GSA Poster Session

The emergence of complex animal life forms is one of the major events in the history of life on Earth and it is often a topic of interest and intense disagreements. One of the biggest obstacles to understanding animal evolution is the perceived difficulty of evolving a complex human body from single-cell organisms. Ernst Haeckel, along with some other 19th century biologists believed that body plan organization of sponges (Porifera) is an intermediate step between protists and the simple multicellular animals, such as cnidarian polyps. According to this view, the innermost layers of animal bodies involved in digestion (the sponge choanoderm and the endodermally derived cnidarian gastrodermis or bilaterian gut) were homologous structures. While neglected for a century, this view recently received support from studies comparing expression of several developmental regulatory genes in sponges, cnidarians, and bilaterians. In this project, we will investigate and compare global gene expression profiles of sponge, cnidarian and bilaterian tissues, especially the choanoderm with endoderm, the pinacoderm with ectoderm, and putative sponge larval sensory cells with neuronal and sensory cells of cnidarians and bilaterians. In addition to well-established cnidarian and bilaterian models (including sea anemones and mammals), we will use an emerging sponge model, Sycon capricorn (Calcarea). To generate tissue-specific transcriptomes, we will use the recently developed single-cell sequencing technology, Drop-Seq. We will then map the obtained transcriptomes of the cell types using a combination of in-silico and laboratory approaches. Lastly, we will compare the identified cell types between the selected models to assess their homology. Testing this hypothesis will not only bring us closer to answering the question “where do we come from?”, but it will also generate extensive data that will provide a foundation and resource for understanding the molecular background of evolutionary and developmental origin of complex animal cells and tissues.

Understanding sequence diagnostic signatures associated with mutagenesis mechanisms can facilitate the development of more accurate models for identifying disease causing mutagens. In most genetic variation catalogs, variant data are derived from a mixture of mutagenic processes. This presents a challenge to assigning the mechanistic origins of an individual variant. Information regarding the mechanistic origin of point mutations is present in surrounding DNA sequence. These motifs can reflect the combination of chemical and biochemical influences of neighbouring bases on mutagenesis. We assess whether information from sequence neighborhood can be used to identify mutations resulting from the potent chemical mutagen, ENU. ENU is a synthetic chemical employed in mutagenesis studies, introducing novel point mutations to genomes. We developed a machine learning classifier to discriminate between ENU-induced and spontaneous point mutations in the mouse germline. Our classification results reveal that a combination of k-mer size and representation of second-order interactions among nucleotides was able to improve classification performance in comparison to the naive classifier approach.

Horizontal gene transfer (HGT) is increasingly recognized as a major evolutionary force driving adaptation in prokaryotes. However, the environmental factors that drive the opportunity and relative success of HGT events among natural bacterial populations have yet to be empirically evaluated among closely related strains at the landscape level. Here, we quantified HGT among closely related strains of a plant-associated bacteria, Bradyrhizobium japonicum, using whole genome data and evaluated the predictive power of two major factors frequently hypothesized to affect signals of HGT in natural populations, spatial proximity and ecological similarity. By evaluating HGT among strains sampled in a spatially explicit design across a complex environmental landscape spanning large environmental gradients (e.g. climate, soil and plant characteristics), while accounting for phylogenetic history, our analyses revealed two major results. Firstly, that HGT was more likely to occur when bacterial isolates were sampled in the same or nearby locations supporting the hypothesis that spatial proximity increases the opportunity for HGT. Secondly, that HGT was much more likely between bacterial isolates collected from different locations with similar environmental conditions, despite these locations (in some cases) being hundreds of kilometers apart. This pattern supports the prediction that HGT between dissimilar environments is less likely to be observed because there is a higher probability of receiving maladaptive genes, leading to HGT events that are not selectively maintained in the environment. The results of our analyses provide empirical evidence for the important role of HGT in bacterial adaptation, and the potential for bacteria to adapt to environmental change.

