Data

Minderoo Foundation’s OceanOmics Program

Australian Ocean Data Network
Goncalves, Priscila ; Corrigan, Shannon ; Rauschert, Sebastian ; Burnell, Stephen ; Bayer, Philipp
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=https://catalogue.aodn.org.au/geonetwork/srv/eng/catalog.search#/metadata/5c648e8a-e40e-4d1b-a676-272f2e748eae&rft.title=Minderoo Foundation’s OceanOmics Program&rft.identifier=https://catalogue.aodn.org.au/geonetwork/srv/eng/catalog.search#/metadata/5c648e8a-e40e-4d1b-a676-272f2e748eae&rft.description=The overarching goal of the Minderoo Foundation’s OceanOmics Program is to revolutionise how we measure, understand, and ultimately conserve life in our oceans. The program focuses on the advancement and implementation of environmental DNA (eDNA) technologies at speed and scale, in the context of biodiversity monitoring and marine conservation. This includes (1) designing, evaluating and deploying scalable and standardised eDNA laboratory procedures; (2) generating reference genome resources for marine vertebrate species; (3) developing novel open-source computational approaches for analysis of eDNA data; and (4) deploying such technologies and resources in the field at scale, covering both spatial and temporal dimensions, including high-throughput automated and/or autonomous solutions for seawater sampling and eDNA isolation. To accelerate the generation of eDNA data for Australian marine environments, the program will collect seawater samples for eDNA analyses throughout the Commonwealth marine estate. Over the past 2.5 years (2021-2023), we have visited and produced data from a number of Australian Marine Parks within the North-West and South-West networks. To date, our main output is sequencing data from Australian waters for fish community description, with the raw sequencing reads deposited in the European Nucleotide Archive (ENA), one bioproject per expedition area.Maintenance and Update Frequency: quarterlyStatement: Metabarcoding analysis of marine eDNA samples for characterisation of fish community assemblages (targeting fragments of 16S and 12S rRNA genes). Supplemental information: eDNA is isolated from seawater samples from filtration (0.45 µm filters) and submitted to extraction. Fragments of 16S and 12S rRNA genes are amplified by qPCR and sequenced on an Illumina NextSeq2000 platform (2x150 bp). Sequencing data is analysed by a custom, open-source metabarcoding pipeline with taxonomic annotation of fish species performed based on nucleotide records available at ENA.&rft.creator=Goncalves, Priscila &rft.creator=Corrigan, Shannon &rft.creator=Rauschert, Sebastian &rft.creator=Burnell, Stephen &rft.creator=Bayer, Philipp &rft.date=2023&rft.coverage=westlimit=94.915797; southlimit=-38.618302; eastlimit=131.338415; northlimit=-8.322025&rft.coverage=westlimit=94.915797; southlimit=-38.618302; eastlimit=131.338415; northlimit=-8.322025&rft.coverage=uplimit=60; downlimit=1&rft.coverage=uplimit=60; downlimit=1&rft_rights=Creative Commons Attribution 4.0 International License https://creativecommons.org/licenses/by/4.0/&rft_rights=The citation in a list of references is: Citation author name/s (year metadata published), metadata title. Citation author organisation/s. File identifier and Data accessed at (add http link).&rft_rights=Data, products and services from IMOS are provided as is without any warranty as to fitness for a particular purpose.&rft_subject=oceans&rft_subject=Genome sequencing&rft_subject=Amplicon sequencing&rft_subject=Actinopterygii&rft_subject=Chondrichthyes&rft_subject=FISHERIES&rft_subject=EARTH SCIENCE&rft_subject=AGRICULTURE&rft_subject=AGRICULTURAL AQUATIC SCIENCES&rft_subject=FISH&rft_subject=BIOLOGICAL CLASSIFICATION&rft_subject=ANIMALS/VERTEBRATES&rft_subject=BIODIVERSITY FUNCTIONS&rft_subject=BIOSPHERE&rft_subject=ECOLOGICAL DYNAMICS&rft_subject=COMMUNITY DYNAMICS&rft_subject=INDIGENOUS/NATIVE SPECIES&rft_subject=SPECIES/POPULATION INTERACTIONS&rft_subject=States, Territories (Australia) | States, Territories (Australia) | Western Australia&rft_subject=Coastal Cities / Towns (Australia) | Coastal Cities / Towns (Australia) | Perth, WA&rft_subject=Coastal Waters (Global) | Coastal Waters (Global) | Papua New Guinea Coast&rft_subject=Countries | Countries | Australia&rft_subject=Global / Oceans | Global / Oceans | East Indian Ocean&rft_subject=Global / Oceans | Global / Oceans | Indian Ocean&rft.type=dataset&rft.language=English Access the data
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Data, products and services from IMOS are provided "as is" without any warranty as to fitness for a particular purpose.

