– ABOUT
Plant Pathogen ‘Omics Initiative
Plant diseases cost Australia millions of dollars each year as they reduce productivity, increase the cost of production, impact on our ability to trade both locally and internationally and adversely affect our environment and biodiversity.
With rising temperatures and more severe weather events, experts predict increased risks of pest and disease outbreaks. Preparedness and awareness are national priorities, requiring data-driven decision-making. Researchers and industry stakeholders in Australia and internationally are integrating ‘omics data into developing resistant varieties and biosecurity surveillance programs. However, gaps in referential data, especially over space and time, hinder progress, while existing data can be difficult to access.
Established in 2021, the Bioplatforms-supported Plant Pathogen ‘Omics Initiative is generating high quality molecular reference data for plant pathogens in Australia. This data will be developed through collaboration with the national plant pathogen community.
OBJECTIVES
The Plant Pathogen Initiative is generating referential genomic data to achieve the following aims:
- Generate molecular reference data: Collaborate nationally to develop high-quality data for Australian plant pathogens.
- Support research in plant protection: Enhance understanding of pathogen evolution, taxonomy, and aid in biocide and resistant variety development.
- Enhance biosecurity surveillance: Improve incursion detection and develop rapid diagnostic tests for plant pathogens.
DATA
For further information and to view and access initiative data, please go to the Bioplatforms Australia Data Portal.
PROJECTS
| Species name | Project summary | Data strategy | Project Lead | Partners |
|---|---|---|---|---|
| Legume viruses - Alfamovirus, Cucumovirus, Polerovirus, Potyvirus | This project uses high-throughput sequencing to analyse Norfolk Island biosecurity samples, supporting pathogen detection and risk management to protect Australian and Norfolk Island agriculture and economy. | Whole genome sequencing (Illumina short-read) | John Thomas | The University of Queensland, Australian Department ofAgriculture, Water and Environment (DAWE) |
| Broad bean wilt virus 1 and 2 (BBWV-1, BBWV-2) | The project is characterising and sequencing historical and recent isolates of Broad bean wilt virus 1 and 2 (BBWV-1, BBWV-2) to address gaps in genomic data for Australian strains. It seeks to enhance understanding of BBWV's genomic diversity and its role in crop disease epidemics, and to produce high-quality reference genomes to aid agricultural research and management. | Whole genome sequencing (Illumina short-read) | Murray Sharman | Queensland Department of Agriculture and Fisheries, Grains Research and Development Corporation, Queensland Alliance for Agriculture and Food Innovation. |
| Cotton bunchy top virus 1 and 2 (CBTV-1, CBTV-2), Cotton leafroll dwarf virus (CLRDV) | This project focuses on characterising and sequencing isolates of Cotton bunchy top virus and Cotton leafroll dwarf virus to understand their genomic diversity and assess potential threats to Australian cotton production. The genomic data will support improved biosecurity diagnostics, inform breeding strategies for durable resistance, and contribute to global knowledge of these economically significant poleroviruses. | Whole genome sequencing (Illumina short-read) | Murray Sharman | Department of Agriculture and Fisheries, Queensland, International Centre for Agricultural Research in the Dry Areas, Cotton Research and Development Corporation, CSIRO. |
| Johnsongrass mosaic virus (JGMV) | This project focuses on sequencing and analysing the genomes of Johnsongrass mosaic virus, a plant virus affecting maize, sweet corn, and sorghum in Australia. By generating genomic data from historical and contemporary isolates, the project aims to understand the genetic diversity and resistance-breaking potential of JGMV strains, contributing to improved disease management and breeding strategies. | Whole genome sequencing (Illumina short-read) | Murray Sharman | Department of Agriculture and Fisheries Queensland |
| Potato virus Y (PVY) | This project aims to characterise the genetic diversity of Potato virus Y (PVY), a significant pathogen in horticultural crops, using next-generation sequencing of archived isolates from diverse hosts and locations in Australia. The outcomes will provide insights into PVY strain diversity, its association with disease symptoms, and inform improved disease management strategies. | Whole genome sequencing (Illumina short-read) | Fiona Filardo | Department of Primary Industries and Fisheries, Queensland Alliance for Agriculture and Food Innovation, Agriculture Victoria, Department of Primary Industries, Parks, Water and Environment, Tasmania. |
| Tobacco streak virus (TSV) | This project focuses on studying the Tobacco streak virus (TSV) by sequencing several isolates from different strains and geographical locations in Australia. The aim is to understand the genetic diversity of TSV, its potential for reassortment, and its impact on plant host resistance, particularly in sunflower and mungbean crops, to improve disease management strategies. | Whole genome sequencing (Illumina short-read) | Murray Sharman | Queensland Department of Primary Industries and Fisheries |
| Ralstonia sp | This project focuses on the genomic characterization of Ralstonia species in Australia, particularly Ralstonia pseudosolanacearum and Ralstonia solanacearum, which affect a wide range of crops. The aim is to create accurate diagnostics, identify potential host plants, and determine the geographical distribution and spread of these pathogens to inform disease management strategies. | Reference genome (PacBio HiFi) Phylogenomics (Illumina short-read) | Paul Campbell | Queensland Department of Primary Industries and Fisheries, Agriculture Victoria |
| Various (Dickeya spp., Pectobacterium spp, Erwinia spp., other soft rotting Enterobacteriaceae) | The project aims to generate genomic data for various soft rot bacteria (including Dickeya, Pectobacterium, and Erwinia species) affecting a range of plant hosts across Australia. This data will aid in identifying and characterising Australian isolates, understanding pathogen variability, and improving biosecurity measures through population genetics, phylogenomics, and reference genome generation. | Reference genome (PacBio HiFi) Phylogenomics (Illumina short-read) | Toni Chapman | NSW Department of Primary Industries, NRE Tasmania, DJPR Victoria, DPIRD Western Australia, DAF Queensland |
