Data

Population genetics dataset for Antarctic krill (Euphausia superba): Restriction site-associated DNA sequencing (RAD-seq) and mtDNA sequencing

Australian Antarctic Division
Deagle, B. ; DEAGLE, BRUCE E.
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=info:doi10.4225/15/556FAB354BE19&rft.title=Population genetics dataset for Antarctic krill (Euphausia superba): Restriction site-associated DNA sequencing (RAD-seq) and mtDNA sequencing&rft.identifier=10.4225/15/556FAB354BE19&rft.publisher=Australian Antarctic Data Centre&rft.description=This restriction site associated DNA sequencing (RAD-seq) dataset for Antarctic krill (Euphausia superba) includes raw sequence data and summaries for 148 krill from 5 Southern Ocean sites. A detailed README.pdf file is provided to describe components of the dataset. DNA library preparation was carried out in two separate batches by Floragenex (Eugene, Oregon, USA). RAD fragment libraries (SbfI) were sequenced on an Illumina HiSeq 2000 using single-end 100 bp chemistry. As there is no reference genome for Antarctic krill, a set of unique 90 bp sequences (RAD tags) was assembled from 17.3 million single-end reads from an individual krill. We obtained over a billion raw reads from the 148 krill in our study (a mean of 6.8 million reads per sample). The reference assembly contained 239,441 distinct RAD tags. The core genotype dataset exported for downstream data filtering included just those SNPs with genotype calls in at least 80% of the krill samples and contained 12,114 SNPs on 816 RAD tags.Sample collection table (comma separated):Southern Ocean Location, Sample Size, Austral Summer, Latitude, Longitude, IDEast Antarctica (Casey), 21, 2010/2011, 64S, 100E, CasEast Antarctica (Mawson), 22, 2011/2012. 66S, 70E, MawLazarev Sea, 38, 2004/2005 and 2007/2008, 66S, 0E, LazWestern Antarctic Peninsula, 16, 2010/2011, 69S, 76W, WAPRoss Sea, 23, 2012/2013, 68S, 178E, RossProgress Code: completedStatement: DNA sequencing done by: Floragenex, Inc. 4725 Village Plaza Loop, Suite 200 Eugene, OR 97401 USA Most of the SNP markers were from multi-copy genomic regions.&rft.creator=Deagle, B. &rft.creator=DEAGLE, BRUCE E. &rft.date=2015&rft.coverage=westlimit=-76; southlimit=-69; eastlimit=178; northlimit=-64&rft.coverage=westlimit=-76; southlimit=-69; eastlimit=178; northlimit=-64&rft_rights=These data are publicly available for download from the provided URL.&rft_rights=Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/legalcode&rft_rights=This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/). Please follow instructions listed in the citation reference provided at http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_4015_Population_Genetics when using these data.&rft_rights=This metadata record is publicly available.&rft_subject=oceans&rft_subject=biota&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL)&rft_subject=EARTH SCIENCE > BIOSPHERE > ECOLOGICAL DYNAMICS > SPECIES/POPULATION INTERACTIONS > POPULATION DYNAMICS&rft_subject=Genome&rft_subject=DNA&rft_subject=ADS > Automated DNA Sequencer&rft_subject=LABORATORY&rft_subject=SHIPS&rft_subject=AMD/AU&rft_subject=CEOS&rft_subject=AMD&rft_subject=CONTINENT > ANTARCTICA&rft_subject=OCEAN > SOUTHERN OCEAN&rft_subject=GEOGRAPHIC REGION > POLAR&rft.type=dataset&rft.language=English Access the data
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Attribution 4.0 International (CC BY 4.0)
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These data are publicly available for download from the provided URL.

This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/). Please follow instructions listed in the citation reference provided at http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_4015_Population_Genetics when using these data.

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Full description

This restriction site associated DNA sequencing (RAD-seq) dataset for Antarctic krill (Euphausia superba) includes raw sequence data and summaries for 148 krill from 5 Southern Ocean sites. A detailed README.pdf file is provided to describe components of the dataset. DNA library preparation was carried out in two separate batches by Floragenex (Eugene, Oregon, USA). RAD fragment libraries (SbfI) were sequenced on an Illumina HiSeq 2000 using single-end 100 bp chemistry. As there is no reference genome for Antarctic krill, a set of unique 90 bp sequences (RAD tags) was assembled from 17.3 million single-end reads from an individual krill. We obtained over a billion raw reads from the 148 krill in our study (a mean of 6.8 million reads per sample). The reference assembly contained 239,441 distinct RAD tags. The core genotype dataset exported for downstream data filtering included just those SNPs with genotype calls in at least 80% of the krill samples and contained 12,114 SNPs on 816 RAD tags.

Sample collection table (comma separated):

Southern Ocean Location, Sample Size, Austral Summer, Latitude, Longitude, ID

East Antarctica (Casey), 21, 2010/2011, 64S, 100E, Cas
East Antarctica (Mawson), 22, 2011/2012. 66S, 70E, Maw
Lazarev Sea, 38, 2004/2005 and 2007/2008, 66S, 0E, Laz
Western Antarctic Peninsula, 16, 2010/2011, 69S, 76W, WAP
Ross Sea, 23, 2012/2013, 68S, 178E, Ross

Lineage

Progress Code: completed
Statement: DNA sequencing done by: Floragenex, Inc. 4725 Village Plaza Loop, Suite 200 Eugene, OR 97401 USA Most of the SNP markers were from multi-copy genomic regions.

Data time period: 2012-01-01 to 2013-12-31

This dataset is part of a larger collection

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178,-64 178,-69 -76,-69 -76,-64 178,-64

51,-66.5

text: westlimit=-76; southlimit=-69; eastlimit=178; northlimit=-64

Subjects
ADS > Automated DNA Sequencer | AMD | AMD/AU | CEOS | CONTINENT > ANTARCTICA | DNA | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL) | EARTH SCIENCE > BIOSPHERE > ECOLOGICAL DYNAMICS > SPECIES/POPULATION INTERACTIONS > POPULATION DYNAMICS | GEOGRAPHIC REGION > POLAR | Genome | LABORATORY | OCEAN > SOUTHERN OCEAN | SHIPS | biota | oceans |

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Other Information
Download the dataset (GET DATA > DIRECT DOWNLOAD)

url : https://data.aad.gov.au/eds/4116/download

Public information for AAS project 4015 (PROJECT HOME PAGE)

url : https://projects.aad.gov.au/report_project_public.cfm?project_no=AAS_4015

Citation reference for this metadata record and dataset (VIEW RELATED INFORMATION)

url : http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_4015_Population_Genetics

Identifiers
ACN 633 798 857