The Genomics for Australian Plants Framework Initiative (GAP) consortium, formed by Bioplatforms Australia in partnership with researchers from the Australian State and National Herbaria, has published 29 reference genomes for key Australian flowering plant species in a recent PLOS One publication. The resource represents a significant genomics contribution to the understanding and conservation of Australia’s unique flora and also addresses a key gap in global plant genomics, where the majority of sequencing efforts have been concentrated on commercially important species and crop plants.
The 29 plant species were chosen for their scientific importance, conservation value and evolutionary significance, with many representing plant groups that have never before had a reference genome published prior to this effort. For example, Archirhodomyrtus beckleri, commonly known as small-leaved myrtle or rose myrtle, is an evergreen shrub belonging to the myrtle family (Myrtaceae). It is at risk of extinction from the incursion and establishment of myrtle rust in Australia. Considerable research is being undertaken to understand these susceptible taxa and to identify potential mechanisms of resistance. Other species such as Dendrocnide excelsa, the giant stinging tree, have considerable potential for therapeutic agents related to their stinging toxins; and Eremophila drummondii, a member of the iconic Australian emu-bush group, has a significant role in traditional Aboriginal medicine and is at the centre of current chemical research for natural product discovery and pharmaceutical development.
The partnerships created from the Genomics for Australian Plants Framework Initiative (GAP) consortium highlight the scientific value of Australia’s botanic gardens and herbaria, and the creation of genomics resources for research, conservation and understanding evolution. Researchers and Bioplatforms sequencing facilities within the GAP consortium with different expertise including high molecular weight DNA extraction, long-read sequencing expertise and bioinformatics expertise, worked closely with Botanic Gardens around the country to select, prepare, sequence and assemble the genomes to help fill in key gaps within the flowering plants tree of life. The living plants that have been sequenced are also maintained in the respective Botanic Gardens to ensure researchers are able to sample and add on additional sequence data in future to address their own research questions and to strengthen the genomics data that is made available through the GAP Initiative.
All the genome data, specimen information and bioinformatics workflows have been made publicly available to create an enduring resource for researchers in Australia and globally. These plant genomes also mark an important step in filling in major gaps in Australia’s tree of life and contribute to global efforts in cataloguing and the use of genomics data to accelerate new discoveries for application in conservation, medicinal discoveries and pharmaceutical development.
Other reference genomes that have been created as part of the GAP Initiative include: Acacia pycnantha, golden wattle, the Australian national floral emblem; Telopea speciosissima, waratah, the floral emblem of New South Wales, and Tasmannia lanceolata, also known as Mountain Pepper, a culinary spice, Aboriginal food flavouring and traditional Aboriginal medicine.
The Genomics for Australian Plants Framework Initiative consortium (https://www.genomicsforaustralianplants.com/consortium/) is supported by funding from Bioplatforms Australia (enabled by the Commonwealth Government National Collaborative Research Infrastructure Strategy, NCRIS), the Ian Potter Foundation, Royal Botanic Gardens Foundation (Victoria), Royal Botanic Gardens Victoria, the Royal Botanic Gardens and Domain Trust, the Council of Heads of Australasian Herbaria, Australian National Herbarium, CSIRO and the Department of Biodiversity, Conservation and Attractions, Western Australia. The provision of computing and data resources was provided by the Australian BioCommons Leadership Share (ABLeS) program, which is co-funded by Bioplatforms Australia (enabled by NCRIS), the National Computational Infrastructure and Pawsey Supercomputing Research Centre.
Image credit: Eremophila drummondii by Rachael Fowler