumour suppressors and oncogenes that deregulate the genetic programmes that control intestinal turnover and homeostasis. The zebrafish intestinal epithelium shares extensive phenotypic and genetic homology with the mammalian intestine, providing a genetically tractable model organism for the discovery and characterisation of novel genes required for intestinal development. Increased knowledge of the genetic control of intestinal development may reveal new therapeutic avenues for the treatment of CRC. The Liverplus mutagenesis screen identified zebrafish embryos defective in endoderm organ morphogenesis, including the intestinal mutant setebos, described herein. This study reports the positional cloning of the setebos mutant locus, identifying a premature stop codon as the responsible mutation in the gene nucleolar protein 8 (nol8). Microinjection of wildtype nol8 mRNA rescued setebos developmental abnormalities whereas morpholino oligonucleotide-mediated knockdown of Nol8 phenocopied setebos morphology in wildtype embryos, providing functional proof that nol8 is the mutated locus underlying the setebos phenotype. This study demonstrated that Nol8 is essential for zebrafish survival and that nol8 mRNA is widely expressed in actively proliferating tissues of the zebrafish embryo at 72 hours post fertilisation (hpf), when developmental abnormalities in setebos mutants first become apparent. Northern blot analyses revealed that setebos mutants accumulate an intermediate ribosomal RNA (rRNA) orthologous to mammalian 36S at the expense of downstream 32S rRNA; defects predicted to result in reduced biogenesis of 28S rRNA. Bioanalyzer analyses confirm that setebos mutants are preferentially impaired for 28S biogenesis. 28S, 5.8S and 18S rRNA molecules combine with ribosomal proteins to form functional ribosomes, which are essential for translation and cellular growth. Defects in ribosome biogenesis have been shown to activate the tumour suppressor Tp53, resulting in cell cycle arrest. Tp53 is activated in the setebos mutant, resulting in upregulation of pro-cell cycle arrest genes, including the N-terminally truncated isoform of Tp53, ?113tp53. While this provides a mechanism for the hypoplasia observed in the tissues of the setebos embryo, including the intestinal epithelium, craniofacial cartilages, eyes, liver and pancreas, inactivation of Tp53 signalling in the setebos mutant failed to obviously alter setebos morphology. Nevertheless, activation of Tp53 signalling was found to significantly extend survival of setebos embryos, identifying an important biological role for Tp53 in cells undergoing ribosomal stress. Multiple human syndromes have been linked to abnormal ribosome biogenesis (ribosomopathies), and several predispose to cancer. Zebrafish haploinsufficient for 17 different ribosomal proteins also display increased cancer susceptibility (Amsterdam et al. 2004; Lai et al. 2009). Tp53 is inactivated in these zebrafish tumours, suggesting that inactivation of Tp53 may be a key event in tumour formation in these animals. In summary, setebos provides an ideal in vivo model to further characterise the link between defective ribosome biogenesis, Tp53 signalling and cancer. Since disruption of Nol8 function preferentially impairs the growth of several highly proliferative embryonic zebrafish tissues in the absence of Tp53 signalling, inhibition of Nol8 may provide a therapeutic avenue for the treatment of Tp53 mutant tumours.