The Continuous Plankton Recorder (CPR) has been used to characterise zooplankton biodiversity along transects covering hundreds of thousands of kilometres in the Southern Ocean CPR survey. We investigated the potential to use DNA metabarcoding (species identification from DNA mixtures using high-throughput DNA sequencing) as a tool for rapid collection of taxonomic data from CPR samples.  In our study, zooplankton were collected on CPR silks along two transects and identified using standard microscopic methods and by sequencing a mitochondrial COI marker. DNA increased the number of metazoan species identified and provided high resolution taxonomy of groups problematic in conventional surveys (e.g. larval echinoderms and hydrozoans).  Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from large plankton such as krill masked the presence of smaller species. Overall, the genetic data represents a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing this powerful DNA metabarcoding approach from the current snapshot studies to the requirements of a long-term monitoring program. Given the continually increasing efficiency of DNA metabarcoding, it is almost certain this approach combined with underway sampling will play an important role in characterising the status and trends of key species in future Southern Ocean monitoring programs.

The olive flounder Paralichthys olivaceus, is one of the most economically important marine aquaculture species, with a selective breeding program to increase aquaculture production in Korea. Production of monosex female stocks is desirable in commercial production since females grow faster and mature later than males. Understanding the sex determination mechanism and developing sex-associated markers will shorten the time for the development of all-female production, thus decreasing the costs of farming. The sex determination mechanism is presently unknown in olive flounder. In this study, we found the sex-associated single nucleotide polymorphism (SNP) markers by next-generation sequencing together with bioinformatics analysis. There were 18,867 SNP loci between males and females. 3 SNP markers, that show significant differences in sexes, were identified, and all of these markers were located in chromosome 9. In order to validate sex-associated markers, artificial gynogenetic diploid, which are genetically females, was produced. A genotype analysis on these 3 SNP markers in males and females showed that female, gynogenetic diploid, and pseudomales are 100% homozygous and 90% in male individuals are heterozygous. The ratio of males are not 100% heterozygous because homozygous females, due to environmental factors controlling sex differentiation in females, are sex-reversed pseudomales. Meanwhile, around 1:1 sex ratio was observed in a total of 450 juvenile offspring from three other families. To culture all-female juvenile olive founders, we analyzed SNP genotypes in 100 males. The selected 10 pseudomales mated with genetically confirmed females, and SNP genotypes of their juveniles were then determined. As a result, these juveniles were 100% females genetically. The development of these sex-associated markers and results of their molecular sexing in different populations provide strong evidence for a sex determination system of female homogametry or male heterogametry (XX/XY) in olive flounder.

The genus Onobrychis contains more than 150 species. Some of these species are cultivated widely in some parts of the world as forage legume due to their beneficial traits such as, high protein content, high yield, high digestibility, cold tolerance and drought tolerance. Taxonomic identification of the Onobrychis species is challenging due to variation and lack of morphological diversity. Additionally, species of this genus have different base chromosome number of either n=7 or n=8 and polyploidy is a common phenomenon in the genus.
Identification of the species within the genus Onobrychisand determining their chromosome numbers are crucial before initiating any plant breeding program for the genus. This is beacause of the potential issues such as genetic incompatibility and sterility that may occur during the crossings, which may waste the limited available resources such as material and human resources.
 
In this study, we used flow cytometry to determine nuclear DNA content of 38 Onobrychis acessions from nine species, maintained by The Margot Forde Germplasm Center (MFGC), Palmerston North, New Zealand for the first time. Based on the results of the study, 2C nuclear DNA content of the accessions varied between 1.0 and 2.87 pg. These results indicate that the collection includes both diploids and polyploids. Except one accession of O. viciifolia and two accessions of O. transcaucasia, all other accessions of these two cultivated species are tetraploid (2n=28). Therefore, these three accessions should be further investigated to confirme their label information by distinguishing the accessions taxonomically. Further, the results of the study indicate that all accessions or the contents of their seed packets are pure as they don't include plants with different ploidy levels or misidentified seeds although only a few plants per accession were analysed.
Acknowledgements: This study was supported by a TUBITAK grant (TOVAG-215O526). 

