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OAS accession Detail for 0299430
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| accessions_id: | 0299430 | archive |
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| Title: | Sample collection information and sequence accessions at the National Center for Biotechnology Information (NCBI) for whole genome sequencing of eelgrass (Zostera marina) collected at Bodega and Tomales Bay, CA, USA from July to September 2019 (NCEI Accession 0299430) |
| Abstract: | This dataset contains biological and survey - biological data collected in the North Pacific Ocean from 2019-07-16 to 2019-09-30. These data include species. The instruments used to collect these data include Agarose Gel Electrophoresis System, Automated DNA Sequencer, and Fluorometer. These data were collected by John J. Stachowicz of University of California-Davis as part of the "Using genomics to link traits to ecosystem function in the eelgrass Zostera marina (ZosteraEcoGenomics)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2024-07-02. The following is the text of the dataset description provided by BCO-DMO: Whole Genome Sequencing of Eelgrass Bodega and Tomales Bay Dataset Description: Methods and Sampling: We collected 2 to 3 shoots attached by a rhizome from fifteen putative genets (separated by approximately 5 to 10 meters) at 14 sites across Tomales Bay and Bodega Harbor in California from a height below 0.0 mean lower low water (MLLW) (i.e., not sampling the uppermost or lowermost vertical distribution of Zostera marina ). For two of the sites sampled in Bodega Harbor (Mason's Marina and Westside Park), we also collected a deeper set of specimens (at least -0.6 meters below MLLW) to test for genetic differences between shallower versus deeper plants. We transported plants back to the University of California, Davis in a cooler with ice packs, and stored them for no more than 1 day in a recirculating seawater table before dissecting out the tissue from within the leaf sheath of all shoots within a genet and they were then flash-frozen in liquid nitrogen and stored at -80 degrees Celsius (°C). Using the inner leaf sheath tissue allowed us to minimize the amount of noneelgrass DNA by selecting tissue that was free of epibionts and had lower chloroplast concentrations. We extracted DNA from up to 200 milligrams (mg) of frozen tissue by grinding with a plastic pestle and liquid nitrogen in a 1.5 milliliter (mL) tube until powdered and then by using a modified CTAB chloroform extraction (see details and references in Schiebelhut et al., 2023). Briefly, tissue was resuspended in 800-microliter (μL) CTAB (0.1 M Tris-HCl [pH 8.0], 0.02 M EDTA [pH 8.0], 3% CTAB, 1.4 M NaCl, 0.2% β-mercaptoethanol), after the first chloroform isoamyl alcohol step, the upper aqueous phase was transferred to a new tube and treated with 2 μL of RNAse A at 37°C for 1 hour, followed by an additional chloroform-isoamyl alcohol step before completing the remaining steps. We quantified DNA on a Qubit fluorometer and adjusted the concentration to ~13 nanograms per microliter (ng/μL); in cases where the concentration was lower than 17 ng/μL the concentration was not adjusted. DNA quality was visually assessed on a 2% agarose gel. We submitted genomic DNA for 240 individuals to the Genomics and Bioinformatics Services Texas A&M Agrilife Research Centre (College Station, Texas, USA) for library preparation using the high-throughput PerkinElmer NEXTFLEX Rapid XP DNA-Seq Kit and paired-end 150 base pair (bp) sequencing (targeting 10× coverage with ~5.8 Gb/sample) on two lanes of a NovaSeq 6000 S4 X. |
| Date received: | 20240702 |
| Start date: | 20190716 |
| End date: | 20190930 |
| Seanames: | Greater Farallones National Marine Sanctuary, North Pacific Ocean |
| West boundary: | -123.06 |
| East boundary: | -122.846 |
| North boundary: | 38.333 |
| South boundary: | 38.105 |
| Observation types: | biological, survey - biological |
| Instrument types: | fluorometer |
| Datatypes: | SPECIES IDENTIFICATION |
| Submitter: | |
| Submitting institution: | Biological and Chemical Oceanography Data Management Office |
| Collecting institutions: | University of California, Davis |
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| Platforms: | |
| Number of observations: | |
| Supplementary information: | |
| Availability date: | |
| Metadata version: | 1 |
| Keydate: | 2024-11-29 15:49:38+00 |
| Editdate: | 2024-11-29 15:50:13+00 |