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ItemStructure(University of Melbourne, 2010)MLK2 is a serine/threonine kinase with a N-terminal SH3 domain and a centrally located dual leucine zipper region that defines the mixed lineage kinase family. Motifs for interaction with the small Rho-like GTPases, 14-3-3 signalling adaptor proteins, as well as for nuclear import and export have been identified in MLK2 and other MLK family members, providing the capacity for a large number of diverse interactions. MLK2 extracted from over-expressing cells is catalytically active and long-term over-expression is lethal. A study of the contribution of the SH3 domain, catalytic domain and dual leucine zipper region to the overall activity of MLK2 was undertaken. This investigation utilised targeted mutagenesis to alter the coding sequence of conserved amino acids to produce non-functional and constitutively active protein domains. The SH3 domain contributes to the regulation of catalytic activity by binding within the protein C-terminal domain. Once released from auto-inhibition, the SH3 domain interacts with dynamin and is capable of activating dynamin I GTPase activity, thereby increasing the rates of dynamin mediated endocytosis. Both auto-inhibition and dynamin activation is ablated by substitution of a praline residue within the conserved binding cleft of the SH3 domain. Dim�risation via the dual leucine zipper region is required to achieve full catalytic activity. Substitution within the catalytic domain produced a kinase-inactive protein that was used throughout the study. In addition, this inactive variant also demonstrated the requirement for phosphorylation of the activation loop prior to an increase in catalytic activity. Membrane localisation of MLK2 was demonstrated to be independent of catalytic activity and SH3 domain or leucine zipper binding capacity. MLK2 is a member of the MAPKKK family capable of activating the c-jun N terminal kinases via MKK4 and MKK7. The use of kinase negative MKK4 confirmed the ability of MLK2 to signal to JNK through an alternative MKK protein. Kinase negative MLK2 was a target for JNK phosphorylation producing a pattern of phosphopeptide TLC-TLE spots with commonalities to autophosphorylated MLK2. Phosphorylation was concentrated within the C-terminal half of the protein where no large functional domains have been identified but a number of smaller motifs are found. Retrophosphorylation was proposed to have a positive effect on MLK2, sustaining activity and signalling that ultimately leads to apoptosis. Stable expression of GFP tagged MLK2 was only achieved with kinase inactive or truncated protein coding constructs, confirming the lethal effect of over-expressing active MLK2. Kinase negative MLK2 expression decreased cell doubling rates, increased the number of fine membrane projections and trafficked to the nucleus in a cell-cycle dependent manner. The CRIB domain allowed for interaction between Cdc42, Rad and MLK2. MLK2 was proposed to influence cytoskeletal remodelling in response to Cdc42 and Rad activation leading to stimulation of the JNK pathway. Finally, MLK2 was has been shown to have a role in the progression of the neurodegenerative pathology of Alzheimer�s disease. Stimulation of the JNK pathway, coupled with the ability to mediate receptor activation by modulation of rates of endocytosis theoretically places MLK2 in a key position in the response to excitory amino acid excitotoxicity, in Huntington�s disease, and to apoER2 activation in Alzheimer s disease. The characterisation of the contributions made by SH3 domain, catalytic domain and dual leucine zipper region to the overall activity of MLK2 will allow for the design and optimisation of novel therapeutic targets aimed at reducing MLK2 activity, opening up new scope for disease management.
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ItemThe roles of a novel group of plastid transporters in glutathione metabolism in arabidopsis(University of Melbourne, 2010)The tripeptide glutathione (GSH) is an important compound with a broad spectrum of functions in plants, including stress responses and is a key element of the intracellular redox buffer that protects cells from oxidation. In Arabidopsis GSH is synthesized in two enzymatic steps by GSH1, found exclusively in the plastids, forming the pathway intermediate ?-glutamylcysteine (?-EC) and then by GSH2 which is located in both plastids and cytosol. This suggests a mechanism for ?-EC export from the plastids and, because the majority of GSH2 transcripts (90%) encode the cytosolic isoform, it is believed that the cytosol may be the main compartment for GSH biosynthesis. In addition, GSH may be efficiently transported between the two compartments to maintain proper homeostasis. However, comparatively little is understood about the mechanisms that control and interconnect these two subcellular GSH pools. The identification and characterization of a novel family of transporters, the CRT Like Transporters (CLTs), has provided further insights into glutathione metabolism in Arabidopsis. The CLT1 gene was originally identified in a screen for mutants resistant to L-Buthionine-SR-sulfoximine (BSO), a synthetic compound used to specifically inhibit GSH1 and GSH biosynthesis. Two paralogues in Arabidopsis, CLT2 and CLT3, were identified and all three CLTs are localized to the plastids. Previous studies have shown the clt1clt2clt3 triple mutant is GSH-deficient in roots and cadmium-sensitive suggesting a role for the CLTs in transporting ?-EC and/or GSH between the plastid and cytosol compartments. In this study redirecting GSH1 activity or GSH biosynthesis exclusively to the cytosol by complementing the Arabidopsis gsh1 and gsh2 mutants with E. coli GSHA and GSHB, respectively, has no significant impact on phenotypes or stress resistance suggesting efficient exchange of ?-EC and GSH between the plastid and cytosol compartments. The use of redox-sensitive roGFP2 reporters in combination with confocal imaging with monochlorobimane and measurements of cytosolic thiols has demonstrated that the clt1clt2clt3 mutant is GSH-deficient in the cytosol but not the plastid in both roots and shoots consistent with a predicted role for CLTs in ?-EC and/or GSH transport. The Arabidopsis gsh2 mutant accumulates high levels of ?-EC in the cytosol. However, the combination of the clt1clt2clt3 mutations with gsh2 did not decrease ?-EC levels suggesting CLTs may not contribute to ?-EC transport in vivo. To further study the roles of the CLTs separately on ?-EC and GSH transport in planta different clt mutations were introduced into transgenic lines expressing plastid- or cytosol-targeted GSH2. These observations suggest that de novo GSH biosynthesis in wildtype Arabidopsis occurs largely in the plastids and that CLT2 and CLT1/CLT3 are mainly involved in ?-EC and GSH export, respectively, in planta.
