– 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:
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- 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. |
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
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