 
Bi-allelic Single Nucleotide Polymorphism (SNP) markers of variable length are useful for population genetic studies, where genetic variation is determined by a single nucleotide change in a certain locus among individuals within or between populations. In doing so, a large portion of the sequenced data (either side of the SNPs) remain unused. These data can contain information that is valuable beyond population genetics studies. In this study we used DArTseq (Diversity Array Technology) derived SNP markers developed from a non-model Australian native freshwater fish Golden perch (Macquaria ambigua) to demonstrate the use of such markers for comparative genome analysis.           The specific aim of the study was to identify gene-associated SNP markers and the associated homologies with evolutionary conserved genes.  A total of 6,776 markers were concatenated to create a hypothetical genome (representing 3–10% of the actual genome), which was used to find sequence homologies with multiple fish species. We identified sequence homologies for 18 evolutionary conserved genes (cd9b, plk2b, rhot1b, sh3pxd2aa, si:ch211-148f13.1, si:dkey-166d12.2, zgc:66447, atp8a2, clvs2, lyst, mkln1, mnd1, piga, pik3ca, plagl2, rnf6, sec63, ubr2) along with an ancestral  syntenic block (euteleostomi Block_210) conserved across vertebrates. Repetitive sequences covered approximately 12.2% of the hypothetical genome where DNA transposon, LTR and non-LTR retrotransposons are most abundant. A hierarchical pattern of the number of sequence homologies with phylogenetically close species validated the approach for reproducibility. This new approach of using SNP markers for comparative genome analysis may provide insight into the genomes of non-model species in addition to population genetic information

By modifying gene regulatory networks (GRNs) present the last common ancestor of the Eumetazoa (cnidarians and bilaterians), animals evolved a diversity of complex body plans. Yet, the question of what specific changes in GRNs facilitated the emergence of complex animal bodies remains largely unexplored. My Honours project explores the evolutionary history of a GRN which specifies endomesoderm and its derivatives (gut and muscle tissue) during embryogenesis. Though endomesoderm specification in Eumetazoa is well-studied, little is known about the mechanisms that specify its potential homologues in earlier evolving metazoans. Sponges (Porifera) are considered one of the oldest surviving animal lineages, and are emerging models for exploring evolution of developmental GRNs. Components of the canonical Wnt pathway (a key element of the endomesoderm GRN) are expressed in a potential endomesoderm homologue – the choanoderm – in the calcareous sponge Sycon. However, whether the Wnt pathway plays a role in sponge choanoderm specification similar to its role in eumetazoan endomesoderm is unknown. Using custom-raised antibodies against TCF, the transcription factor of the canonical Wnt pathway, and a ChIP-Seq protocol developed for Sycon capricorn, I will identify Wnt target genes and compare them to those known to be involved in endomesoderm specification in cnidarians. The results of my study will shed light on the evolutionary relationship between the sponge choanoderm and the eumetazoan endomesoderm.

Lymphoma is the sixth most common form of cancer, with 90% of cases belonging to a heterogeneous group of lymphomas called Non-Hodgkin Lymphoma (NHL). One of the most common types of NHL, Diffuse Large B Cell Lymphoma (DLBCL), is characterized into two subtypes on the basis of differential gene expression: Activated B Cell (ABC) and Germinal Centre (GC), of these ABC is the most aggressive and least curable form. Recurrent somatic mutations in MYD88 were initially identified in ABC-DLBCL patients. MYD88 is an adaptor protein that transmits innate immune signalling from Toll-like receptor (TLR) and interleukin-1 (IL-1) receptor to the nuclear factor-kappa B (NF-B) pathway, for immune and inflammatory responses. The most frequent MYD88 mutation in lymphoma is a single amino acid variant L265P, identified in approximately 30% of ABC-DLBCL and 90% of Waldenström Macroglobulinemia (WM) patients. Apart from the L265P mutation, additional mutations in MYD88 have been reported in lymphoma. Moreover, genome-wide analysis of ABC-DLBCL and WM indicates that MYD88 L265P is preferentially found in combination with mutations in the B-cell antigen component CD79B and chemokine receptor CXCR4, which result in further induction of NF-κB pathway.
We are currently investigating the role of MYD88 in both normal development and immune cell function. For this purpose, we have developed Drosophila melanogaster and mouse model systems. In the fly model, we are investigating potential effects of Myd88 knockdown and CRISPR-generated Myd88 I335P substitutions (designed to mimic oncogenic MYD88 L265P) on hematopoietic development and immunity. In the mouse model, compound mutations (MYD88 loss-of-function together with MYD88 L265P) are being examined to determine potential of MYD88 L265P as a therapeutic target. Further to this, we are testing the combined effect of the MYD88 L265P mutation and CD79B mutations in our B cell lymphoma mouse models.
 

