– ABOUT
Genomics for australian plants
Australia’s unique flora is the result of millions of years of isolated evolution prior to collision with the Asian continent. There are an astounding 24,000 species of native vascular plants, many of which are found nowhere else in the world.
Australian native plants are vital for multiple sectors, including agriculture, forestry, fisheries, aquaculture, and tourism. They hold significant cultural importance for Indigenous communities, supporting their history, innovation, culture, spirituality, and economics for millennia. Genomic characterisation aids in managing and conserving native species, which have faced disturbances since European settlement.
Genomic approaches reveal key insights for plant evolution and conservation, aiding management decisions. Despite limited characterisation of plant genomes, genomic data offers vast potential for identifying traits and informing various applications, including biofuel production, drug development, and crop breeding.
Since its outset in 2018, the Bioplatforms Genomics for Australian Plants Initiative has sequenced and assembled representative plant genomes to enhance herbaria and botanic garden collections nationwide with genomic data, fostering long-term conservation and understanding of Australia’s unique flora. You can find out more on the Genomics for Australian Plants website.
OBJECTIVES
Through this program of research, the creation of referential genomic data resources of Australian native plants will:
- Sequence and assemble Australian plant genomes to enhance conservation, utilisation, and understanding of plant diversity.
- Build genomic capacity across Australian Botanic Gardens and Herbaria for collaborative data management and application.
- Develop tools to use genetic data for identifying and classifying biodiversity, aiding conservation management and decision-making.
DATA
For further information and to view and access initiative data, please go to the Bioplatforms Australia Data Portal.
PROJECTS
| Scientific name | Common name | Data Strategy | Project Lead |
|---|---|---|---|
| Acacia pycnantha | Golden Wattle | Reference genome (PromethION, 10X, Illumina [RNA]) | Daniel Murphy |
| Archirhodomyrtus beckleri | Rose myrtle | Reference genome (PromethION) | David Cantrill |
| Austrobaileya scandens | Austrobaileya | Reference genome (PromethION, PacBio-HiFi) | Darren Crayn |
| Bellendena montana | Mountain Rocket | Reference genome (PacBio-HiFi) | David Cantrill |
| Berberidopsis beckleri | Montane tape vine | Reference genome (PacBio-HiFi) | Jeremy Bruhl |
| Callicoma serratifolia | Black Wattle | Reference genome (PromethION) | David Cantrill |
| Dampiera purpurea | Mountain or Purple dampiera | Reference genome (PacBio-HiFi) | David Cantrill |
| Dendrocnide excelsa | Giant Stinging Tree | Reference genome (PacBio-HiFi) | David Cantrill |
| Denhamia bilocularis | Orangebark | Reference genome (PacBio-HiFi) | David Cantrill |
| Doryanthes excelsa | Gymea lily | Reference genome (PromethION, PacBio-HiFi) | David Cantrill |
| Elaeocarpus reticulatus | Blueberry ash, Fairy petticoats, Koda | Reference genome (PacBio-HiFi) | David Cantrill |
| Eremophila drummondii | Drummond’s Eremophila | Reference genome (PacBio-HiFi, Illumina) | Rachael Fowler |
| Eucryphia lucida | Leatherwood | Reference genome (PromethION) | David Cantrill |
| Eupomatia laurina | Bolwarra, copper laurel, native guava | Reference genome (PacBio-HiFi) | David Cantrill |
| Flindersia xanthoxyla | Yellow-wood, Long jack | Reference genome (PacBio-HiFi) | David Cantrill |
