BACKGROUND

The Bioplatforms Australia-supported Plant Pathogen ‘Omics Initiative has the broad aim of generating a national library of ‘omics data to support the goals and missions of the plant health community in preparing, managing and mitigating plant disease outbreaks across Australia’s agricultural sectors.

The program will generate high quality molecular reference data for plant pathogens in Australia. This data will be developed through collaboration with the national plant pathogen community and will be used as a foundational data asset to support:

  1. fundamental research and development in plant protection (e.g., understanding the emergence and evolution of pathogens in crop systems, resolving taxonomy and race structure, informing biocide development, etc.)
  2. an effective national biosecurity surveillance system (e.g., incursion detection, rapid diagnostics tests, etc.)

In order to develop an enduring data asset, the initiative will work with key groups across Australia to implement a series of standardised protocols (from sampling to metadata and sequencing) as well as standardised software and bioinformatics tools for fit-for-purpose workflows that a transparent and repeatable.

PHASE 1 – GENOMICS  

Phase 1 of the initiative will focus on creating a library of genomic data for established plant pathogens that impact the spectrum of agricultural plant industries. This will focus on bacteria, viruses, fungi and nematodes. Data will be created, as needed, across two areas:

  1. High quality reference genomes
  2. Population genetics & phylogenomics

Phase 2 will investigate exotic pathogens, as well as other ‘omics i.e. proteomics, metabolomics and phenomics.

PRIORITY SPECIES

The Plant Pathogen ‘Omics Initiative has worked with state and territory agencies, Rural Development Corporations and academic groups to produce a list of starting pathogen species for genomic sequencing.

  • The list does not necessarily focus on pathogens that pose the most potential threat, but rather those species where having genomic/genetic data would be immediately useful for Research & Development and/or biosecurity applications.
  • The current list focuses mainly on established pathogens only. Exotics are to be explored in future stages.
  • We anticipate that this will be a living list, and will be updated over time and as consultations continue.
  • We understand that some data already exists for listed species and we’ll undertake a thorough stocktake on gaps before any new projects begin.

The list of priority pathogens can be found here.

PARTNERSHIP FRAMEWORK

  1. The project currently has $1 million in funding to support sequencing costs within the Bioplatforms Australia-supported facilities.
  2. Project, data and metadata management will be provided by Bioplatforms Australia.
  3. This is not a competitive grant opportunity. This initiative is a national collaboration to deliver data products of relevance to plant protection researchers and practitioners. The initiative will cover the sequencing costs, and we seek to collaborate with the national plant pathogen community to design and deliver on-the-ground project outcomes.
  4. The Plant Pathogen ‘Omics Initiative is seeking partners to lead species-focused projects and assist us in the form of:
    • Project coordination
    • Sample metadata provision (a template will be provided and must be completed and received prior to sample submission)
    • Sample provision (in collaboration with vouchered collections groups to confirm pathogen ID)
    • DNA extraction (with support/guidance from the program consortium)
    • Sample shipping to the appropriate sequencing facility
    • Bioinformatics/data analysis (with support and standardised access to compute and tools via the consortium and the Australian BioCommons)
  5. Project leaders and collaborators will get primary access to data outputs for publication or other collaboration purposes under a 12-month embargo period.

REQUEST FOR PARTNERSHIP PROCESS

  • Proposed projects must select a species listed on the priority list.
  • We encourage you to engage with other departments who have also listed their interest in the same pathogen to see how you might work together on the project, e.g., contributing isolates for the same end use etc. Interested parties are listed in the requesting organisation/s (Column D) (requesting organisations are also very welcome to lead projects). The key contact details for these groups are listed in the “Contacts” tab of the priority list.
  • Where we receive more than one proposal for the same species, we will facilitate a collaboration across the submitting groups.

INSTRUCTIONS FOR APPLYING

  1. Please read all of the information on this page before completing the project proposal document.
  2. Please download the proposal template here – Request for Partnership Application Template
  3. Complete one document for each species.
  4. Address all criteria listed.
  5. Answers to all the criteria should not exceed 4 pages.

Deadline: EXTENDED to COB Friday 20th May, 2022.

Submissions: Please email the completed RFP document to Mabel Lum, mlum@bioplatforms.com, with subject: Plant Pathogen RFP – [Species name].

Parties interested in participating in the Plant Pathogen ‘Omics Initiative, including this RFP, are welcome to get in contact with Mabel Lum at any time.

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