Chromosomes may contain sex-specific genes or sequences that can reveal their sex determination mode (XY or ZW) when sex chromosomes are cryptic or homomorphic. Sex –linked markers can also reveal sex determining genes and even the genetic architecture of sex chromosomes. It has been hypothesised that the differential methylation of the promoters of genes at sex-specific temperatures is involved in sex determination and also involved in differentiation of sex chromosomes, yet a full understanding of this mechanism is still yet unknown. Although, differences in gene methylations occurring between genetic males and females have been observed in several species of fishes and turtles, information on these differences at genetic marker level is yet lacking. Methylation DArTseq, a genotyping by sequencing (GBS) approach, employs a combination of genome complexity reduction and next generation sequencing methods and have the potential to identify differential gene methylation between sexes. In this study, we investigated oriental garden lizard (Calotes versicolor) genome by using this method to discover sex-linked markers that are differentially methylated. Both methylation sensitive and non-sensitive restriction enzymes were used (m-DArTseq and DArTseq) and we analysed in silico DArTseq markers (presence and absence) for sex-linkage. From m-DArTseq, 12 markers were identified to be substantially methylated in females and 2 in males (from 7 females and 7 males). Of these, 2 markers were only found in females. We also identified 241 female and 142 male specific markers from DArTseq, of which 60 were only found in females and 5 were only found in males (from 4 females and 4 males). Our preliminary data suggest, like other dragon lizards, Calotes versicolor also has a female heterogametic (ZZ/ZW) system. We are currently screening larger sample size to validate the efficacy of these markers.

Spotted-tailed quolls (Dasyurus maculatus) occupied Kangaroo Island (KI), South Australia, for over 50,000 years but became locally extinct following European settlement of the island in 1836. As the top-order mammalian predator on KI when Europeans arrived, spotted-tailed quolls played a significant role in maintaining healthy ecosystem function. The reintroduction of spotted-tailed quolls to KI could return some of these ecological benefits, as welll as establish another refuge population of these animals that are under threat on the Australian mainland and Tasmania. Two subpecies of spotted-tailed quoll (mainland and Tasmanian) are recognised; however, the subspecies that inhabited KI in the past is currently unknown. While the extant subspecies are difficult to distinguish based on skeletal morphology, they are genetically distinct. Here, we extracted ancient DNA from five fossil specimens from Kelly Hill Cave (KI), morphologically identified as D. maculatus. Using next-generation sequencing, we confirmed the morphological identifications of the fossil specimens, and amplified a 450 bp region of the mitochondrial D-loop to determine the subspecific affiliation(s) of KI's D. maculatus, and therefore the subspecies that would be the most appropriate candidate for reintroduction of spotted-tailed quolls to KI. We find that all fossil specimens are most closely related to the Tasmanian subspecies, but form a distinct monophyletic clade. As this clade may prove to be a new subspecies with further research, we advocate that any reintroduction of D. maculatus to KI seeks to establish a genetically diverse comparative population, possibly sourcing individuals from both the mainland and Tasmania.

A large proportion of eukaryotic genomes are comprised of repetitive sequences such as Transposable elements, transposons in short. Uncontrolled propagation of transposons causes catastrophic DNA damage on one hand, occasional new transposon insertions provide additional regulatory elements for the host gene expression. From the genetic screen for factors involved in transposon silencing in Drosophila germline, we identified factors that help the splicing of piwi gene, the central gene in the piRNA pathway in Drosophila. RNA sequencing revealed that there are two independent mechanisms that facilitate the splicing of two different introns of piwi. Interestingly, both introns contain evolutionarily recent transposon insertions, which likely made the splicing of those introns difficult. We found an evolutionary arms race where transposons harm the host defence pathway while the host immunises transposon insertions by aiding the splicing of suboptimal introns.

After some 20 years of river structure theoretical and field studies in genetics, their structure and scale effects are poorly understood for Australia. Some field observations conflict with theory developed from and explored by modelling.


In this poster we illustrate current work using extensive genomic SNP datasets (DaRTSeq) from shrimp, turtle, smelt and yabby sampling, along the main Eastern river systems.


Our research is aimed at examining the relationship between aquatic species’ genetic and riverine distance measures, and the relative importance of river network topologies (linear vs dendritic) in shaping these. The results of testing theoretical predictions of constrained gene flow in dendritic systems, and increased among-site diversity among headwater populations in different taxa and basins are shown and discussed.