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ItemInvestigating the mechanisms of zinc homeostasis in Arabidopsis thaliana(University of Melbourne, 2010)Zn is an element essential for all forms of life, and either Zn-deficiency or excess Zn can have serious biological consequences. In plants, Zn levels are controlled by a number of physiological and cellular mechanisms to maintain appropriate physiological concentrations of Zn. This study further characterises the HMA2 and HMA4 transporters by developing a novel technique using the Zn fluorophore Zinpyr-1. A procedure for the use of Zinpyr-1 in Arabidopsis roots was developed and validated which allowed the visualisation and relative quantification of Zn. This technique showed that both hma4 and hma2/hma4 mutants differed in the amount of Zn and its distribution compared to wildtype or hma2. This correlates to previous data showing that hma4 and hma2/hma4 are Zn-deficient in shoots but accumulate Zn in roots. Thus we can say that this Zn- deficiency in shoot occurs due to an inability to load Zn into the xylem for transport to the shoot. To investigate the regulation of Zn-homeostasis, Zn-deficient and hma2/hma4 plants were compared to wildtype in micro-array experiments to test whether plants respond systemically to Zn- deficiency. hma2/hma4 plants are Zn-deficient in shoots but over-accumulate Zn in roots, so genes co-regulated in hma2/hma4 roots and shoots, and genes co-regulated in hma2/hma4 roots and Zn- deficient wildtype roots were identified. 52 and 27 genes were identified in these comparisons respectively as regulated >2-fold in the same direction. These were considered robust as their co-regulation was observed in four measurements, two technical replicates of two biological replicates. promoter
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ItemPopulation genetics and ecology of the lucerne flea, sminthurus viridis, with applications for control(University of Melbourne, 2010)The lucerne flea, Sminthurus viridis (Collembola: Sminthuridae), is a major pest of broadacre grains and pasture throughout southern Australia. Current control methods for this pest rely heavily on the prophylactic use of broad spectrum pesticides and are unlikely to be sustainable. Development of an integrated pest management (IPM) strategy is needed. However, this requires a greater understanding of the biology, ecology and genetics of S. viridis. This thesis aims to address this by examining the population genetics and life-cycle of this pest, as well as investigating chemical and biological control methods. Laboratory pesticide bioassays were used to compare the response of S. viridis with the redlegged earth mite (Halotydeus destructor) to six broad spectrum pesticides. Sminthurus viridis displayed significantly higher pesticides tolerance than H. destructor and the tolerance differences were greater for the synthetic pyrethroids than the organophosphorous pesticides. This indicates that application rates for S. viridis should be greater than H. destructor and that organophosphates are likely to provide the most effective control of this pest. Seasonal abundance patterns and summer diapause response of S. viridis in south-eastern Australia were investigated using field and shade-house experiments. The seasonal activity agreed with previous studies and parameters predicting autumn emergence were defined. A summer-diapausing egg stage was also confirmed, with diapause eggs accumulating across the season. These results suggest autumn emergence of S. viridis can be predicted for target control strategies, but late-season spraying strategies may be difficult to implement. The species status, mode of reproduction and population genetics of S. viridis were examined using microsatellite markers I developed, together with allozymes and a mitochondrial DNA marker. A single, sexually reproducing species was found with limited gene flow between Australian populations. Genetic similarity between some distant populations was also shown, indicating that wind or human-mediated long-distance dispersal occurs. These findings suggest that management strategies may be more effective when locally developed and need to consider the effects of human- mediated dispersal. The impact of the predatory mite, Bdellodes lapidaria, for controlling S. viridis and its susceptibility to several pesticides were assessed using laboratory and field experiments. Bdellodes lapidaria was more susceptible to the synthetic pyrethroids in the laboratory, but was not affected by pesticide applications in the field. In addition, no detectable predator-prey relationship was found between these species. These results indicate that B. lapidaria is not strongly susceptible to pesticides in the field and may not be an effective predator of S. viridis. Overall, this thesis contributes important knowledge of the pesticide tolerance, life- cycle, population genetics and biological control of S. viridis. These findings highlight ways to improve the effectiveness and sustainability of control methods and bring closer the development of an integrated pest management strategy for S. viridis.
