REQUEST FOR PARTNERSHIP GUIDELINES
The Australian Avian Genomics Initiative is now calling for project proposals to collaboratively develop critical genomics resources for Australian bird species.
The call includes activities to generate:
- Reference Genomes (with an associated priority list to fill in gaps)
- Population genetics and Phylogenomics
- Other beneficial ‘omics resources, including metabolomics and proteomics
AUSTRALIAN AVIAN GENOMICS INITIATIVE
REQUEST FOR PARTNERSHIP TEMPLATE
PRIORITY SPECIES LIST FOR REFERENCE GENOME REQUESTS
THE AUSTRALIAN AVIAN GENOMICS INITIATIVE – BACKGROUND
Australia is home to approximately 830 species of birds, of which 43% are endemics that are only found here. There have been substantial efforts, particularly internationally in avian genomics and phylogenomics. However, central gaps remain in the reference data available for Australian bird species.
The Australian Avian Genomics Initiative aims to build a foundation of molecular data to advance our understanding and conservation of Australia’s unique bird species. This durable data resource generated by the initiative will include gap-filling reference genomes for Australian representatives of all bird families in Australia, and increasing capacity for cutting-edge studies using phylogenomic, population genomic, and other ‘omic approaches.
Our aim is to accelerate research in bird genomics in areas that Australia is uniquely placed to make its mark on the world stage. We are promoting a focus on understanding the evolution of traits. Especially traits that are uniquely Australian or those that impact on species survival and adaptation to Australia’s harsh environments. For example: What are the molecular underpinnings of drought tolerance or non-tolerance, adaptation to the arid zone, detection of infrasound (how waterbirds locate water after rainfall events)? Are there common genetic controls of plumage evolution and plumage mimicry? Vocal mimicry? What has driven the evolution of traits involved in co-evolution of birds and plants, or in nectarivory, co-operative breeding, construction of mud nests or migration and nomadism and the spectrum in-between those extremes?
We also aim to support the promotion of novel and innovative research using genomic (or other ‘omics) approaches to meet critical biodiversity and conservation needs. From better understanding the prevalence of avian diseases in reservoir species, to estimating extinction risk for data deficient species, and accelerating the discovery and resolution of species, subspecies, and genetically distinct populations for conservation management.
A FOCUS ON ADVANCING OUR KNOWLEDGE ON AUSTRALIA’S UNIQUE BIRDS
This Request for Partnership is a non-competitive, collaborative, opportunity to create referential biomolecular data to help Australia’s birds.
The below themes represent some examples where biomolecular data can bring substantial value to research. Partnership projects are not expected to address all of these topics, and we will consider other topics not listed here.
RESEARCH THEMES
- Adaptation to Australia’s unique environments
- Evolution of traits
- Invasive species
- Avian disease
- Conservation efforts with applied use
- Genomic resources for poorly understood and data deficient species/subspecies
- Taxonomy, species identification, biodiversity investigation
The initiative welcomes partnership requests with various analytic designs such as:
- Reference genomes on the list of priority groups and species defined (see below)
- Population genomics (SNPs, re-sequencing)
- Phylogenomics
- Multi-omics project including one or more omics
Gap analysis on existing genomics resource for Australian relevant bird species.
A review of existing genomics resources (reference genomes) available for Australian relevant bird species was conducted. Australia hosts 107 families of birds covering 968 species. As of the records from early December 2023, a total of 527 reference genomes from Australian species have been generated and can be publicly accessible. This is mapping to 91.5% of the Australian families of birds, covering 98.6% of the Australian relevant species. All families of Australian relevant species have a mapping reference genome from an international species. Out of the 413 genera of Australian birds, 82% mapped to an available reference genome from an Australian species and more than 88% mapped to a reference genome from any international species.
This shows the increasing worldwide effort in generating genomic referential information. To strengthen this effort, the Initiative will prioritise the generation of reference genome for families and genera lacking genomic resources.
The list of target groups and species for the generation of reference genomes can be found here.
REQUEST FOR PARTNERSHIP
Projects are encouraged to target an applied theme and will be assessed based on the following criteria
- Project team: contains the expertise to complete the project and collaborates with relevant stakeholders, including industry or collection partners
- Rationale: designed to enhance knowledge of Australia’s birds by the generation of novel broad utility (reusable) data
- Timely sample availability: access to existing samples, or the ability to collect samples in a timely manner (with detailed timeline), that are suitable for extracting the necessary material
- Co-contribution: the team must be capable of marshalling the resources necessary to complement Bioplatforms Australia project investment (biomolecular data generation and access to high end compute resources – NCI and Pawsey), in order to bring the project to completion. Sample collection and data analysis are to be supported by co-investment (in time) from the researcher. The ability to conduct value-add analyses is highly desirable.
- Scale of the request: The scale of support will ensure a return on Bioplatforms national investment according to the initiative objectives.
It should be noted that this is not a competitive grant opportunity and the Australian Avian Genomics Initiative will endeavour to support projects that aim to enhance Australia’s knowledge and application of birds. Project assessment will be guided by Bioplatforms Australia facilities and the Australian Avian Genomics Advisory Committee.
NOTES:
- We encourage interested parties with low to no expertise in genomics to get in touch with the initiative contacts to discuss potential opportunities.
- The Bioplatforms initiatives aim to support the Australian research community. We welcome proposals from international researchers on Australian-relevant birds, however, the proposal must have a meaningful collaboration with Australian researchers.
The processing of the material is also required to be carried through the Bioplatforms network of facilities and the data to be managed through the Bioplatforms data portal according to the Data use and Communications policy.
INSTRUCTIONS FOR APPLYING
- Please ensure you have read all information on this page before completing the Request for Partnership (RFP) document.
- Please download the proposal template – Request for Partnership Application Template
- Complete and submit one document per species of interest. Where a project may be addressing a question that spans multiple species (or genera), please submit one document per project question and include an appendix list of the species of interest.
- Address all criteria/questions listed in the document.
- Answers to all the criteria should not exceed 6 pages.
Deadline: COB Thursday 28th March 2024
Submissions: Please email the completed document to Sophie Mazard, smazard@bioplatforms.com, with the subject: Avian Initiative RFP1 – [Project name summary]
Contact information:
Dr Sophie Mazard, Program Manager smazard@bioplatforms.com
Sarah Richmond, General Manager Scientific Programs srichmond@bioplatforms.com