Sex of most species in animal kingdom has classically been considered to be determined via one of two mechanisms: genotypic sex determination (sex determined at the time fertilization by genetic factors which independent of environmental influence) or environmental sex determination (sex determined by environmental factors that act after fertilization). However, in Bassiana duperreyi and Pogona vitticeps, genetic sex determination can be over-ridden by extreme temperatures during incubation resulting in sex reversal. Altered climate regimes are increasingly being considered one of the major threats for reptiles, especially for species with temperature-dependent sex determination, possibly leading to population declines and extinctions.
The aim of this project is to determine the ecological and evolutionary implications of sex reversal in the wild. Therefore, putative Y-chromosome markers will be identified using subtractive genomics. We will then use these markers to assess the rate of sex reversal across a high altitude to low altitude gradient from the Australian Alps to the Victorian coast to determine the rate of sex reversal in nests and among adults.
This project will address our knowledge gap on understanding the ecological consequences of global warming on reptiles and our new data will stimulate the development of predictive models that could help predict the effect on global warming on reptile populations in Australia on reptile sex ratios. In addition, this project will serve as a model for species at risk of extinction from climate change to focus on future research to test on-the-ground management strategies to mitigate the effects of climate in local populations.

The cellular microenvironment of the stem cell niche orchestrates the complex cellular interactions essential to stem cell self-renewal and differentiation. Proper organization and positioning of the niche is critical for preventing stem cell loss and tissue degeneration, or conversely, the emergence of cancer stem cells (CSCs) capable of unbridled proliferation. However, the mechanisms of oncogenic changes in the tumour microenvironment are still unclear. Here, we use the Drosophila model organism to demonstrate that the RNA recognition motif (RRM) protein Half-pint (Hfp) is important for germline stem cell niche signalling in vivo. Half-pint (Hfp), the Drosophila ortholog of the human tumour suppressor FIR, has been attributed to dual functions in mRNA splicing and transcription, particularly as a repressor of the MYC oncogene (Mitchell, 2010). Our exciting preliminary data demonstrate that depletion of the RNA recognition motif (RRM) protein Half-pint (Hfp) specifically in the Drosophila ovarian stem cell niche drives a phenomenon not previously reported; formation of an ectopic stem cell niche able to drive germline tumour formation. Interestingly the ability of depletion of Hfp in the stem cell niche to establish an ectopic niche, capable of non-autonomously driving germline stem cell tumours, was not dependent on MYC. Based on our observation that Hfp can bind genes in addition to MYC, we aim to determine 1) the direct Hfp binding targets in specifically in niche cells using Tandem-DamID and 2) identify targets responsible for the ectopic niche and germline tumour phenotype. Thus, we will identify the how Hfp regulates germline stem cell signalling, which will provide insight into oncogenic changes in the cancer microenvironment that might support cancer stem cell formation. 

In addition to the tumour cells, breast tumours contain other cell types such as fibroblasts, adipocytes, inflammatory and immune cells. Together with the extracellular matrix, these non-tumour cells compose the tumour microenvironment (TME). Complex interactions occur between tumour cells and the TME that can inhibit or stimulate tumour cell growth, metastasis and/or chemoresistance.  While treatment of tumours with chemotherapeutic agents such as Abraxane, leads to apoptosis of tumour cells, it can also have consequences for the cellular makeup and transcriptional profile of the TME and these, like the increased infiltration of macrophages, may have detrimental effects.

Transcriptome profiling of whole tumours from mice injected with tumour cell lines and treated with combinations of chemotherapeutic drugs has provided novel insights into pathways affected by different agents and diagnostic signatures. However, differences in the cellular composition of tumours from treated mice can have confounding effects and increase variation in whole tumour transcriptomes. To be able to examine the effects of co-treatment of Abraxane with another drug, we performed RNA-seq on tumours from mice injected with the human breast cancer cell line MDA-MB-231. We then separated reads mapped to the human and mouse genomes in silico, creating tumour and TME transcriptomes for control, Abraxane, drug and combination treated mice. 

Separation of the tumour and TME profiles revealed that while in the tumour cells, co-addition of the drug potentiated Abraxane’s inhibitory effect on cell cycle genes and promotional effect on antigen presentation genes, in the TME it inhibited genes involved in the inflammation and migration responses and promoted genes involved in lipid and xenobiotic metabolism.