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ItemPopulation genetics and ecology of the lucerne flea, Sminthurus viridis, with applications for control( 2010)The lucerne flea, Sminthurus viridis (Collembola: Sminthuridae), is a major pest of broadacre grains and pasture throughout southern Australia. Current control methods for this pest rely heavily on the prophylactic use of broad spectrum pesticides and are unlikely to be sustainable. Development of an integrated pest management (IPM) strategy is needed. However, this requires a greater understanding of the biology, ecology and genetics of S. viridis. This thesis aims to address this by examining the population genetics and life-cycle of this pest, as well as investigating chemical and biological control methods. Laboratory pesticide bioassays were used to compare the response of S. viridis with the redlegged earth mite (Halotydeus destructor) to six broad spectrum pesticides. Sminthurus viridis displayed significantly higher pesticides tolerance than H. destructor and the tolerance differences were greater for the synthetic pyrethroids than the organophosphorous pesticides. This indicates that application rates for S. viridis should be greater than H. destructor and that organophosphates are likely to provide the most effective control of this pest. Seasonal abundance patterns and summer diapause response of S. viridis in southeastern Australia were investigated using field and shade-house experiments. The seasonal activity agreed with previous studies and parameters predicting autumn emergence were defined. A summer-diapausing egg stage was also confirmed, with diapause eggs accumulating across the season. These results suggest autumn emergence of S. viridis can be predicted for target control strategies, but late-season spraying strategies may be difficult to implement. The species status, mode of reproduction and population genetics of S. viridis were examined using microsatellite markers I developed, together with allozymes and a mitochondrial DNA marker. A single, sexually reproducing species was found with limited gene flow between Australian populations. Genetic similarity between some distant populations was also shown, indicating that wind or human-mediated longdistance dispersal occurs. These findings suggest that management strategies may be more effective when locally developed and need to consider the effects of humanmediated dispersal. The impact of the predatory mite, Bdellodes lapidaria, for controlling S. viridis and its susceptibility to several pesticides were assessed using laboratory and field experiments. Bdellodes lapidaria was more susceptible to the synthetic pyrethroids in the laboratory, but was not affected by pesticide applications in the field. In addition, no detectable predator-prey relationship was found between these species. These results indicate that B. lapidaria is not strongly susceptible to pesticides in the field and may not be an effective predator of S. viridis. Overall, this thesis contributes important knowledge of the pesticide tolerance, lifecycle, population genetics and biological control of S. viridis. These findings highlight ways to improve the effectiveness and sustainability of control methods and bring closer the development of an integrated pest management strategy for S. viridis.
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ItemIdentifying downstream targets of FILAMENTOUS FLOWER, a YABBY transcription factor that promotes organ polarity and lateral growth in Arabidopsis( 2017)Angiosperm leaves are typically polar structures with a distinct arrangement of cell types along the adaxial-abaxial (upper-lower) axis. Studies of leaf development in the model dicot plant Arabidopsis thaliana have shown that adaxial-abaxial patterning is not only associated with the formation of distinct cell types, but also triggers growth along the lateral axis leading to the formation of the leaf blade or lamina. Adaxial-abaxial patterning factors identified in a variety of plants including Arabidopsis, Antirrhinum and maize are either small regulatory RNAs or transcription factors. Although first categorized as being involved in adaxial-abaxial patterning, the YABBY (YAB) family of transcription factors is now thought to play a pivotal role in coordinating various developmental programs involved in leaf blade formation. As part of an approach to identify targets of the Arabidopsis YAB gene FILAMENTOUS FLOWER (FIL), this study generated transgenic lines with inducible FIL activity. Constitutive activation of FIL resulted in the partial abaxialisation of leaves and reduced blade growth, phenotypes that have previously been attributed to ectopic YAB expression. Further analysis showed that constitutive FIL activity increased the rate of cell cycle progression in specific regions of the developing leaf, as well as increasing sensitivity to exogenously applied auxin. The latter phenotype was inferred from increased activity of an auxin-signalling reporter, suggesting that FIL modulates auxin responses in Arabidopsis. Transcriptional profiling with microarrays was subsequently used to monitor genome-wide changes in gene expression following FIL activation. This analysis identified groups of genes that were either positively or negatively regulated by FIL and extensive testing of a subset of these genes showed that some were direct targets. On the basis of these results it is proposed that FIL functions as both a transcriptional activator as well as repressor during leaf development. Among the positively regulated genes identified as FIL targets, two are well-known abaxial patterning factors, KANADI1 (KAN1) and AUXIN RESPONSE FACTOR4 (ARF4). Given the well-defined role these factors play during leaf development, this study focused on their regulation. Analysis of mutant lines lacking activity of the leaf-expressed YABs revealed a significant reduction in KAN1 expression, but not ARF4 expression. These results confirm that FIL is a regulator of KAN1, but presumably regulates ARF4 in combination with other factors. In conclusion, this study identified direct targets of the bifunctional plant transcription factor FIL. Finding that two of these targets promote abaxial cell identity during leaf development supports the case for YABs being important polarity regulators. Given the expression pattern of the YABs, it is argued that YABs are unlikely to function upstream of KAN1/ARF4. Instead, a model is proposed in which YABs promote adaxial/abaxial patterning through a system of positive feedback loops that ultimately maintain the activity of these early abaxial patterning genes during leaf blade formation.
