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

• Format: Dataset
• Language: unknown
• Published: Australian Ocean Data Network
• Subjects: biota; oceans; EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL); Genome; DNA; ADS > Automated DNA Sequencer; LABORATORY; SHIPS; AMD; AMD/AU; CEOS; CONTINENT > ANTARCTICA; OCEAN > SOUTHERN OCEAN; GEOGRAPHIC REGION > POLAR; Antarctic; Southern Ocean; Antarctic Peninsula; East Antarctica; Austral; Ross Sea; Lazarev; Lazarev Sea; Antarc*; Antarctic Krill; Antarctica; Euphausia superba
• Online Access: https://researchdata.edu.au/population-genetics-dataset-mtdna-sequencing/2818962

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. 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