The q-profile is a continuum that includes common measures of genetic differentiation: allelic richness (q= 0), Shannon (q=1) and Fst (q=2).  Using all three measures is expected to give the best chance of detecting genetic patterns, because each measure has specific sensitivities. For example, Fst is a commonly used measure of genetic distance; however, due to the overemphasis on common types (alleles), patterns of differentiation in rare alleles may be missed. Conversely, allelic richness has an overemphasis on rare types and is thus prone to sampling errors. Information measures (Shannon) weight alleles proportional to their abundance and allow for the detection of patterns for both rare and common alleles. While the benefits of Shannon measures of genetic diversity have been demonstrated in the theoretical literature, empirical genetic studies using Shannon are uncommon, with preference to Fst or allelic richness. By using all three, we test these measures on empirical data sets of plant populations across NSW as well as analogous simulated data to determine the scenarios to which each method is best applied.

 

Devil facial tumour disease (DFTD) has decimated wild populations of Tasmanian devils since its emergence. As the disease has the ability to avoid immune detection, it spreads rapidly both through populations and within individual hosts. Only a very few devils have been observed to spontaneously recover from the disease which is otherwise invariably fatal. In one north-western population, West Pencil Pine (WPP), it has been observed that some devils have spontaneously cleared the cancer where it had previously been considered 100% fatal. These individuals were sampled in the wild with evidence of DFTD tumours that were recorded to have shrunk or disappeared on subsequent sampling trips. We sequenced the whole genomes of 11 Tasmanian devils and combined them with 2 previously published devil genomes to obtain a sample set of 7 devils with regressed tumours and 6 controls. A genome-wide association (GWAS) was conducted to determine if any regions segregated between cases (regressed devils) and controls. Candidate regions arising from the genome were searched to identify any genes that may be involved in the ability for the host to overcome DFTD infection. Following targeted sequencing in an additional 13 controls and one regressed animal from WPP, the significant association of SNPs in and around the PAX3 gene was retained. The PAX3 gene is a regulatory gene involved with developmental pathways through regulation of intermediate targets such as bone morphogenic proteins (BMPs). As such PAX3 has been associated with the development and metastasis of many cancers due to its regulatory activity. PAX3 is also involved in angiogenesis through its interaction with VEGF. It is possible that PAX3 expression in the regressed devils results in reduced angiogenesis in the tumour microenvironment, leading to slowed tumour growth and eventual regression. Further research is required to confirm the involvement of PAX3 in DFTD regression.

 

Glioma, the most common primary brain tumour, is a highly heterogeneous disease arising from glial cell types including astrocytes and oligodendrocytes. These slow growing but invasive tumours are difficult to treat with unpredictable outcomes, necessitating an analysis of their molecular basis to improve prognosis and treatment. Far upstream binding protein 1 (FUBP 1), a single stranded DNA binding protein, was first discovered as a transcriptional activator of the MYC oncogene. Consistently with this function, FUBP1 is upregulated in many tumour types, including breast, liver, bladder, kidney lung cancer and glioblastoma. However, in oligodendroglioma FUBP1 is one of the top-ranked mutated genes predicted to result in loss-of-function, suggesting that FUBP1 has capacity for anti-proliferative effects in this context. Interestingly, FUBP1 mutations frequently co-occur with loss-of-function mutations in Capicua (CIC), a downstream regulatory factor of receptor tyrosine kinase (RTK) signaling pathways. Although FUBP1 and CIC are predicted to behave as tumour suppressors in glial lineage tumours, the capacity of mutations in either gene alone or in combination for driving glioma has not been fully understood. Hence, in order to identify the effect of deleted FUBP1 and CIC in glial cells and brain development, our research employs Drosophila which has been widely used for studying mechanisms of tumourigenesis due to the conservation of key molecular pathways involved in human cancer. In Drosophila, Capicua/CIC has characterized roles in regulating cell fate, while the role of human CIC has not been fully elucidated. Moreover, Drosophila FUBP1 (called Psi) plays conserved molecular functions in regulating expression of MYC. Therefore, the individual and cooperative effects of FUBP1/Psi and/or CIC/Capicua depletion on glial lineage behaviour and brain development in Drosophila will provide insights into molecular mechanisms underlying glioma development. Additionally, we aim to determine whether FUBP1 and/or CIC mutation(s) drive tumorigenesis, using mouse xenograft glioma models.

A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic plant pathogenic fungi. To answer this, high quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long-reads using the FALCON-Unzip assembler. RNA-seq datasets were used to infer high quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high inter-haploid diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When investigating genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors, and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales. In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant pathogenic fungus previously hidden in collapsed and fragmented genome assemblies. In addition, it will enable the community to identify to date unknown effector proteins that are recognized by the plant immune system.