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ItemThe genetic basis of resistance to the Ryanodine Receptor modulator chlorantraniliprole in Drosophila melanogaster( 2017)The development of synthetic insecticides in the mid 20th century lead to a revolution in pest control. However, issues with environmental toxicity, adverse human exposure and insecticide resistance have meant new safer alternative pest control methods are required. Chlorantraniliprole belongs to a promising new class of insecticides that exert control by targeting the Ryanodine Receptor. As this class, the group 28 synthetic diamides, has a unique chemistry and a mode of action that is distinct from most insecticides, its market share has rapidly increased since it was first introduced in 2007. Here, I use genomic, transcriptomic and phenotypic analyses of the Drosophila Genetic Reference Panel (DGRP) to examine the way chlorantraniliprole interacts with an insect’s biology. This research reveals that a novel muscle- associated gene, Stretchin Myosin Light Kinase, is strongly associated with resistance in the DGRP. In addition, a co-expressed set of detoxification enzymes, under control of the Cap ‘n Collar/Keap1 pathway were found to be constitutively up-regulated in a subset of the DGRP and that their transcriptional abundance was correlated with survivorship on chlorantraniliprole. Transgenic ‘knock up’ of one of these putative detoxification enzymes, Cyp12d1, confers increased resistance to chlorantraniliprole and resistance to the related compound cyantraniliprole. Furthermore, a lab selection experiment based on a large Australian population of D. melanogaster also confirms an association between Cyp12d1 and resistance. This contributes to a growing body of evidence suggesting that cytochrome P450 enzymes play a role in chlorantraniliprole resistance. Through the quantitative genetic approaches employed, it is possible to demonstrate that the genetic architecture underpinning resistance changes with dose. Furthermore, as the DGRP was established before the introduction of chlorantraniliprole this study demonstrates that alleles of large effect are pre- existing in naïve populations and such alleles may increase in frequency as this class of insecticides become more widespread. Finally, this study illustrates the systems genetic approach offers unprecedented power to understand the biology perturbed by insecticides.