| Gastrolobium racemosum | Net-leaved poison | Reference genome (PromethION) | David Cantrill |
| Gymnostoma australianum | Daintree pine, Daintree oak | Reference genome (PacBio-HiFi) | David Cantrill |
| Gymnostoma australianum | Daintree pine or Daintree oak | Reference genome (PacBio-HiFi) | David Cantrill |
| Hedycarya angustifolia | Austral mulberry | Reference genome (PacBio-HiFi) | David Cantrill |
| Hibbertia scandens | Climbing guinea flower | Reference genome (PromethION, Illumina) | Michelle Waycott |
| Isopogon anethifolius | Narrow-leaf drumsticks | Reference genome (PromethION) | David Cantrill |
| Kingia australis | Kingia, Bullanock | Reference genome (PacBio-HiFi) | David Cantrill |
| Lepidosperma gladiatum | Coast sword-sedge | Reference genome (PacBio-HiFi) | David Cantrill |
| Leucochrysum albicans | Hoary Sunray | Reference genome (PacBio-HiFi) | Alexander Schmidt-Lebuhn |
| Nothofagus cunninghamii | Tasmanian myrtle | Reference genome (PacBio-HiFi) | David Cantrill |
| Pelargonium australe | Native storksbill, austral storksbill) | Reference genome (PacBio-HiFi) | Michael Roach |
| Phebalium stellatum | Phebalium stellatum | Reference genome (PacBio-HiFi, PromethION [RNA], Hi-C) | Rose Andrew, Ash Jones |
| Phyllanthus gunnii | Scrubby spurge | Reference genome (PacBio-HiFi) | David Cantrill |
| Pultenaea daphnoides | Large-leaf bush-pea | Reference genome (PacBio-HiFi) | David Cantrill |
| Quintinia fawkneri | Climbing quintinia | Reference genome (PromethION) | David Cantrill |
| Roepera similis | White twinleaf | Reference genome (PacBio-HiFi) | David Cantrill |
| Tasmannia lanceolata | Mountain pepper, Tasmanian pepperberry | Reference genome (PacBio-HiFi) | Mathew Lewsey, Alexandre Fournier-Level |
| Telopea speciosissima | NSW Waratah | Reference genome (PromethION, 10X, Hi-C) | Jason Bragg |
| Thelymitra variegata | Queen of Sheba orchid | Reference genome (Pacbio-HiFi) | Katharina Nargar |
| Wahlenbergia ceracea | Waxy bluebell | Reference genome (PacBio-HiFi, Hi-C) | Jemimah Hamilton, Ash Jones |
| Xanthorrhoea johnsonii | Johnson’s grass tree | Reference genome (PacBio-HiFi, PromethION [DNA,RNA], Hi-C) | Todd McLay, Ash Jones |
| Acacia and related mimosoid legume phylogenomics | Phylogenomics (Bait capture - Illumina) | Dan Murphy | |
| Alismatales (Alismatids) | Phylogenomics (Bait capture - Illumina) | Michelle Waycott | |
| Boronieae | Australian Rutaceae | Phylogenomics (Bait capture - Illumina) | Harvey Orel |
| Drosera | Sundews | Phylogenomics (Bait capture - Illumina) | Michelle Waycott |
| Ericaceae | Epacrids, southern heaths | Phylogenomics (Bait capture - Illumina) | Darren Crayn |
| Fabaceae tribe Mirbelieae | Bush peas | Phylogenomics (Bait capture - Illumina) | James Clugston |
| Hibbertia | Guinea flowers | Phylogenomics (Bait capture - Illumina) | Michelle Waycott |
| Lasiopetaleae (Malvaceae) | Phylogenomics (Bait capture - Illumina) | Kelly Shepherd | |
| Myrtaceae tribe Chameulaucieae | Waxflower | Phylogenomics (Bait capture - Illumina) | Michelle Waycott |
| Persoonia | Geebung, Snottygobble | Phylogenomics (Bait capture - Illumina) | Gareth Holmes |
| Santalaceae (Viscaceae & Amphorogynaceae) | Mistletoes | Phylogenomics (Bait capture - Illumina) | Benjamin Anderson |
| Stylidiaceae | Triggerplant family | Phylogenomics (Bait capture - Illumina) | Juliet Wege |
| Tecticornia & Salicornia | Samphires | Phylogenomics (Bait capture - Illumina) | Kelly Shepherd |
| Teucrium | Germander | Phylogenomics (Bait capture - Illumina) | Trevor Wilson |