| Various (Dickeya spp., Pectobacterium spp., Other Enterobacteriaceae) | This project aims to generate genomic data for Australian isolates of Pectobacterium spp. and Dickeya spp., which cause blackleg and soft rot in various horticultural crops, particularly potatoes. The goal is to explore genetic diversity across isolates, improve diagnostic assays, and contribute to disease management and biosecurity strategies in Australia. | Reference genome (PacBio HiFi) | Alison Dann | Department of Natural Resources and Environment Tasmania, Department of Jobs, Precincts and Regions, Department of Primary Industries, New South Wales, Department of Primary Industries and Regional Development, Western Australia, Department of Agriculture and Fisheries, Queensland. |
| Various Pseudomonas spp. | This project aims to use genomic sequencing to identify various Pseudomonas species found in Australia, with a focus on determining the accuracy of molecular identification methods such as the CTS gene and training MALDI-TOF for fast diagnostics. The collaboration involves several Australian research institutions, each contributing isolates, DNA extraction, and genomic data analysis expertise to enhance biosecurity and disease monitoring. | Reference genome (PacBio HiFi) Phylogenomics (Illumina short-read) | Toni Chapman | NSW Department of Primary Industries, NRE Tasmania DJPR Victoria, DPIRD Western Australia, DAF Queensland, DAWE NSW |
| Ascochyta fabae | This project aims to investigate the genetic diversity and virulence factors of Ascochyta fabae, a fungal pathogen affecting faba beans, by sequencing and analysing a comprehensive set of isolates from various years and locations. The genomic data generated will provide insights into the pathogen's evolution, population shifts, and the development of resistance, assisting in disease management and breeding efforts for resistant faba bean varieties. | Reference genome (PacBio HiFi) Population genetics (Illumina short-read) | Sara Blake | South Australian Research and Development Institute, SA Genomics Centre |
| Ascochyta lentis | This project aims to investigate the genomics and population dynamics of Ascochyta lentis, the pathogen responsible for Ascochyta blight in lentils, which causes significant crop yield losses. By sequencing and analyzing isolates from different lentil varieties and geographical regions, the research will focus on understanding genetic diversity, virulence, and aggressiveness in pathogen populations to inform breeding, disease management, and crop protection strategies. | Population genetics (Illumina short-read) | Sara Blake | South Australian Research and Development Institute, SA Genomics Centre |
| Blumeria graminis f. sp. tritici (Bgt) | This project aims to sequence the genome of Blumeria graminis, the fungal pathogen responsible for wheat powdery mildew, to better understand its biology, genetic diversity, and mechanisms of virulence. The findings will help identify key genes involved in pathogenicity and adaptation, informing strategies for improving wheat disease resistance. | Pangenome (Illumina short-read) | James Hane | Curtin University, WA Department of Primary Industries and Regional Development |
| Colletotrichum lupini | This project focuses on generating genomic resources for Colletotrichum lupini, the fungal pathogen causing anthracnose in lupin crops. By sequencing the pathogen’s genome and transcriptome, the project aims to improve understanding of its genetic diversity, pathogenicity, and population dynamics, helping to develop better disease management strategies for lupin production in Australia. | Pangenome (Illumina short-read) | Manisha Shankar and Geoff Thomas | Curtin University, WA Department of Primary Industries and Regional Development |
| Diaporthe toxica | The project aims to generate genomic data on Diaporthe toxica, a fungal pathogen causing lupinosis in livestock and impacting lupin production in Australia. By analyzing genomic sequences, the project seeks to investigate pathogen diversity, evolution, and pathogenicity, with applications for disease management and crop protection. | Pangenome (Illumina short-read) | Manisha Shankar and Geoff Thomas | Curtin University, WA Department of Primary Industries and Regional Development |
| Eutypella sp. | This project aims to characterise the genomes of two novel Eutypella species responsible for reoccurring wilt in cotton crops in Queensland, Australia. The genomic data will support the development of molecular diagnostic tools, explore pathogen diversity, and inform management strategies for this emerging disease. | Reference genome (Illumina short-read) | Linda Smith | Queensland Department of Agriculture and Fisheries, CSIRO. |
| Fusarium oxysporum f. sp. vasinfectum | This project focuses on studying Fusarium oxysporum f. sp. vasinfectum (Fov), a pathogen causing Fusarium wilt in Australian cotton. By sequencing and comparing isolates of Fov from different time periods, the research aims to investigate the pathogen's genetic diversity, virulence evolution, and develop faster diagnostic tools to support effective disease management strategies. | Reference genome (Illumina short-read) | Linda Smith | Queensland Department of Agriculture and Fisheries, CSIRO. |
| Fusarium oxysporum f.sp. cubense (Foc) | This project aims to generate whole genome sequence data for 24 representative isolates of Fusarium oxysporum f.sp. cubense (Foc) to improve molecular diagnostic assays for identifying different races and vegetative compatibility groups (VCGs) of this devastating banana pathogen. The genomic data will help design more specific and sensitive diagnostic tools to support better management and control of Panama disease, which impacts banana production globally. | Reference genome (PacBio HiFi) | Tuan Nguyen | Queensland Department of Agriculture and Fisheries, Northern Territory Department of Industry, Tourism and Trade, The University of Queensland |
| Fusarium pseudograminearum | This project aims to advance the genomic understanding of Fusarium pseudograminearum, the primary cause of crown rot in wheat and barley, by generating a comprehensive reference genome and exploring population genetics and pathogenicity factors. The research will enhance diagnostic tools and provide insights into pathogen evolution and resistance, helping to mitigate crop losses caused by this destructive soilborne disease. | Pangenome (Illumina short-read) | Manisha Shankar and Daniel Huberli | Curtin University, WA Department of Primary Industries and Regional Development |
| Leptosphaeria maculans | This project aims to generate a high-quality, telomere-to-telomere pan-genome of Leptosphaeria maculans (blackleg fungus), the most significant disease of canola worldwide, causing up to 30% annual yield losses in Australia. By sequencing and analysing isolates from diverse international locations, including Australia, the resulting pan-genome will enhance understanding of the pathogen's virulence evolution and guide improved disease management strategies. | Reference genome (PacBio HiFi, Hi-C) | Angela Van de Wouw | University of Melbourne, University of Western Australia |
