Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples
Data stored in a Dryad package (doi:10.5061/dryad.c75sj) associated with the publication: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples Authors: Bruce Deagle , Laurence Clarke , John Kitchener, Andrea Polanowski,...
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Australian Antarctic Data Centre
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Online Access: | https://researchdata.ands.org.au/initial-evaluation-dna-recorder-samples/992335 https://doi.org/10.5061/dryad.c75sj https://data.aad.gov.au/metadata/records/AAS_4313_Genetic_CPR http://nla.gov.au/nla.party-617536 |
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ftands:oai:ands.org.au::992335 2023-05-15T15:33:50+02:00 Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples DEAGLE, BRUCE (hasPrincipalInvestigator) DEAGLE, BRUCE (processor) Australian Antarctic Data Centre (publisher) Spatial: northlimit=-52.48278; southlimit=-52.48278; westlimit=155.03906; eastLimit=155.03906; projection=WGS84 Temporal: From 2015-04-06 to 2015-04-20 https://researchdata.ands.org.au/initial-evaluation-dna-recorder-samples/992335 https://doi.org/10.5061/dryad.c75sj https://data.aad.gov.au/metadata/records/AAS_4313_Genetic_CPR http://nla.gov.au/nla.party-617536 unknown Australian Antarctic Data Centre https://researchdata.ands.org.au/initial-evaluation-dna-recorder-samples/992335 fbc3f902-2288-42cd-83a7-d40ab31ca5a0 doi:10.5061/dryad.c75sj AAS_4313_Genetic_CPR https://data.aad.gov.au/metadata/records/AAS_4313_Genetic_CPR http://nla.gov.au/nla.party-617536 Australian Antarctic Data Centre biota oceans ZOOPLANKTON EARTH SCIENCE BIOSPHERE AQUATIC ECOSYSTEMS PLANKTON EUPHAUSIIDS (KRILL) BIOLOGICAL CLASSIFICATION ANIMALS/INVERTEBRATES ARTHROPODS CRUSTACEANS ECHINODERMS HYDROZOANS CNIDARIANS DNA BARCODING DNA SEQUENCES CPR > Continuous Plankton Recorder R/V AA > R/V Aurora Australis GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN dataset ftands https://doi.org/10.5061/dryad.c75sj 2020-01-05T21:37:30Z Data stored in a Dryad package (doi:10.5061/dryad.c75sj) associated with the publication: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples Authors: Bruce Deagle , Laurence Clarke , John Kitchener, Andrea Polanowski, Andrew Davidson. Molecular Ecology Resources. The Continuous Plankton Recorder (CPR) has been used to characterise zooplankton biodiversity along transects covering hundreds of thousands of kilometres in the Southern Ocean CPR survey. Plankton collected by the CPR is currently identified using is classical taxonomy (i.e. using a microscope and morphological features). We investigated the potential to use DNA metabarcoding (species identification from DNA mixtures using high-throughput DNA sequencing) as a tool for rapid collection of taxonomic data from CPR samples. In our study, zooplankton were collected on CPR silks along two transects between Tasmania and Macquarie Island. Plankton were identified using standard microscopic methods and by sequencing a mitochondrial COI marker. Data provided in the Dryad Data entry include the DNA sequences (Illumina MiSeq) recovered, the morphological identifications and the R-code used to analyse these data. The results from our study show that a DNA-based approach increased the number of metazoan species identified and provided high resolution taxonomy of groups problematic in conventional surveys (e.g. larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from larger plankton (such as krill) masked the presence of smaller species. Overall, the genetic data represents a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing this powerful DNA metabarcoding approach from the current snapshot studies to the requirements of a long-term monitoring program. Dataset aurora australis Macquarie Island Southern Ocean Research Data Australia (Australian National Data Service - ANDS) Davidson ENVELOPE(-44.766,-44.766,-60.766,-60.766) Southern Ocean ENVELOPE(155.03906,155.03906,-52.48278,-52.48278) |
institution |
Open Polar |
collection |
Research Data Australia (Australian National Data Service - ANDS) |
op_collection_id |
ftands |
language |
unknown |
topic |
biota oceans ZOOPLANKTON EARTH SCIENCE BIOSPHERE AQUATIC ECOSYSTEMS PLANKTON EUPHAUSIIDS (KRILL) BIOLOGICAL CLASSIFICATION ANIMALS/INVERTEBRATES ARTHROPODS CRUSTACEANS ECHINODERMS HYDROZOANS CNIDARIANS DNA BARCODING DNA SEQUENCES CPR > Continuous Plankton Recorder R/V AA > R/V Aurora Australis GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN |
