Dataset: Whole Genome Sequencing of Eelgrass Bodega and Tomales Bay

Name: 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
Published: 2024-04-10
Keywords: seagrass, genetics, Local adaptation, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.924786.1

Spatial Extent: N:38.3334 E:-122.846 S:38.105 W:-123.06

Tomales Bay and Bodega Harbor in California

Temporal Extent: 2019-07-16 - 2019-09-30

Project:

Using genomics to link traits to ecosystem function in the eelgrass Zostera marina (ZosteraEcoGenomics)

Principal Investigator:

John J. Stachowicz (University of California-Davis, UC Davis)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-04-10

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

This dataset includes 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, California, USA from July and September of 2019. Sequence Read Archive (SRA) Experiments and BioSamples can be accessed from the NCBI BioProject PRJNA887384 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA887384/). Results summary as described in Scheibelhut, et al. (2023): We examine genomic signals of selection in the eelgrass Zostera marina across temperature gradients in adjacent embayments. Although we find many genomic regions with signals of selection within each bay there is very little overlap in signals of selection at the SNP level, despite most polymorphisms being shared across bays. We do find overlap at the gene level, potentially suggesting multiple mutational pathways to the same phenotype. Using polygenic models we find that some sets of candidate SNPs are able to predict temperature across both bays, suggesting that small but parallel shifts in allele frequencies may be missed by independent genome scans. Together, these results highlight the continuous rather than binary nature of parallel evolution in polygenic traits and the complexity of evolutionary predictability.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2024-04-10	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.924786.1	2024-07-02

Methods & 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.

BCO-DMO Processing

- 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".

Data Files

File
924786_v1_whole_genome_sequencing_eelgrass.csv (Comma Separated Values (.csv), 25.73 KB) MD5:a76e9bc7e49dcd3c4208f11121ccd512 Primary data file for dataset ID 924786, version 1

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1829976

Deployments

None available yet

Instruments

Agarose Gel Electrophoresis System

Supplied Name: 2% agarose gel

Supplied Description:

Instrument Type

Generic Name: Agarose Gel Electrophoresis System

Acronym: agarose gel electrophoresis system

Generic 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.

Automated DNA Sequencer

Supplied Name: NovaSeq 6000 S4 X

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Fluorometer

Supplied Name: Qubit fluorometer

Supplied Description:

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
accession	NCBI accession number	unitless	Genbank_accession
sample_name	sample name	unitless	sample
bioproject_accession	NCBI BioProject number	unitless	BioProject
Site	Geographic Site Name	unitless	site
organism	Organism name	unitless	species
collection_date	Date of sample collection Format: %Y-%m-%d	unitless	date
isolation_source	Upper (0 m mllw) vs Lower (-0.5 to -1.0 m mllw) intertidal zone	unitless	site_descrip
latitude	latitude	decimal degrees	lat
longitude	longitude	decimal degrees	lon