http://lod.bco-dmo.org/id/dataset/924786
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2024-04-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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
2024-04-10
publication
2024-04-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-07-02
publication
https://doi.org/10.26008/1912/bco-dmo.924786.1
John J. Stachowicz
University of California-Davis
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Stachowicz, J. J. (2024) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-04-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.924786.1 [access date]
Whole Genome Sequencing of Eelgrass Bodega and Tomales Bay Dataset Description: Methods and Sampling: <p>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 <em>Zostera marina</em>). 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).</p>
<p>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&amp;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.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829976 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829976
completed
John J. Stachowicz
University of California-Davis
530-752-1113
Department of Evolution and Ecology 1 Shields Ave
Davis
CA
95616
USA
jjstachowicz@ucdavis.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
accession
sample_name
bioproject_accession
Site
organism
collection_date
isolation_source
latitude
longitude
2% agarose gel
NovaSeq 6000 S4 X
Qubit fluorometer
theme
None, User defined
NCBI Genbank nucleotide accession
sample identification
NCBI BioProject accession
site
species scientific name (binomial)
date
site description
latitude
longitude
featureType
BCO-DMO Standard Parameters
Agarose Gel Electrophoresis System
Automated DNA Sequencer
Fluorometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Using genomics to link traits to ecosystem function in the eelgrass Zostera marina
https://osprey.bco-dmo.org/project/777102
Using genomics to link traits to ecosystem function in the eelgrass Zostera marina
<p><em>NSF Award Abstract:</em><br />
Seagrass ecosystems provide important services to coastal regions, including primary production, carbon storage, nutrient cycling, habitat for fisheries species, and erosion control. At the same time, eelgrass is threatened by direct destruction, pollution, and other human impacts on the environment. We know that genetic diversity in eelgrass enhances seagrass bed growth and persistence, but application of this knowledge to restoration and conservation is limited. This work will guide restoration programs by considering what specific aspects of diversity are important to conservation and restoration of seagrass ecosystems, helping to guide the selection of source material to improve restoration success (which is often low). The project integrates the effects of multiple components of diversity and clarifies the extent to which genetic and ecological uniqueness can predict ecosystem functions.</p>
<p>Intellectual Merit: Genetic diversity as measured by the number of genetically distinct individuals (genets) in an assemblage influences critical ecosystem functions in a wide range of ecosystems. Functional diversity, the presence of key traits, or population flexibility to respond to environmental change are all potential mechanisms underlying these patterns, but distinguishing among them requires a clear link between genetic diversity and the phenotypes present in an assemblage. The investigators, and others, have previously demonstrated that genet diversity in eelgrass (Zostera marina) increases stand productivity, animal community diversity, and resilience to environmental change. These genet diversity effects are associated with increases in genetically determined trait diversity. Predicting trait diversity without having to measure traits of every genet remains a major barrier to wider application of functional diversity approaches in restoration and management. In this project, the investigators assess the association between Single Nucleotide Polymorphisms (SNPs) across the genome and performance-related traits that we will measure at the individual, population, and seascape-scale. They also assess environmental correlates of trait differentiation from field sampling. Finally, the research team will compare the predictive power of genomic SNP diversity versus other metrics of intraspecific diversity for the functioning (productivity, invertebrate abundance) of field planted eelgrass assemblages. If genomic variation can reliably be used to predict functional traits, then the value of genomic sequencing efforts for informing management will be greatly enhanced. Broader Impacts: Seagrass restoration and mitigation is currently of major interest in California and elsewhere and the project results will inform current initiatives regarding eelgrass management in California through the state's Ocean Protection Council. In addition to recruiting individual students from diverse backgrounds to work on the project, the project broadens participation of students in STEM fields through its partnership with three existing outreach/training programs at UC Davis.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
ZosteraEcoGenomics
largerWorkCitation
project
eng; USA
oceans
-123.06
-122.846
38.105
38.3334
2019-07-16
2019-09-30
In Zostera marina beds worldwide, including western and eastern margins of both the Atlantic and Pacific Oceans. Project centered in Bodega Bay, CA 38.31 N; 123.059 W
0
BCO-DMO catalogue of parameters from 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
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/924796.rdf
Name: accession
Units: unitless
Description: <p>NCBI accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/924797.rdf
Name: sample_name
Units: unitless
Description: <p>sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/924798.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject number</p>
http://lod.bco-dmo.org/id/dataset-parameter/924799.rdf
Name: Site
Units: unitless
Description: <p>Geographic Site Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/924800.rdf
Name: organism
Units: unitless
Description: <p>Organism name</p>
http://lod.bco-dmo.org/id/dataset-parameter/924801.rdf
Name: collection_date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/924802.rdf
Name: isolation_source
Units: unitless
Description: <p>Upper (0 m mllw) vs Lower (-0.5 to -1.0 m mllw) intertidal zone</p>
http://lod.bco-dmo.org/id/dataset-parameter/924803.rdf
Name: latitude
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/924804.rdf
Name: longitude
Units: decimal degrees
Description: <p>longitude</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
26344
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/f49b7b16-45c7-4692-b6bf-49cb28f91cee/content
download
https://doi.org/10.26008/1912/bco-dmo.924786.1
download
onLine
dataset
<p>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 <em>Zostera marina</em>). 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).</p>
<p>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&amp;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.</p>
Specified by the Principal Investigator(s)
- Imported original file "WGS_LS_TomalesBodega.xlsx" into the BCO-DMO system.
- Converted date field to YYYY-MM-DD format.
- Saved the final file as "924786_v1_whole_genome_sequencing_eelgrass.csv".
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2% agarose gel
2% agarose gel
PI Supplied Instrument Name: 2% agarose gel Instrument Name: Agarose Gel Electrophoresis System Instrument Short Name:agarose gel electrophoresis system Instrument Description: A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.
NovaSeq 6000 S4 X
NovaSeq 6000 S4 X
PI Supplied Instrument Name: NovaSeq 6000 S4 X Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Qubit fluorometer
Qubit fluorometer
PI Supplied Instrument Name: Qubit fluorometer Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/