spellingShingle |
biota oceans ZOOPLANKTON EARTH SCIENCE BIOSPHERE AQUATIC ECOSYSTEMS PLANKTON EUPHAUSIIDS (KRILL) BIOLOGICAL CLASSIFICATION ANIMALS/INVERTEBRATES ARTHROPODS CRUSTACEANS ECHINODERMS HYDROZOANS CNIDARIANS DNA BARCODING DNA SEQUENCES CPR > Continuous Plankton Recorder R/V AA > R/V Aurora Australis GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
topic_facet |
biota oceans ZOOPLANKTON EARTH SCIENCE BIOSPHERE AQUATIC ECOSYSTEMS PLANKTON EUPHAUSIIDS (KRILL) BIOLOGICAL CLASSIFICATION ANIMALS/INVERTEBRATES ARTHROPODS CRUSTACEANS ECHINODERMS HYDROZOANS CNIDARIANS DNA BARCODING DNA SEQUENCES CPR > Continuous Plankton Recorder R/V AA > R/V Aurora Australis GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN |
description |
Data stored in a Dryad package (doi:10.5061/dryad.c75sj) associated with the publication: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples Authors: Bruce Deagle , Laurence Clarke , John Kitchener, Andrea Polanowski, Andrew Davidson. Molecular Ecology Resources. The Continuous Plankton Recorder (CPR) has been used to characterise zooplankton biodiversity along transects covering hundreds of thousands of kilometres in the Southern Ocean CPR survey. Plankton collected by the CPR is currently identified using is classical taxonomy (i.e. using a microscope and morphological features). We investigated the potential to use DNA metabarcoding (species identification from DNA mixtures using high-throughput DNA sequencing) as a tool for rapid collection of taxonomic data from CPR samples. In our study, zooplankton were collected on CPR silks along two transects between Tasmania and Macquarie Island. Plankton were identified using standard microscopic methods and by sequencing a mitochondrial COI marker. Data provided in the Dryad Data entry include the DNA sequences (Illumina MiSeq) recovered, the morphological identifications and the R-code used to analyse these data. The results from our study show that a DNA-based approach increased the number of metazoan species identified and provided high resolution taxonomy of groups problematic in conventional surveys (e.g. larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from larger plankton (such as krill) masked the presence of smaller species. Overall, the genetic data represents a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing this powerful DNA metabarcoding approach from the current snapshot studies to the requirements of a long-term monitoring program. |
author2 |
DEAGLE, BRUCE (hasPrincipalInvestigator) DEAGLE, BRUCE (processor) Australian Antarctic Data Centre (publisher) |
format |
Dataset |
title |
Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_short |
Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_full |
Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_fullStr |
Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_full_unstemmed |
Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_sort |
data from initial evaluation of dna metabarcoding for processing continuous plankton recorder samples |
publisher |
Australian Antarctic Data Centre |
url |
https://researchdata.ands.org.au/initial-evaluation-dna-recorder-samples/992335 https://doi.org/10.5061/dryad.c75sj https://data.aad.gov.au/metadata/records/AAS_4313_Genetic_CPR http://nla.gov.au/nla.party-617536 |
op_coverage |
Spatial: northlimit=-52.48278; southlimit=-52.48278; westlimit=155.03906; eastLimit=155.03906; projection=WGS84 Temporal: From 2015-04-06 to 2015-04-20 |
long_lat |
ENVELOPE(-44.766,-44.766,-60.766,-60.766) ENVELOPE(155.03906,155.03906,-52.48278,-52.48278) |
geographic |
Davidson Southern Ocean |
geographic_facet |
Davidson Southern Ocean |
genre |
aurora australis Macquarie Island Southern Ocean |
genre_facet |
aurora australis Macquarie Island Southern Ocean |
op_source |
Australian Antarctic Data Centre |
op_relation |
https://researchdata.ands.org.au/initial-evaluation-dna-recorder-samples/992335 fbc3f902-2288-42cd-83a7-d40ab31ca5a0 doi:10.5061/dryad.c75sj AAS_4313_Genetic_CPR https://data.aad.gov.au/metadata/records/AAS_4313_Genetic_CPR http://nla.gov.au/nla.party-617536 |
op_doi |
https://doi.org/10.5061/dryad.c75sj |
_version_ |
1766364433291935744 |