Genomics for Australian Plants

###Citation Guidelines __Bioplatforms Initiative DOI__: - 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 - Genomics for Australian Plants Initiative, 2018, 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. __To cite the general initiative__: - 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 - 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]. ###Acknowledgement Statement We would like to acknowledge the contribution of the Genomics for Australian Plants Initiative 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), 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, CSIRO, Centre for Australian National Biodiversity Research and the Department of Biodiversity, Conservation and Attractions, Western Australia.. __Citing and acknowledging the Australian BioCommons Leadership Share (ABLeS) program__ Please use the acknowledgement below if you have accessed the ABLeS program: https://australianbiocommons.github.io/ables/acknowledgements/ 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. ###Data Portal resources - [Programmatic access to the Bioplatforms Data Portal](https://github.com/BioplatformsAustralia/dataportal-usersupport/blob/master/programmatic_access.md) - [Bioplatforms Data Portal support - GitHub resource](https://github.com/BioplatformsAustralia/dataportal-usersupport) ###Useful plant resources - [Compilation of sequenced plant genomes](https://www.genomicsforaustralianplants.com/compilation-of-sequenced-plant-genomes/) - [Researcher directory – Phylogenomics](https://www.genomicsforaustralianplants.com/researcher-directory-phylogenomics/) - [Reference genomes protocols](https://www.genomicsforaustralianplants.com/protocols/) ###Key project information - [Data access (consortium members only)](https://data.bioplatforms.com/organization/pages/bpa-plants/data-access) - [Project contacts](https://data.bioplatforms.com/organization/pages/bpa-plants/contacts) - [Consortium members](https://www.genomicsforaustralianplants.com/consortium/) - [Collaborative Agreement, __Data Policy__ and Communications Policy](https://www.genomicsforaustralianplants.com/agreements-policies/) - __[Acknowledging the consortium](https://www.genomicsforaustralianplants.com/acknowledging-the-consortium/)__ - When using Genomics for Australian Plants Framework Initiative data, please acknowledge the Consortium and Bioplatforms Australia support using the following wording at this __[link here.](https://www.genomicsforaustralianplants.com/acknowledging-the-consortium/)__ ###For more information, please visit: - Genomics for Australian Plants Initiative [Consortium webpage and project updates](https://www.genomicsforaustralianplants.com/) - Genomics for Australian Plants Initiative [Twitter](https://twitter.com/PlantsAus) - Genomics for Australian Plants Initiative [Open Science Framework (consortium access only)](https://osf.io/gkdjx/) - Genomics for Australian Plants Initiative [Bioplatforms webpage](https://bioplatforms.com/projects/genomics-for-australian-plants/) ###Data notes The [Nagoya Protocol](https://www.cbd.int/abs/) on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity is an international agreement which addresses the sharing of benefits arising from the utilization of genetic resources. It entered into force on 12 October 2014, 90 days after the date of deposit of the fiftieth instrument of ratification. The Australian Government has ratified the Nagoya Protocol but not yet implemented it. Specimens which are collected for the Genomics for Australian Plants initiative prior to the Nagoya protocol are indicated as such in the sample metadata. Researchers providing plant material collected after 11 October 2014 have provided assurance that the material complies with current best practice under the relevant federal and/or state legislation. ###Introduction Plants are the backbone of all life on Earth and a key resource for human well-being. Climate change can affect plant diversity as species that are unable to adapt are particularly vulnerable. Australia’s unique flora is under threat from due to varying degrees of disturbance or neglect since the first Europeans came to Australia and from climate change. Genomic approaches offer the possibility of unlocking the enormous information in nuclear genomes for plant evolutionary and conservation studies to significantly improve conservation management decisions. The central resource for this initiative will be derived from herbaria and botanic gardens (living collections) around the country. The addition of genome sequencing data will add significant value to the collections and contribute to the development of new methods and capabilities. ###Aims The Initiative has three key aims: • Sequence and assemble representative Australian plant genomes across across the plant tree of life to enable better conservation, utilisation and understanding of Australia’s unique plant diversity; • Build genomic capacity across Australian Botanic Gardens and Herbaria to create networks collaborating in the collection, management, dissemination and application of genomic data for Australian plants; • Provide tools to enable genetic data to be used to identify and classify biodiversity at a range of scales and to use these tools to inform conservation management and enable better decision making.