Biology subjects

Downs, J.

Publications and source records attributed to Downs, J..

9 recordsLinked to original sources

bioRxiv2026

Global population genomics and pangenome of the clubroot pathogen link clonal expansion and effector diversification to resistance breakdown in canola

Clubroot disease, caused by the obligate biotrophic protist Plasmodiophora brassicae, threatens Brassica crops worldwide. Novel pathogen virulence frequently breaks resistance in agricultural crops, and yet explanations for isolate evolution remain unknown. We combined whole genome sequencing of 192 isolates from 24 countries with a pangenome analysis of 55 high-quality complete or nearly complete genome assemblies and performed functional effector analyses to investigate potential mechanisms of virulence emergence. Three major phylogenetic clusters were identified, including two highly clonal lineages with contrasting virulence profiles, and a genetically diverse population retaining signatures of recombination. Our findings support a model in which genome-wide purifying selection maintained core genome integrity, while effector genes evolved under less constraint. Despite a compact closed pangenome, we identified chromosome 17 as a major hotspot of single nucleotide and structural variations, transposable elements and expansion of ankyrin repeat effectors. Within the variable chromosome 17, PbAnk2 alleles from virulent and avirulent isolates encoded proteins with distinct predicted structures. PbAnk2 interacted with the Arabidopsis co-chaperone DJC31 in yeast two-hybrid and BiFC assays, whereas co-immunoprecipitation did not detect an interaction for the allele found in isolates that break CRa-mediated resistance, suggesting that allelic variation may alter PbAnk2's association with DJC31. These findings reveal the clonal expansion of virulent isolates and connect it to effector diversification that led to resistance breakdown and establish a genomic framework for pathogen surveillance and durable clubroot resistance.

genomics↗

bioRxiv2025

Phylogenomics and effector analysis of Plasmodiophora brassicae genomes unveils a unique and highly divergent clade in Australia

Clubroot, caused by the protist pathogen Plasmodiophora brassicae, is a soilborne disease that leads to significant yield losses in a broad range of brassica crops worldwide. Despite its significant impact on agriculture, genomic and molecular studies of clubroot disease are hindered due to the complex life cycle and the obligate biotrophic nature of the pathogen, which prevents its cultivation in vitro. In addition, several genotypes of P. brassicae are often present as a mixture in a single field sample, making it challenging to resolve high-quality assemblies of individual genomes. Recently, several genomes were assembled for some strains of P. brassicae, however, in-depth genomic analysis of this devastating pathogen remains limited. In this study, we generated complete telomere-to-telomere genome assemblies for three Australian P. brassicae field isolates using PacBio Revio HiFi sequencing combined with chromatin conformation capture technology (Hi-C). Importantly, we could generate two nearly fully phased haplotype genome assemblies from one of the field isolates. Additionally, we sequenced 14 isolates of P. brassicae, sampled from a wide geographical range across Australia using Illumina technology and performed an in-depth global comparative phylogenetic analysis. We revealed that Australian isolates are classified into three different clades, including a highly divergent and unique clade present only in Australia. Comparative analysis showed that the predicted effector profile of the Australian-unique clade is distinct from other clades, further supporting phylogenetic divergence. Altogether, we demonstrate the first haplotype-resolved genome of Australian P. brassicae isolates from a single clubroot field sample, and provide an in-depth phylogenetic analysis of global and Australian isolates. These findings, together with core effector profile analysis, will further advance the research to combat this destructive pathogen.

genomics↗

bioRxiv2025

A phased chromosome-level genome resource for a myrtle rust susceptible Syzygium luehmannii

Syzygium luehmannii is an Australian east coast endemic tree within the family Myrtaceae. Syzygium luehmannii is not known to be highly susceptible to the parasitic fungus causing myrtle rust, Austropuccinia psidii, however infections have been reported in the field, and in controlled inoculations. The capacity for this exotic pathogen to parasitise host trees, suggest that molecular targets are present in susceptible plants. While understanding resistance phenotypes is important for tree breeding and management, determining the key drivers for susceptibility may also provide useful additional research targets to avert infection. While there are several genome resources for plants within the large and globally diverse Syzygium genus, there is no diploid genome assembly (2n = 22), and no genome for S. luehmannii. We assembled the genome for S. luehmannii into the pseudo-phased, 11 chromosome pairs here termed haplotype A (370 Mbp) and B (357 Mbp). We annotated the predicted protein coding genes, and we specifically annotated the nucleotide-binding leucine rich repeat (NLR) type resistance genes as a useful resource for plant:pathogen studies. The high quality of this genome provides a base for studies on myrtle rust resistant and susceptible hosts to understand mechanisms of infection.

genomics↗

bioRxiv2024

Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying responses to Ceratobasidium theobromae

Diseases of Theobroma cacao disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTL). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome-level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide-binding site leucine-rich repeat class (NLR). On investigation, we determined the presence of NLR clusters at informative QTLs, as well as other potential disease response gene candidates. Understanding the genetics underlying resistance and susceptibility to VSD will accelerate the breeding cycle by providing clear targets for molecular screening. Additionally, we provide the first diploid, fully scaffolded and parentally phased genome resource for Theobroma cacao L.

plant biology↗

bioRxiv2022

Wheat pollen uptake of CRISPR/Cas9 RNP-PDMAEMA nanoassemblies results in targeted loss of gene function in progeny