| Phaeosphaeria avenaria f.sp. avenaria | This project focuses on generating high-quality genomic resources for Parastagonospora avenaria f. sp. avenae (Septoria avenae blotch), a fungal pathogen of oats causing significant yield losses in Australia. By sequencing and analysing isolates from diverse Australian populations, the study aims to understand pathogen diversity, population genetics, and virulence markers to improve disease management strategies for growers and researchers. | Reference genome (PacBio HiFi) Phylogenomics (Illumina short-read) | Tara Garrard | South Australian Research and Development Institute, South Australian Genomics Centre, Grains Research and Development Corporation. |
| Parastagonospora nodorum | This project focuses on sequencing and analysing the genome of Parastagonospora nodorum, the pathogen causing nodorum blotch in wheat, to understand its population genetics, pathogenicity, and resistance evolution. The research will leverage advanced bioinformatics approaches to provide insights for improving disease management strategies in Australian wheat production. | Reference genome (Hi-C) | James Hane | Curtin University, WA Department of Primary Industries and Regional Development |
| Puccinia coronata f. sp. Avenae | This project focuses on sequencing the genome of Puccinia coronata f. sp. avenae (oat crown rust), a fungal pathogen causing significant yield losses in Australian oat crops. By generating reference genomes and analysing the genetic diversity of Australian isolates, the initiative aims to uncover mechanisms driving virulence evolution and develop enhanced surveillance tools to support oat breeding programs. | Reference genome (PacBio HiFi, Hi-C) Phylogenomics (Illumina short-read) | Melania Figueroa | CSIRO, Australian National University, Intergrain, Grains Research and Development Corporation. |
| Puccinia striiformis, Puccinia graminis, Puccinia triticina | This project focuses on generating high-quality reference genomes for three major rust fungi species affecting Australian wheat and barley—Puccinia striiformis, P. graminis, and P. triticina. The data will advance understanding of pathogen evolution, support diagnostic development, and enable better management of rust incursions. | Reference genome (PacBio HiFi, transcriptome, Hi-C) Phylogenomics (Illumina short-read) | Robert F. Park | The University of Sydney, Australian National University, University of New South Wales, NSW Department of Primary Industries, WA Department of Primary Industries and Regional Development, South Australian Research and Development Institute. |
| Pyrenophora teres f maculata | This project focuses on genomic research to combat Pyrenophora teres, the fungal pathogen causing net blotch in barley, a significant threat to Australia's $3 billion barley industry. Using advanced sequencing and bioinformatics, the team aims to investigate pathogen diversity, genome structure, and virulence factors to improve disease resistance and inform management strategies. | Pangenome (Illumina short-read) | James Hane | Centre for Crop and Disease Management, Curtin University, WA Department of Primary Industries and Regional Development, University of Southern Queensland, Murdoch University. |
| Pyrenophora teres f. teres | This project focuses on Pyrenophora teres f. teres, the fungal pathogen responsible for net form net blotch in barley, a significant threat to Australian barley crops. Researchers aim to generate high-quality genomic resources and conduct population genetics and phylogenomics to better understand the pathogen's diversity, evolution, and virulence, informing improved disease management strategies. | Population genetics (Illumina short-read) | Tara Garrard | South Australian Research and Development Institute, South Australian Genomics Centre. |
| Pyricularia oryzae Cavara (syn. Magnaporthe oryzae) | This project aims to generate genomic resources for Australian isolates of Pyricularia oryzae, the fungal pathogen causing rice blast disease, a significant threat to rice and turf industries. By sequencing and analysing the genomes of local isolates, the project will provide insights into pathogen diversity and virulence, aiding disease management and biosecurity efforts under changing climatic conditions. | Reference genome (PacBio HiFi) Phylogenomics (Illumina short-read) | Ben Stodart and Nirodha Weeraratne | Charles Sturt University, Queensland Plant Pathology Herbarium, Australian Genome Research Facility. |
| Rhizoctonia solani AG8 | This project focuses on genomic and transcriptomic studies of Rhizoctonia solani AG8, a major soilborne pathogen affecting cereal crops like wheat, barley, and oats in Australia. By leveraging population genetics, comparative genomics, and advanced bioinformatics, the initiative aims to uncover the pathogen's genetic diversity, pathogenicity factors, and adaptive mechanisms to support sustainable disease management strategies. | Reference genome (PacBio HiFi) Pangenome (Illumina short-read) | Manisha Shankar and Daniel Huberli | Curtin University, WA Department of Primary Industries and Regional Development |
| Rhynchosporium commune | The project aims to generate high-quality genomic resources for Rhynchosporium commune, the fungal pathogen responsible for barley leaf scald, by sequencing Australian isolates to investigate genetic diversity, virulence, and resistance markers. This research will support the development of better pathogen management strategies and improve the understanding of the pathogen's evolution and its impact on barley production in Australia. | Reference genome (PacBio HiFi) | Tara Garrard | South Australian Research and Development Institute, South Australian Genomics Centre. |
| Pucciniastrum minimum | This project aims to generate genomic and transcriptomic data for Thekopsora minima, a rust fungus impacting the Australian blueberry industry. The research will focus on population genetics, phylogenomics, and genome sequencing to improve pathogen detection, monitor its spread, and inform control strategies in affected regions. | Reference genome (PacBio HiFi) | Tamieka Pearce | Tasmanian Institute of Agriculture, Department of Natural Resources and Environment Tasmania - Biosecurity Tasmania, Southern Cross University. |
| Austropuccinia psidii (fungi) + Syzygium luehmannii (host) | This project aimed to develop sequencing and chromosome-level assembly methods for infected plant samples, using the pandemic strain of myrtle rust and its interaction with Riberry as a case study. By leveraging HiFi and Hi-C data, it sought to model host-pathogen genotypes in woody species, addressing gaps in understanding disease resistance in perennial plants. | Whole genome sequencing (PacBio HiFi and HiC) | Peri Tobias | The University of Sydney |