| Typhonium | Arum lilies, Dead horse lilies | Phylogenomics (Bait capture - Illumina) | Matthew Barrett |
| Xanthorrhoe | Grass trees, yacca, balga | Phylogenomics (Bait capture - Illumina) | Todd McLay |
| Allocasuarina section Cylindropitys | She-oaks | Conservation genomics (ddRAD) | Marlien van der Merwe |
| Cassia species in Queensland | Conservation genomics (ddRAD) | Laura Simmons | |
| Geleznowia verrucosa species complex | Yellow bells | Conservation genomics (ddRAD) | Kelly Shepherd |
| Gompholobium species in Queensland | Conservation genomics (ddRAD) | Laura Simmons | |
| Isopogon buxifolius complex | Conservation genomics (ddRAD) | Rachel Binks | |
| Lepidosperma fimbriatum | Conservation genomics (ddRAD) | Russell Barrett | |
| Lepidosperma laterale | Conservation genomics (ddRAD) | Jeremy Bruhl | |
| Olearia ramulosa | Twiggy Daisy Bush | Conservation genomics (ddRAD) | Andre Messina |
| Paracaleana gracilicordata / P. granitica complex (flying duck orchids) | Conservation genomics (ddRAD) | Katharina Nargar | |
| Samadera bidwillii | Conservation genomics (ddRAD) | Laura Simmons | |
| Synaphea stenoloba complex | Conservation genomics (ddRAD) | Rachel Binks | |
| Wurmbea dioica subsp. alba complex | Conservation genomics (ddRAD) | Rachel Binks | |
| Zieria species | Conservation genomics (ddRAD) | Mike Bayly |
PARTNERS
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advisory committee members
KEY INFORMATION
ACKNOWLEDGEMENT INFORMATION
Bioplatforms Initiative DOI: https://doi.org/10.25953/3108-3v82
Umbrella Bioproject ID: PRJNA1075727
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:
Genomics for Australian Plants Initiative, 2018, https://doi.org/10.25953/3108-3v82
To cite a specific dataset:
The Genomics for Australian Plants Initiative, 2018, https://doi.org/10.25953/3108-3v82, [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 Genomics for Australian Plants Initiative Consortium (https://www.genomicsforaustralianplants.com/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), as well as the Ian Potter Foundation, the Royal Botanic Gardens Foundation (Victoria), the Royal Botanic Gardens Victoria, the Royal Botanic Gardens and Domain Trust, the Council of Heads of Australasian Herbaria, CSIRO, Centre for Australian National Biodiversity Research and the Department of Biodiversity, Conservation and Attractions, Western Australia.
If relevant, also credit other organisations involved in the collection of the particular dataset you are using, as listed in the ‘project_lead’ and ‘project_collaborators’ in the metadata record.
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Citing and acknowledging the Australian BioCommons Leadership Share (ABLeS) program
Please use the acknowledgement below if you have accessed the ABLeS program: https://australianbiocommons.
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Associated publication
The Genomics for Australian Plants (GAP) Framework Initiative – developing genomic resources for understanding the evolution and conservation of the Australian flora
https://doi.org/10.1071/SB24022
CONTACT US
Program Manager
Mabel Lum – Bioplatforms Australia
mlum@bioplatforms.com
Science Lead
David Cantrill – Royal Botanic Gardens of Victoria
David.Cantrill@rbg.vic.gov.au
General Manager – Science Programs
Sarah Richmond – Bioplatforms Australia
srichmond@bioplatforms.com
DATA AND COLLABORATION POLICY
Data generated through this initiative is subject to a Data policy, Collaboration policy and Communication policy.