Dataset: Shoots sampled for whole genome sequencing

Name: Shoot measurements (sheath length and width) for the eelgrass (Zostera marina) shoots sampled for whole genome sequencing collected from Bodega and Tomales Bay, CA, USA from July to September 2019
Published: 2024-04-10
Keywords: plant morphology, seagrass, eelgrass, oceans

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Cite This Dataset

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:

Current State:

Data not available

Shoot measurements (sheath length and width) for the eelgrass (Zostera marina) shoots sampled for whole genome sequencing collected from Bodega and Tomales Bay, CA, USA from July to September 2019

Abstract:

This dataset provides shoot measurements for the shoots sampled for whole genome sequencing for Tomales Bay and Bodega Harbor (see related datasets for access to sequence data). Sheath width is measured on the terminal shoot using calipers at the abscission point (point where leaves emerge from the sheath). Sheath length is measured using a ruler to the nearest mm from the base to the abscission point. These data were used to record any differences in plant phenotype among the populations sampled. Shoot Length was not measured since it is susceptible to breakage and density was not measured as we could not ascribe density to a genetic individual.

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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 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 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 measuring the terminal shoot sheath width using calipers and sheath length using a ruler. The sheath width was measured at the abscission point and the length from the abscission point to the base of the shoot. Once measurements were made, we dissected out the tissue from within the leaf sheath and flash-froze them in liquid nitrogen and stored at -80 degrees Celsius (°C).

BCO-DMO Processing

- Imported original file "Zm_TomBod_morpohmetrics.xlsx" into the BCO-DMO system.
- Imported original file "WGS_LS_TomalesBodega.xlsx" into the BCO-DMO system.
- Added the "collection_date" column from "WGS_LS_TomalesBodega.xlsx" to the shoot morphometrics file, matching on individual sample ID number
- Converted date field to YYYY-MM-DD format.
- Saved final file as "924808_v1_shoots_sampled_for_sequencing.csv".

More Information about this dataset

Funding Sources

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

Deployments

None available yet

Instruments

calipers

Supplied Description:

Instrument Type

Generic Name: calipers

Generic Description:

A caliper (or "pair of calipers") is a device used to measure the distance between two opposite sides of an object. Many types of calipers permit reading out a measurement on a ruled scale, a dial, or a digital display.

ruler

Supplied Description:

Instrument Type

Generic Name: ruler

Generic Description:

A device used for measuring or for drawing straight lines, consisting of an elongated piece of rigid or semi-rigid material marked with units for measurement. Device that allows one or more physical dimensions of a sample or specimen to be determined by visible comparison against marked graduations in units of measurement of dimension length.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
INDV	sample name	unitless	sample
SITE	B=Bodega Bay; T= Tomales Bay; two letter code indicates site within each Bay from Schiebelhut et al 2023.	unitless	site
collection_date	Date of sample collection Format: %Y-%m-%d	unitless	date
Latitude	Latitude	decimal degrees	lat
Longitude	Longitude	decimal degrees	lon
sheath_length	length of the seagrass sheath from the base to the abscission point	millimeters (mm)	length
sheath_width	width of the sheath at the abcission point	millimeters (mm)	width
depth	intertidal (0 to - 0.5m below mllw) or subtidal (deeper than 0.5 m below MLLW)	unitless	site_descrip
mean_temp_C	mean temperature at the site during the day of sampling	degrees Celsius	temp

Database

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Dataset: Shoots sampled for whole genome sequencing