| Puccinia striiformis f.sp. tritici | This project aims to investigate the genomic and transcriptional differences between four major lineages of Puccinia striiformis f.sp. tritici (wheat stripe rust) in Australia to understand their infection mechanisms and virulence diversity. Through long-read sequencing of infected wheat samples, the team will analyze both pathogen and host responses to identify key genetic factors influencing disease severity and resistance durability. | Transcriptomics (ONT RNA) | Benjamin Schwessinger and Mareike Moeller | The Australian National University, The University of Sydney, Cereal Rust Laboratory at the University of Sydney, Grains Research and Development Corporation, Department of Agriculture, Fisheries, and Forestry, ARC Discovery Project. |
| Plasmodiophora brassicae | This project aims to generate a high-quality genomic reference for Plasmodiophora brassicae (Clubroot), a soil-borne pathogen impacting Brassica crops across Australia. Through genome sequencing of Australian isolates, the research will explore the pathogen’s phylogenetic structure, functional mechanisms of secreted proteins, and potential plant resistance strategies. | Reference genome (PacBio HiFi, Hi-C, Illumina RNA) Phylogenomics (Illumina short-read) | Maxim Prokchorchik | The University of Sydney, DPI-NSW, NSW DPI Herbarium. |
| Meloidogyne arenaria, Meloidogyne hapla, Meloidogyne incognita, Meloidogyne javanica | These projects focus on characterising virulence-related molecular markers and understanding the epigenetic determinants of virulence in root-knot nematodes (Meloidogyne spp.), which are major agricultural pests globally and in Australia. By sequencing genomes and transcriptomes of multiple species, this research aims to identify markers for race identification, support crop selection, and aid in developing resistant crop cultivars. | Reference genome (PacBio HiFi, Hi-C) | Daniel Huston | CSIRO, Charles Darwin University, Norther Territory Department of Industry, Tourism and Trade, Plant Health Laboratories. |
| Beet pseudo-yellows virus (BPYV), Strawberry crinkle virus (SCV), Strawberry mottle virus (SMoV), Strawberry mild yellow edge virus (SMYEV), Strawberry pallidosis-associated virus (SPaV), Strawberry vein banding virus (SVBV) and Strawberry necrotic shock virus (SNSV) | BPYV, SCV, SMoV, SMYEV, SPaV, SVBV and SNSV are the most important strawberry viruses that occur worldwide including Australia. These viruses cause diseases that impact the quality of yield of strawberry plants in Australia. The genetic diversity of these strawberry viruses in Australia is not known due to lack of any genome sequences of Australian strawberry isolates. Genome sequencing and genetic characterisation of Australian isolates will result in reference sequences of these viruses and enable the development of improved and sensitive diagnostics for these strawberry viruses occurring in Australia. | Whole genome sequencing (Illumina short-read) | Joanne Mackie | Agriculture Victoria |
| Plant viruses Norfolk Island | This project examines the composition of the plant virome on Norfolk Island, and external territory of Australia. Norfolk Island was settled soon after the First Fleet arrived in Sydney in January 1788 and thus is one of the oldest agroecosystems in Australia. The virus specimens that form the basis of this project were collected as part of plant biosecurity surveys of Norfolk Island in 2014. The diseased plants that were sampled were primarily vegetables, but some are garden ornamentals and one an endemic rainforest plant. Preliminary diagnoses have been done and virus particles observed under the electron microscope in many cases, but identification to species level can only be done by sequencing. It is expected that most of the virus records will be new to science, new virus records for the region, or new host records for viruses that already occur in the region. | Whole genome sequencing (Illumina short-read) | Andrew Geering | The University of Queensland, Queensland Department of Primary Industries |
| Various Rhizobiaceae including Agrobacterium spp., Allorhizobium spp., Rhizobium spp., Neorhizobium spp. | The Rhizobiaceae family in Australia includes both plant pathogens and beneficials, with its taxonomy still evolving due to advances in genome sequencing. Recent single amplicon sequencing of Australian isolates suggests misidentifications by earlier methods. To clarify the population structure, we plan to sequence genomes for phylogenetic analysis and establish reference isolates to refine taxonomy. Rhizobiaceae pathogens can harm crops like grapevines, but genera such as Rhizobia, Bradyrhizobia, and Mesorhizobia contribute significantly to legume agriculture, providing an estimated $3.5 billion annually in nitrogen fixation. Accurate identification is crucial, given their long-term soil viability. | Reference genome (PacBio HiFi), Population genetics (Illumina short-read) | Toni Chapman | NSW Department of Primary Industries and Regional Development, Queensland DPI |
| Streptomyces scabiei | Streptomyces scabiei is a species of Actinobacteria causing the disease common scab on potato and tuber crops. It is found worldwide with losses varying depending on management practices. The bacterium infects the exterior layers of the potato/tuber, entering via natural openings or small wounds. Once inside the tuber, the bacterium consumes carbohydrates, producing unwanted, distasteful lesions, rendering the fruit unmarketable. The spores of S. scabiei are long-lived and can spread in soil, water, or on the wind. Recent research suggests that very close relatives of S. scabiei are particularly active in the wheat rhizosphere, where it does not cause disease. However, it is not clear if these microbes have the genetic capacity to cause disease in tuber species, or if they represent non-pathogenic isolates. This work would therefore generate genomic data to identify the genomic diversity of S. scabiei in Australian soils and their potential for pathogenicity in potato. | Reference genome (PacBio HiFi) | Lachlan Dow | CSIRO Agriculture & Food |
