The Genomics for Australian Plants (GAP) framework initiative – developing genomic resources for understanding the evolution and conservation of the Australian flora

Lalita Simpson; David J. Cantrill; Margaret Byrne; Theodore R. Allnutt; Graham J. King; Mabel Lum; Ziad Al Bkhetan; Rose L. Andrew; William J. Baker; Matthew D. Barrett; Jacqueline Batley; Oliver Berry; Rachel M. Binks; Jason Bragg; Linda Broadhurst; Gillian Brown; Jeremy J. Bruhl; Richard J. Edwards; Scott Ferguson; Félix Forest; Johan Gustafsson; Timothy A. Hammer; Gareth D. Holmes; Christopher J. Jackson; Elizabeth A. James; Ashley Jones; Paul J. Kersey; Ilia J. Leitch; Olivier Maurin; Todd G. B. McLay; Daniel J. Murphy; Katharina Nargar; Lars Nauheimer; Hervé Sauquet; Alexander N. Schmidt-Lebuhn; Kelly A. Shepherd; Anna E. Syme; Michelle Waycott; Trevor C. Wilson; Darren M. Crayn

doi:10.1071/SB24022

RESEARCH ARTICLE (Open Access)

The Genomics for Australian Plants (GAP) framework initiative – developing genomic resources for understanding the evolution and conservation of the Australian flora

Lalita Simpson ^A , David J. Cantrill ^B ^C , Margaret Byrne ^D , Theodore R. Allnutt ^B , Graham J. King ^E , Mabel Lum ^F , Ziad Al Bkhetan ^G , Rose L. Andrew ^H , William J. Baker ^I ^K , Matthew D. Barrett

^A , Jacqueline Batley ^L , Oliver Berry ^M , Rachel M. Binks ^D , Jason Bragg ^N , Linda Broadhurst ^O , Gillian Brown ^P , Jeremy J. Bruhl

^H , Richard J. Edwards ^Q ^R , Scott Ferguson

^S , Félix Forest ^I , Johan Gustafsson ^G , Timothy A. Hammer

^T ^U , Gareth D. Holmes

^B , Christopher J. Jackson ^B , Elizabeth A. James ^B , Ashley Jones

^S , Paul J. Kersey ^I , Ilia J. Leitch ^I , Olivier Maurin ^I ^J , Todd G. B. McLay ^B ^C ^V , Daniel J. Murphy ^B ^C ^W , Katharina Nargar

^A ^X , Lars Nauheimer

^A , Hervé Sauquet ^W ^Y , Alexander N. Schmidt-Lebuhn

^O , Kelly A. Shepherd ^Z ^AA , Anna E. Syme ^G , Michelle Waycott

^T ^U , Trevor C. Wilson

^Y and Darren M. Crayn

^A ^P ^X ^AB ^*

+ Author Affiliations

- Author Affiliations

^A Australian Tropical Herbarium, James Cook University Nguma Bada Campus, Smithfield, Qld 4878, Australia.

^B Royal Botanic Gardens Victoria, Melbourne, Vic. 3004, Australia.

^C School of BioSciences, The University of Melbourne, Parkville, Vic. 3010, Australia.

^D Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983, Australia.

^E Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.

^F Bioplatforms Australia Ltd, Sydney, NSW 2109, Australia.

^G Australian BioCommons, The University of Melbourne, Parkville, Vic. 3010, Australia.

^H Botany & N.C.W. Beadle Herbarium, University of New England, Armidale, NSW 2351, Australia.

^I Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.

^J Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium.

^K Department of Biology, Aarhus University, Ny Munkegade 116, DK-8000 Aarhus C, Denmark.

^L School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia.

^M CSIRO Environomics Future Science Platform, Indian Ocean Marine Research Centre, University of Western Australia, Crawley, WA 6009, Australia.

^N Research Centre for Ecosystem Resilience, Botanic Gardens of Sydney, Sydney, NSW 2000, Australia.

^O Centre for Australian National Biodiversity Research (a joint venture of Parks Australia and CSIRO), GPO Box 1700, Canberra, ACT 2601, Australia.

^P Queensland Herbarium and Biodiversity Science, Department of Environment, Tourism and Science, Brisbane Botanic Gardens, Toowong, Qld 4066, Australia.

^Q Minderoo OceanOmics Centre at UWA, Oceans Institute, University of Western Australia, Perth, WA 6009, Australia.

^R Evolution and Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia.

^S Research School of Biology, Australian National University, Canberra, ACT 0200, Australia.

^T School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia.

^U Botanic Gardens and State Herbarium, North Terrace, Adelaide, SA 5000, Australia.

^V National Biodiversity DNA Library, CSIRO, Parkville, Vic. 3010, Australia.

^W Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.

^X National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT 2601, Australia.

^Y National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia.

^Z Western Australian Herbarium, Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983, Australia.

^AA School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia.

^AB Centre of Excellence for Indigenous and Environmental Histories and Futures, James Cook University Nguma Bada Campus, Smithfield, Qld 4878, Australia.

^* Correspondence to: darren.crayn@jcu.edu.au

Handling Editor: Caroline Puente-Lelievre

Australian Systematic Botany 38, SB24022 https://doi.org/10.1071/SB24022

Submitted: 18 July 2024 Accepted: 13 March 2025 Published: 7 May 2025

© 2025 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)

Abstract

The generation and analysis of genome-scale data – genomics – is driving a rapid increase in plant biodiversity knowledge. However, the speed and complexity of technological advance in genomics presents challenges for the widescale use of genomics in evolutionary and conservation biology. We introduce and describe a national-scale collaboration conceived to build genomic resources and capability for understanding the Australian flora: the Genomics for Australian Plants (GAP) Framework Initiative. We outline (a) the history of the project including the collaborative framework, partners and funding; (b) GAP principles such as rigour in design, sample verification and documentation, data management and data accessibility; and (c) the structure of the consortium and the four associated activity streams (reference genomes, phylogenomics, conservation genomics and training), with the rationale and aims for each of these. We show, through discussion of successes and challenges, the value of this multi-institutional consortium approach and the enablers, such as well-curated collections and national collaborative research infrastructure, all of which have led to a substantial increase in capacity and delivery of biodiversity knowledge outcomes.

Keywords: Angiosperms353, Australian flora, conservation, genomics, phylogenomics, population genetics, reference genomes, systematics, taxonomy.

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