The utility of CRISPR in plants has remained limited by the dual difficulties of delivering the molecular machinery to target cells and the use of somatic cell techniques that require tissue culture-based de novo organogenesis. We developed 5-10 nm isodiametric polyplex nanoassemblies, comprising poly [2-(dimethylamino)ethylmethacrylate] PDMAEMA (PD) polycationic linear homopolymers and CRISPR/Cas9 ribonucleoproteins (RNPs), that enable endocytosis-driven RNP uptake into pollen grains. Pollen from wheat plants (genotype Gladius+Sr50), homozygous for monogenic Sr50-mediated resistance to stem rust (Puccinia graminis f. sp. tritici -Pgt), were incubated with RNP/PD nanoassemblies targeting the dominant, Sr50 rust resistance gene. The treated pollen grains were then used to fertilize Gladius+Sr50 florets and the resulting M1 plants were tested for loss of Sr50 function via rust resistance screens. The identification of fully susceptible M1 seedlings indicated that the Sr50 RNPs acted on both alleles, indicating they were transferred via the treated pollen to the zygote. The ability to readily deliver CRISPR RNPs to reproductive cells via biodegradable, polymeric nanocomplexes has significant implications for the efficiency of gene editing in plants.

plant biology↗

bioRxiv2020

Improved RAD51 binders through motif shuffling based on the modularity of BRC repeats

Exchanges of protein sequence modules support leaps in function unavailable through point mutations during evolution. Here we study the role of the two RAD51-interacting modules within the eight binding BRC repeats of BRCA2. We created 64 chimeric repeats by shuffling these modules and measured their binding to RAD51. We found that certain shuffled repeats were stronger than any of the natural repeats, suggesting balancing of relative properties in BRC repeats. Surprisingly, the contribution from the two modules was poorly correlated with affinities of natural repeats, with weak BRC8 repeat containing the most effective N-terminal module. The binding of the strongest chimera, BRC8-2, to RAD51 was improved by -2.44 kCal/mol compared to the strongest natural repeat, BRC4. Crystal structure of RAD51:BRC8-2 complex shows an improved interface fit and an extended {beta}-hairpin in this repeat. BRC8-2 was shown to function in human cells, preventing the formation of nuclear foci after ionizing radiation.

biochemistry↗

bioRxiv2019

Cyclin-dependent-like kinase 5 is required for pain signalling in both human neurons and mouse models

Cyclin-dependent-like kinase 5 (Cdkl5) gene mutations lead to an X-linked disorder that is characterized by infantile epileptic encephalopathy, developmental delay and hypotonia. However, we found that a substantial percentage of these patients also report a previously unrecognised anamnestic deficiency in pain perception. Consistent with a role in nociception, we discovered that Cdkl5 is expressed selectively in nociceptive dorsal root ganglia (DRG) neurons in mice and in iPS-derived human nociceptors. CDKL5 deficient mice display defective epidermal innervation and conditional deletion of Cdkl5 in DRG sensory neurons significantly impairs nociception, phenocopying CDKL5 deficiency disorder in patients. Mechanistically, Cdkl5 interacts with CaMKII to control outgrowth as well as TRPV1-dependent signalling, which are disrupted in both Cdkl5 mutant murine DRG and human iPS-derived nociceptors. Together, these findings unveil a previously unrecognized role for Cdkl5 in nociception, proposing an original regulatory mechanism for pain perception with implications for future therapeutics in CDKL5 deficiency disorder.\n\nOne Sentence SummaryCyclin-dependent-like kinase 5 (Cdkl5) controls nociception in patients and murine models of Cdkl5 deficiency disorder via CaMKII-dependent mechanisms

neuroscience↗

bioRxiv2019

Toward A Reproducible, Scalable Framework for Processing Large Neuroimaging Datasets

Emerging neuroimaging datasets (collected through modalities such as Electron Microscopy, Calcium Imaging, or X-ray Microtomography) describe the location and properties of neurons and their connections at unprecedented scale, promising new ways of understanding the brain. These modern imaging techniques used to interrogate the brain can quickly accumulate gigabytes to petabytes of structural brain imaging data. Unfortunately, many neuroscience laboratories lack the computational expertise or resources to work with datasets of this size: computer vision tools are often not portable or scalable, and there is considerable difficulty in reproducing results or extending methods. We developed an ecosystem of neuroimaging data analysis pipelines that utilize open source algorithms to create standardized modules and end-to-end optimized approaches. As exemplars we apply our tools to estimate synapse-level connectomes from electron microscopy data and cell distributions from X-ray microtomography data. To facilitate scientific discovery, we propose a generalized processing framework, that connects and extends existing open-source projects to provide large-scale data storage, reproducible algorithms, and workflow execution engines. Our accessible methods and pipelines demonstrate that approaches across multiple neuroimaging experiments can be standardized and applied to diverse datasets. The techniques developed are demonstrated on neuroimaging datasets, but may be applied to similar problems in other domains.

neuroscience↗

bioRxiv2017

A substrate for modular, extensible data-visualization

As the scope of scientific questions increase and datasets grow larger, the visualization of relevant information correspondingly becomes more difficult and complex. Sharing visualizations amongst collaborators and with the public can be especially onerous, as it is challenging to reconcile software dependencies, data formats, and specific user needs in an easily accessible package. We present substrate, a data-visualization framework designed to simplify communication and code reuse across diverse research teams. Our platform provides a simple, powerful, browser-based interface for scientists to rapidly build effective three-dimensional scenes and visualizations. We aim to reduce the gap of existing systems, which commonly prescribe a limited set of high-level components, that are rarely optimized for arbitrarily large data visualization or for custom data types. To further engage the broader scientific community and enable seamless integration with existing scientific workflows, we also present pytri, a Python library that bridges the use of substrate with the ubiquitous scientific computing platform, Jupyter. Our intention is to reduce the activation energy required to transition between exploratory data analysis, data visualization, and publication-quality interactive scenes.

bioinformatics↗