| Ralstonia solanacearum species complex (RSSC) | The Ralstonia solanacearum species complex (RSSC) consists of related bacterial strains causing bacterial wilt disease in a wide range of host plants including banana, tomato, potato, ginger, etc. Once a plant is infected, RSSC strains colonise the xylem, leading to wilt and eventual death of the host. The pathogens are highly dispersible, spreading through contaminated plant tissue, water, farming equipment, and insects. The bacteria can persist in soil for many years and are harboured by asymptomatic weed hosts, making it challenging to detect and control the bacterial wilt, especially when it remains present and latent in the environment. Within the Australian context, the RSSC poses a significant threat to banana production as it includes strains that cause serious banana diseases like Blood disease and Moko disease. Members of the RSSC are classified into five races, six biovars, four phylotypes, and over 195 sequevars, based on their host ranges, biochemical characteristics, and genetic variations. Recently, the RSSC has been reclassified into five distinct species and subspecies. However, the genetic relatedness and differences among the races, biovars, phylotypes, sequevars, species and subspecies within the complex are still poorly understood. This project aims to sequence the whole genomes of various RSSC strains, particularly those associated with banana diseases, to better understand these genetic relationships and identify distinct loci for each group within RSSC, enabling the development of rapid and accurate diagnostic assays for bacterial wilt. The project will also generate a resource of Australian genomes providing a baseline of data for comparative genomic analysis enabling investigations into the population diversity, structure and origin. | Reference genome (PacBio HiFi) | Tuan Nguyen | Queensland Department of Primary Industries, Department of Agriculture & Fisheries Northern Territory Government |
| Ascochyta lentis | Australia is one of the leading producers of lentil after Canada and India. Ascochyta blight caused by Ascochyta lentis is a foliar disease affecting all above-ground parts of lentil (Lens culinaris), causing leaf, stem and pod lesions and leading to significant plant damage and up to 50% yield loss in the field. This project will sequence 50 international and 50 domestic isolates using ONT. Furthermore, long-read RNA-Seq from isolates grown in-vitro and in-planta, for the reference Pathotype 1 and 2 isolates will be generated. The data generated will assist in improving the quality of existing reference genomes to allow accurate isoform-level gene annotation and will contribute to our understanding of the pathogen evolutionary history in Australia and compare the pathogen diversity across the globe. It will also allow identification of key pathogenicity factors in A. lentis that lead to susceptibility in lentil cultivars. | Reference genome (PacBio HiFi) | Lars Kamphuis | Centre for Crop and Disease Management, Curtin University |
| Ascochyta rabiei | Ascochyta Blight caused by the Ascochyta rabiei fungus is a foliar disease affecting all above-ground parts of chickpea (Cicer arietinum), causing leaf, stem and pod lesions and leading to significant plant damage and yield loss. The fungus was introduced to Australia in the 1970s from an unknown source population and, within a few decades, successfully established in all Australian agroecological chickpea growing regions where management is heavily reliant on a combination of fungicide application and host resistance. Management of the disease costs the Australian chickpea industry an estimated $34.9 million in disease control expenses and $4.8 million in yield losses annually. The Australian A. rabiei population is highly clonal due to a genetic bottleneck caused by the introduction into Australia and the presence of a single mating type. Despite this, highly pathogenic isolates are rapidly evolving to overcome resistant chickpea cultivars. The genetic factors underlying this apparent rapid evolution of isolate aggressiveness remain unknown. The data generated through this initiative will assist in improving the quality of existing reference genomes to allow accurate isoform-level gene annotation and will contribute to our understanding of the pathogen evolutionary history in Australia. This in turn will support current research programs focusing on identifying genomic polymorphisms that drive virulence/pathogenicity and their underlying molecular mechanisms. | Reference genome (PacBio HiFi) | Ido Bar | Griffith University, Centre for Crop and Disease Management, Curtin University, NSW DPIRD |
| Austropuccinia psidii | Austropuccinia psidii is a biotrophic fungus, causal agent of myrtle rust in around 480 host species within the Myrtaceae family. The disease manifests through orange pustules on young tissues, resulting in defoliation, reduced production and, in severe cases, plant dieback. Introduced to Australia in 2010, A. psidii has brought significant economic and ecological consequences. It affects nurseries and industries dependent on Myrtaceae plants, including timber and spices. The disease has pushed at least five native plant species to the brink of "critically endangered" status, while around 30 Australian native species are suspected declining. This disruption has altered the ecological balance in affected ecosystems, potentially leading to shifts in biodiversity and ecosystem functioning. Myrtle rust first arrived in Australia in 2010 and exotic strains are the #11 National priority plant pest species from DAFF. There has been no active genetic monitoring of myrtle rust since its arrival in 2010 and we do not know how pathogen populations adapted since 2010. In addition, recent work identified the need to further improve diagnostic tools for exotic strains to increase sensitivity of current methodologies (MS under revision with Plant Disease). We propose to address these two important important knowledge gaps by sequencing additional five isolates from Brazil, that are closely related to the pandemic biotype and resequencing ~100 Australian isolates. These new resources will improve diagnostics in the Australian biosecurity setting. | Reference genome (PacBio HiFi) | Benjamin Schwessinger | Australian National University, University of Sydney, University of São Paulo, DPI NSW |
| Botrytis cinerea | Botrytis cinerea is a high-risk pathogen for development of fungicide resistance, where resistance to one or several chemical fungicide classes has been reported globally across many economically important crops. Successful control of B. cinerea with the use of fungicides is hampered by this resistance development. Biological control agents offering new modes of actions are considered a more sustainable crop protection strategy, yet we know relatively little about potential resistance or variability in efficacy against broad host range pathogens like B. cinerea. This project aims study the genetic differences of 50 distinct B. cinerea strains collected from diverse crops, soils, management practices, and geographic and climatic zones of France, and decode genetic diversity associated with differential sensitivities to current and new crop protection solutions. The outcomes are crucial for elucidating the functional modes of action of new biocontrol agents and are vital for resistance stewardship and improving the durability of new crop protection products. | Population genetics (Illumina short-read) | Marta Gallart | CSIRO Agriculture & Food, INRAE Plant Pathology research unit |