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Brief description

The overarching goal of the Minderoo Foundation’s OceanOmics Program is to revolutionise how we measure, understand, and ultimately conserve life in our oceans. The program focuses on the advancement and implementation of environmental DNA (eDNA) technologies at speed and scale, in the context of biodiversity monitoring and marine conservation. This includes (1) designing, evaluating and deploying scalable and standardised eDNA laboratory procedures; (2) generating reference genome resources for marine vertebrate species; (3) developing novel open-source computational approaches for analysis of eDNA data; and (4) deploying such technologies and resources in the field at scale, covering both spatial and temporal dimensions, including high-throughput automated and/or autonomous solutions for seawater sampling and eDNA isolation. To accelerate the generation of eDNA data for Australian marine environments, the program will collect seawater samples for eDNA analyses throughout the Commonwealth marine estate. Over the past 2.5 years (2021-2023), we have visited and produced data from a number of Australian Marine Parks within the North-West and South-West networks. To date, our main output is sequencing data from Australian waters for fish community description, with the raw sequencing reads deposited in the European Nucleotide Archive (ENA), one bioproject per expedition area.

Lineage

Maintenance and Update Frequency: quarterly
Statement: Metabarcoding analysis of marine eDNA samples for characterisation of fish community assemblages (targeting fragments of 16S and 12S rRNA genes). Supplemental information: eDNA is isolated from seawater samples from filtration (0.45 µm filters) and submitted to extraction. Fragments of 16S and 12S rRNA genes are amplified by qPCR and sequenced on an Illumina NextSeq2000 platform (2x150 bp). Sequencing data is analysed by a custom, open-source metabarcoding pipeline with taxonomic annotation of fish species performed based on nucleotide records available at ENA.

Notes

Credit
This research was led by Minderoo Foundation in collaboration with partner institutions and organisations.
Credit
The work was conducted in Australian Marine Parks under permit series number PA2021-00009, issued by the Director of National Parks, Australia (ror.org/02b3hht72).

Issued: 29 03 2023

Data time period: 2019-10-03

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131.33842,-8.32203 131.33842,-38.6183 94.9158,-38.6183 94.9158,-8.32203 131.33842,-8.32203

113.127106,-23.4701635

text: westlimit=94.915797; southlimit=-38.618302; eastlimit=131.338415; northlimit=-8.322025

text: uplimit=60; downlimit=1

Subjects
AGRICULTURAL AQUATIC SCIENCES | AGRICULTURE | ANIMALS/VERTEBRATES | Actinopterygii | Amplicon sequencing | BIODIVERSITY FUNCTIONS | BIOLOGICAL CLASSIFICATION | BIOSPHERE | COMMUNITY DYNAMICS | Chondrichthyes | Coastal Cities / Towns (Australia) | Coastal Cities / Towns (Australia) | Perth, WA | Coastal Waters (Global) | Coastal Waters (Global) | Papua New Guinea Coast | Countries | Countries | Australia | EARTH SCIENCE | ECOLOGICAL DYNAMICS | FISH | FISHERIES | Genome sequencing | Global / Oceans | Global / Oceans | East Indian Ocean | Global / Oceans | Global / Oceans | Indian Ocean | INDIGENOUS/NATIVE SPECIES | SPECIES/POPULATION INTERACTIONS | States, Territories (Australia) | States, Territories (Australia) | Western Australia | oceans |

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Other Information
(Sequencing data on European Nucleotide Archive (ENA))

uri : https://www.ebi.ac.uk/ena/browser/view/PRJEB63306

Identifiers
  • global : 5c648e8a-e40e-4d1b-a676-272f2e748eae