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ItemThe significance of low level mosaicism in Fragile X Syndrome.( 2017)Fragile X Syndrome (FXS) is the most common single disorder associated with intellectual disability (ID) and autism spectrum disorder (ASD). FXS is fundamentally caused by a trinucleotide CGG sequence repeat expansion within the 5’ untranslated portion of the FMR1 gene, to more than 200 repeats which is called Full Mutation (FM). This is associated with abnormal methylation of this gene’s promoter and silencing of FMR1 expression. To date, the type and severity of the neurocognitive phenotype has been related more closely with the methylation status than with the number of CGG repeats in the FM range. Smaller CGG expansions are called premutation (PM) (55 and 200 CGGs), grey zone (GZ) (45-54 CGGs) and normal size (<44 CGGs) alleles, and are usually associated with presence of an unmethylated FMR1 promoter, and normal FMR1 expression. There is a proportion of FXS individuals in which two or more population of cells can be found, and who are called mosaic or mosaicism. These individuals possess cells with FM and smaller CGG sizes (e.g. Normal, GZ or PM), which lead to milder forms of the FXS phenotype. This PhD explores the clinical and diagnostic significance of low level mosaicism (LLM) and DNA methylation variation amongst different CpG sites within FMR1. The first aim of this study was to define the lower limit of detection LLM of six FMR1 tests currently used in diagnostic laboratories. This was achieved using three FMR1 PCR commercial kits (AmplideXTM, X-Sense and FastFraXTM) targeting the CGG region and three methylation tests (Methylation Specific- Quantitative Melt Analysis [MS-QMA], Sequenom®EpiTYPER system [MALDI-TOF MS] and mSouthern blot) targeting methylation of Exon1/Intron1 boundary region and specific CpG sites within FMR1 promoter. The second aim was to screen a large number of males with ID and ASD of unknown etiology referred for FXS testing to determine the prevalence of mosaicism containing FM together with a normal or GZ allele (cryptic FMR1-FM) who are not being identified as a part of standard FXS testing. This was achieved using MS-QMA and the positive results were confirmed with the FMR1 tests assessed in Aim 1. The third aim of this study was to examine the association between DNA methylation of FMR1 and mRNA levels and severity of intellectual functioning impairment in individuals with a cryptic FMR1-FM identified in Aim 2 and males and females with typical FXS (only FM and PM/FM alleles). Three significant contributions to the FXS field resulting from this PhD are: i) implementation of a new highly sensitive assay for detection LLM missed by standard testing; ii) determination of the prevalence of cryptic FM-FMR1 in males with idiopathic ID/ASD referred for FXS testing; iii) clinical and molecular characterization of LLM and its methylation characterization amongst tissues and CpG sites; and demonstration that LLM levels are significantly correlated with severity of cognitive impairment and ASD as well as FMR1 mRNA levels.
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ItemThe evolution of pathogenicity and isolate variation in Talaromyces marneffei( 2017)The opportunistic fungal pathogen of humans, Talaromyces marneffei, is one of very few pathogens in an order of over a thousand species and the only species that has the capacity to switch between two morphologically distinct growth forms (known as dimorphism). Growth at 25°C results in a saprophytic multicellular, hyphal form while infectious growth in a host occurs as a uninucleate unicellular yeast that resides within phagocytic cells of the immune system. The intracellular niche of T. marneffei differs significantly from the niches of other Talaromycetes. The identification of the mechanisms by which T. marneffei can survive and grow in this intracellular niche is a major aim of this study. Comparisons of the genomes of three closely related non-dimorphic, non-pathogenic species with the T. marneffei genome identified unique features that contribute to niche specific growth and the ability to cause disease. Most significant of these were an overall reduction in genome size and gene number in T. marneffei with substantial gene losses in families responsible for environmental interaction. These and other findings strongly indicate that T. marneffei has adapted to an intracellular host niche distinct from its saprophytic relatives. Against this background of gene loss three gene families were identified that had been significantly expanded in T. marneffei. These expanded gene families showed putative extracellular and cell surface localisation and consisted of cell wall galactomannoproteins (mpl family), aspartyl proteases (pop family) and a family of small proteins with very little functional characterisation in any species (mib family). Genes in the pop, mpl and mib families were over-represented in subtelomeric regions, under positive selection, had copy number variation in T. marneffei isolates and many had high levels of repetitive adjacent sequences including several transposon families. In the host T. marneffei grows as an intracellular pathogen within phagocytes and as such extracellular proteins interact directly with the host. Therefore another aim of this study was to characterise these expanded gene families and their role in pathogenesis. Deletion studies in pop genes revealed roles in yeast cell formation during intracellular growth, while high variability in cell-to-cell protein production for two mib genes suggested a role in cell surface variation when interacting with the host. Understanding the type and degree of variation within the population of a fungal pathogen can reveal its population structure and potential to adapt to stressors such as antifungal compounds. Genome wide variation in the T. marneffei population had yet to be examined therefore an aim of this study was to characterise the degree and type of this variation. To this end several clinical and environmental isolates of T. marneffei were examined for variation in chromosomal structure, which is a common means of generating phenotypic variation in other fungi. While no obvious abnormalities were observed, gene copy number variation in subtelomeric regions was widespread and several strains showed specific small mutations with impacts in antifungal resistance and phenotypic instability. Overall this study has revealed the genomic and genetic changes within T. marneffei and between it and other Talaromycetes. Many of these changes help to explain its unique niche as an intracellular pathogen within an almost entirely non-pathogenic clade. This research also highlights specific genes and gene families with roles in this pathogenesis and identifies potential therapeutic targets and genes involved in host interactions for future investigation.