| Fusarium oxysporum f. sp. Lycopersici | This project aims to produce high quality genome assemblies for Fusarium oxysporum f. sp. lycopercisi (Fol) race 1, race 2, and race 3 isolates associated with Fusarium wilt and yield decline of tomato in Australian tomato production. Globally, Fol races are classified based on their ability to cause disease on tomato cultivars carrying different resistance genes. For instance, isolates that overcome the I1 resistance gene are designated as Race 2 while those that can bypass both I1 and I2 resistance genes are classified as Race 3. Since race classification relies on disease response (phenotype), the genetic mechanisms underlying pathogenicity can vary among isolates within the same race. For example, there is evidence that race 3 isolates in Australia have a different evolutionary origin, and Australian Race 2 isolates can cause disease on tomato cultivars from USA with Race 2 resistance. This project, therefore, will produce high-quality genome assemblies and construct a pangenome of Australian Fol isolates to allow further comparisons with isolates from overseas. Additionally, it will investigate genetic loci associated with pathogenicity and virulence, comparing them with published genomes from other countries. | Reference genome (PacBio HiFi), Pangenome (ONT) | Niloofar Vaghefi | University of Melbourne |
| Fusarium sp. (various species) | We are developing a fungal pathogen metabarcoding surveillance and detection project, in which fungal spores will be collected using spore traps and processed for identification by comparing them to a comprehensive database. For pathogens other than Fusarium, we are utilising the rRNA operon region for detection. However, for Fusarium, we have not yet identified the most informative genomic region for metabarcoding. The project pipeline will integrate Unique Molecular Identifiers (UMI) with long-read sequencing, making it essential to create a database built using markers sequenced through a long-read platform. This project will play a pivotal role in advancing comparative genomics, particularly in helping us identify the most suitable metabarcoding region for Fusarium. Additionally, it will allow us to extract the identified regions from the genome and incorporate them into our database, enhancing the accuracy and efficiency of fungal pathogen detection. Ultimately, the development of this database and the integration of long-read sequencing will significantly improve our ability to monitor and identify Fusarium species present as foliar pathogens for the grains industry. | Reference genome (PacBio HiFi, Hi-C) | Saidi Achari | Department of Energy, Environment and Climate Action |
| Fusarium species | Cotton is the most important fibre crop worldwide. Fusarium oxysporum f. sp. vasinfectum (Fov) is a soil-borne pathogen that infects the plant's vascular system. Its proliferation inside the water-conducting vessels of the plant causes vascular wilt, often leading to plant death. While multiple races of Fov exist globally, isolates originating from Australia form a distinct lineage. Each year, approximately 25 million tons of cotton are produced worldwide, with an estimated value of 12 billion USD. In Australia, the cotton industry generates an annual revenue of 1.9 billion AUD. Yield losses of up to 10% have been associated with the Fusarium wilt of cotton. Recent studies have identified other Fusarium species associated with diseased cotton in Australia. Evidence suggest that Fusarium populations in cotton fields are adapting to a changing climate, contributing to a steady rise in disease incidence. In recent years, Fusarium species such as F. solani, F. proliferatum and F. equiseti have been isolated from cotton plants exhibiting wilting and boll rot symptoms. Furthermore, many F. oxysporum isolates from symptomatic plants have been identified and they do not match known Australian biotypes. These findings underscore the need for further investigation into the pathogenic potential of Fusarium species to cause disease on cotton plants. This collaborative project will enable whole-genome sequencing of selected isolates, generating genomic resources to investigate structural variations in regions associated with virulence and identify effector genes for disease diagnostics. | Reference genome (PacBio HiFi), Population genetics (Illumina short-read) | Andrew Chen | The University of Queensland, Queensland Department of Primary Industries, New South Wales Department of Primary Industries |
| Globisporangium commune | Root rot of pyrethrum caused by Globisporangium commune is an important disease of pyrethrum in Australia. This pathogen was described recently in 2023 and has only been found in Australia, thus far, with the ability to cause damping off and seedling death and significantly reduce root growth. This project aims to produce the first genome assembly of this pathogen, which will be further used for the development of species-specific diagnostics markers to be able to detect and quantify pathogen levels in planta and in the soil. | Reference genome (PacBio HiFi) | Niloofar Vaghefi | University of Melbourne |
| Fungi - multiple species | In round 1 there was a pangenome sequencing project submitted by the CCDM for Blumeria graminis f. sp. tritici, which causes powdery mildew disease on wheat and is therefore of interest to the Australian grains industry. Unlike other round1 projects submitted by CCDM, this project was not able to submit any samples from 2022-24, due to a combination of logistical issues and unique challenges inherent to DNA sample preparation of obligate biotrophic fungi, which requires isolation and live culture on a host plant, and is difficult to amass sufficient quantity. Maintaining live cultures of Bgt is an area of expertise for CCDM staff, however labor involved limits the number that can be maintained at a time, and in 2024 samples that were prepared in bulk for DNA extraction were contaminated with mycoplasmas. In parallel to the Bgt project, other fungal pathogen projects (primarily necrotrophs) proceeded without major issues. From 2022-24 the CCDM bioinformatics project led by James Hane developed new methods relevant to this project: a) EffectorFisher – mines pangenome for protein isoform profiles and test versus disease phenotype to generate a refined set of candidate effector proteins with strong disease phenotype-association b) FRAST – mines pangenome for the 12 loci recognised by FRAC to have mutations that cause known fungicide resistance mutations c) Mycoprocessor – an automated toolkit enabling conversion of raw pangenome sequence data into EffectorFIsher, FRAST and phylogenetic summary reports. The combination of the tools above can provide comprehensive surveys of the effector and fungicide-resistance profiles of a pathogen population from (short-read or better) pangenome sequence data. Significant improvements to effector prediction can also be achieved with disease phenotyping corresponding to the same set of isolates. This round 2 project aims to explore potential solutions to the issues encountered in the round 1 Bgt project, and additionally to expand the scope to include analysis of mixed/co-infected samples. Within the genome assembly phase of MycoProcessor, we have developed an alternate pipeline for mixed samples which performs phylogenetic screening, sorts raw sequence reads into bins relative to a panel species typically observed in species-complexes or on the host of interest, and performs (either de novo or reference-assisted) genome assembly within each bin independently. This has been tested on contaminated samples from Fusarium species complex datasets which were able to produce genome assemblies of sufficient quality to pass through the rest of the MycoProcessor pipeline. Additionally, we seek to test low-template DNA preparation kits on both obligate biotroph and mixed co-infected samples, which in combination with the pipeline above, is intended to circumvent labor-intensive steps of single-sporing and bulk culturing required for standard DNA preparations. This is a moderate risk, high return project compared to standard single species pangenome projects, with the potential to enable feasible pangenome survey for a range of “difficult” fungal pathogens, and to expand the scope of pathogenomic surveys to include co-infected samples of two or more pathogen species. | Pangenome (Illumina short-read) | James Hane | Centre for Crop and Disease Management, Curtin University |
| Neopestalotiopsis spp | Despite extensive research on dieback in woody perennials, its impact on persimmons in Australia remains understudied. Growers have reported dieback symptoms, but the factors predisposing trees to the disease are unclear, hindering effective management. Taguiam et al. (2024) highlighted that different fungal species are responsible for persimmon dieback in various regions. This project aims to identify the fungal pathogens responsible for persimmon dieback in Australia and develop effective management strategies to minimize yield loss. In Australia, Neopestalotiopsis species have been isolated from persimmon trees, including from dieback-affected stems, buds, and calyxes. Pathogenicity tests confirm their role in causing dieback and inducing necrotic leaf lesions upon cross-inoculation. While Neopestalotiopsis has previously been reported to cause leaf spots in persimmons, it has never been associated with dieback disease. This project provides the first report of Neopestalotiopsis as a persimmon dieback pathogen. Key management questions include identifying effective control measures, assessing the pathogen's potential to infect other crops, and evaluating its biosecurity risks. These findings will inform disease monitoring, prevention strategies, and integrated pest management (IPM) approaches, supporting long-term sustainability in persimmon orchards. | Reference genome (PacBio HiFi) | Sandra Savocchia | Charles Sturt University, PIRSA – South Australian Research and Development Institute |
| Paraphoma vinacea | Paraphoma crown rot of pyrethrum caused by Paraphoma vinacea is an important disease of pyrethrum in Australia. This pathogen was described in 2016 and has only been found in Australia, thus far, with the ability to reduce root growth by 40%. This project aims to produce the first genome assembly of this pathogen, which will be further used for the development of species-specific diagnostics markers to be able to detect and quantify pathogen levels in planta and in the soil. | Reference genome (PacBio HiFi) | Niloofar Vaghefi | University of Melbourne |
| Phakopsora pachyrhizi | Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi (Pp), is a major threat of soybean production. Soybean is the 6th most grown crop in the world generating 53% of global oil production and has the highest protein (~40%) content of all food crops. Yield losses due to ASR can reach ~80-100%. In Australia, Pp is present in all soybean-growing regions. Furthermore, Pp has a broad host range up to 150 species including wild relatives of the soybean, thus ensuring a source of inoculum all year round. Current commercial varieties of soybean are susceptible to Pp and require extensive fungicide applications for control, which increases the risk of Pp evolving fungicide resistance. Generating of Pp genome assemblies therefore has the potential for high impact outcomes. | Reference genome (PacBio HiFi, Hi-C), Transcriptomics (Illumina) | Jana Sperschneider | CSIRO |
| Phytophthora cinnamomi | Phytophthora cinnamomi is a soil-borne plant pathogen with a 5000+ host range causing devastating canker, root rot and dieback symptoms. This pathogen impacts natural ecosystems, nurseries, and horticultural crops worldwide and is one of the top 10 most destructive oomycete pathogens based on the extent of economic and ecological damage it has caused worldwide. While it has been observed on forest plantation trees and in natural ecosystems, the most severe economic impact has been on the horticulture industry in Australia. This project will sequence the genomes of 27 representative strains collected from avocado, macadamia and pineapple, strains collected over the past 20 years for which information on their pathogenicity and sometimes host resistance has been assessed. Data generated will provide a valuable resource library of genomes for comparison to determine the genomic significance and evolution of strains from different hosts, geographic regions and crop management practices within Australia. Information that will lead to a better understanding and management of the disease. | Reference genome (PacBio HiFi), Phylogenomics (Illumina short-read) | Sarah Dodd | Department of Primary Industries Queensland, University of Queensland |
| Puccinia melanocephala, Puccinia kuehnii , Macruropyxis fulva | A new pathogen, Macruropyxis fulva, is causing tawny rust of sugarcane in South Africa. The biosecurity risk of M. fulva entering Australia is unknown, with the potential severity of disease undetermined. Additionally, two rust fungi, Puccinia melanocephala (brown rust) and P. kuehnii (orange rust) are currently present in Australia, with orange rust causing yield losses of up to 40%. The molecular status of endemic rusts and their virulence in various areas in Australian sugarcane regions is unknown. Genomic characterisation of M. fulva, P. melanocephala and P. kuehnii will be undertaken to determine the features of fungal rust pathogens infecting sugar cane. This project will enable preparedness for a potential incursion of tawny rust into Australia and an insight into population shifts of the current endemic rust pathogens in Australia. An orange rust epidemic had a devastating impact on sugarcane in 2000. There is currently anecdotal evidence that brown rust is becoming more prevalent. The need to understand the change in the genetic of the two rusts currently in Australia is required to determine whether the isolates present are changing in their virulence. Generating the genomic resources for these three sugar cane pathogens will be the starting point for extensive follow up molecular characterization as part of a Sugar Research Australia funded PhD project within the Plant Biosecurity Training Centre. | Reference genome (ONT, Hi-C),Transcriptomics (Illumina) | Benjamin Schwessinger | Australian National University, Sugar Research Australia |
| Pyrenophora teres f. teres (Ptt) | Pyrenophora teres f. teres (Ptt) exhibits significant genetic diversity due to sexual reproduction, resulting in diverse virulence patterns among isolates. Multiple pathotypes can coexist in the same field, each varying in virulence, allowing Ptt to adapt to environmental changes and host resistance genes. Sequencing different Ptt pathotypes offers insights into genetic diversity, virulence factors, and pathogenicity mechanisms. By comparing genomes, effectors linked to specific pathotypes can be identified, helping to understand how they interact with barley hosts and inform strategies for disease control, resistance breeding, and effective management in barley cultivation. Genome sequencing data generated through this project will be used to identify and compare effectors from different pathotypes of Ptt. | Reference genome (Illumina short-read) | Buddhika Amarasinghe Dahanayaka | University of Southern Queensland |
| Pyrenophora teres f. teres (Ptt) Pyrenophora teres f. maculata (Ptm) | In round1 there were two projects covering Ptt (SARDI) and Ptm (CCDM). A quantitative phenotyping panel was generated for the Ptt dataset by SARDI with collaboration across the GRDC Barley Genomics Consortium. Access to this phenotype data is being sought to enable steps below, but has been met with delays. Non-quantitative phenotyping was also recorded for the Ptm dataset within CCDM. From 2022-24 the CCDM bioinformatics project led by James Hane developed new methods relevant to this project: a) EffectorFisher – mine pangenome for protein isoform profiles and test versus disease phenotype to generate a refined set of candidate effector proteins with strong disease phenotype-association b) FRAST – mine pangenome for the 12 loci recognised by FRAC to have mutations that cause known fungicide resistance mutations c) Mycoprocessor – an automated toolkit enabling conversion of raw pangenome sequence data into EffectorFIsher, FRAST and phylogenetic summary reports. To gain the most benefit from Ptt/Ptm pangenomics using these tools, we need more isolates with both genome and phenotype data. This round 2 project seeks to: a) increase the number of isolates with whole-genome sequencing and corresponding phenotype data, to enable or enhance the reliability of EffectorFisher predictions b) provide a second timepoint relative to the round1 data (i.e. 2024/25 vs 2020-23), for proof-of-concept demonstration that pangenome-based survey of effector protein isoform profiles and fungicide resistance mutations change over time and/or shift in abundance relative to sub-regions at state/national levels… this will support applications of pangenomics for crop disease monitoring, leading to actionable recommendations for crop disease management c) include new pathogen isolates of interest to the Australian grains industry, including those exhibiting: i) recently emerging resistance to RGT Planet in south west WA ii) recently emerging fungicide resistance | Pangenome (Illumina short-read) | James Hane | Centre for Crop and Disease Management, Curtin University |
| Turfgrass nematodes | This project aims to improve diagnostics of plant parasitic nematodes of known concern to Australian agriculture through the sequencing of their 18S ribosomal RNA genes. By using Nanopore sequencing, we will establish a metabarcoding pipeline to efficiently identify and classify nematodes from agricultural soils. Additionally, the project will involve constructing a Multi-Locus Sequence Typing (MLST) system using other marker genes to enhance the resolution of nematode identification and provide more accurate data for pest management strategies. To support the development of the diagnostics development, we will sequence 20 complete nematode genomes, which will assist in identifying the presence and sequence of 18S ribosomal genes as well as aiding in identifying key marker genes for the MLST system. This project will contribute to the understanding of nematode biodiversity, improve pest detection methods, and ultimately support the development of better management practices in agriculture. | Reference genome (PacBio HiFi, Hi-C), Transcriptomics (Illumina) | John Webster | NSW Department of Primary Industries and Regional Development, Western Sydney University |
PARTNERS
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advisory committee members
Jeremy Burdon – Independent Chair
Adrian Dinsdale – The Plant Innovation Centre (PIC@PEQ)
Andrew Gilbert – Bioplatforms Australia
Brendan Rodoni – Agriculture Victoria
Deb Hailstones – NSW DPI
Kim Plummer – La Trobe University
Mark Gibberd – Centre for Crop and Disease Management, Curtin University
Markus Herderich – The Australian Wine Research Institute (AWRI)
Neena Mitter – Queensland Alliance of Agriculture and Food Innovation
Peter Langridge – University of Adelaide
Peter Solomon – Australian National University
Robert Coe – Australian Plant Phenomics Facility
Sarah Richmond – Bioplatforms Australia
KEY INFORMATION
ACKNOWLEDGEMENT INFORMATION
Bioplatforms Initiative DOI: https://doi.org/10.25953/9595-kd09
Umbrella Bioproject ID: PRJNA1098054
Please use this ID when submitting any derived data to a database that is a member of the International Nucleotide Sequence Database Collaboration (INSDC), such as GenBank/NCBI, ENA or DDBJ.
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Citation Guidelines
To cite the general initiative:
Plant Pathogen Omics Initiative, 2021, https://doi.org/10.25953/9595-kd09
To cite a specific dataset:
The Plant Pathogen Omics Initiative, 2021, https://doi.org/10.25953/9595-kd09, [year-of-data-download], [full dataset title], [dataset-access-URL], accessed [date-of-access].
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Acknowledgement Statement
We would like to acknowledge the contribution of the Plant Pathogen Omics Initiative Consortium in the generation of data used in this publication. The Initiative is supported by funding from Bioplatforms Australia, enabled by the Commonwealth Government National Collaborative Research Infrastructure Strategy (NCRIS).
If relevant, also credit other organisations involved in collection of the particular dataset you are using, as listed in the ‘project_lead’ and ‘project_collaborators’ in the metadata record.
CONTACT US
Program Manager
Mabel Lum – Bioplatforms Australia
mlum@bioplatforms.com
Project Chair
Jeremy Burdon
jeremy.burdon@gmail.com
General Manager – Science Programs
Sarah Richmond – Bioplatforms Australia
srichmond@bioplatforms.com
DATA AND COLLABORATION POLICY
Data generated through this initiative is subject to the Data and Collaboration policy. Please review it here.