Dataset: SEEPC Bivalve DNA Barcoding Results

Name: DNA barcode sequencing results for bivalve larvae collected on N. Atlantic cruises at cold seeps sites off of Barbados, the East coast of the U.S. and the Gulf of Mexico (SEEPC project)
Published: 2017-04-21
Keywords: biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.688111.1

Spatial Extent: N:37 E:-58 S:11 W:-95

Temporal Extent: 2011-06 - 2015-07

Project:

Connectivity in western Atlantic seep populations: Oceanographic and life-history processes underlying genetic structure (SEEPC)

Principal Investigator:

Svetlana A. Maslakova (University of Oregon, OIMB)

Co-Principal Investigator:

Craig M. Young (University of Oregon, OIMB)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2017-04-21

Restricted:

Validated:

Yes

Current State:

Final no updates expected

DNA barcode sequencing results for bivalve larvae collected on N. Atlantic cruises at cold seeps sites off of Barbados, the East coast of the U.S. and the Gulf of Mexico (SEEPC project)

Abstract:

DNA barcode sequencing results for bivalve larvae collected on N. Atlantic cruises at cold seeps sites off of Barbados, the East coast of the U.S. and the Gulf of Mexico (SEEPC project). This dataset provides the closest GenBank match for larval bivalve specimens resulting from DNA barcode sequencing, the percent match of the identification, and some information on the specimen collections.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2017-04-21	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.688111.1	2021-05-28

Description

This dataset provides the closest GenBank match for larval bivalve specimens resulting from DNA barcode sequencing, the percent match of the identification, and some information on the specimen collections.

NCBI GenBank accessions are not yet available [2017-04-21]. Please contact the PI for further information.

Methods & Sampling

Bivalve larvae were collected either by MOCNESS or Sentry's SyPRID Sampler. The Multiple Opening and Closing Net Environmental Sensing System has 8 separate plankton nets which can be controlled from the ship, allowing for samples along discrete depth ranges. Sentry’s Precision Robotic Impeller Driven Sampler allows for the collection of larvae from just a few meters off the sea floor. DNA was extracted, purified, amplified, and sequenced using standard lab protocols and universal primers (except where indicated).

Data Processing Description

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- renamed some parameters to BCO-DMO standard
- replaced blanks, '?', '-' with 'nd' (no data)
- reformatted date from m/d/yyyy to yyyy-mm-dd
- removed 'm' from depth values
- converted lat and lon to decimal degrees
- removed or replaced special characters
- added cruise_id and year columns

Version: 2017-02-13 [added EN531 collection data]
Replaces version: 2016-09-30

Data Files

File
bivalve_barcode_log.csv (Comma Separated Values (.csv), 31.20 KB) MD5:adb9f64ba137d7fbb87eb6c1fc9282fb Primary data file for dataset ID 688111

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1030453

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT21-02	SEEPC-Barbados	2012-06-01	R/V Atlantis	Cindy Van Dover (Chief Scientist)	data info
AT26-15	SEEPC GoMex	2014-05-21	R/V Atlantis	Cindy Van Dover (Chief Scientist)	data info
AT29-04	Seep Connectivity WAM Western Atlantic Margin	2015-07-08	R/V Atlantis	Cindy Van Dover (Chief Scientist)	data info
EN531	SEEPC	2013-08-15	R/V Endeavor	Ruoying He (Co-Chief Scientist) Craig M. Young (Co-Chief Scientist) Cindy Van Dover (Contact)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Applied Biosystems 3730xl DNA Analyzer

Supplied Description:

The sequencing was done by Sequetech in California

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.

AUV Sentry

Supplied Name:

Supplied Description:

Fitted out with the SyPRID (Sentry’s Precision Robotic Impeller Driven) Sampler

Instrument Type

Generic Name: AUV Sentry

Generic Description:

The autonomous underwater vehicle (AUV) Sentry is a fully autonomous underwater vehicle capable of exploring the ocean down to 6,000 meters (19,685 feet) depth. Sentry builds on the success of its predecessor the ABE, with improved speed, range, and maneuverability.

Sentry's hydrodynamic shape also allows faster ascents and descents. Sentry carries a superior science sensor suite and an increased science payload enabling it to be used for both mid-water and near-seabed oceanographic investigations. Sentry produces bathymetric, sidescan, subbottom, and magnetic maps of the seafloor and is capable of taking digital bottom photographs in a variety of deep-sea terrains such as mid-ocean ridges, deep-sea vents, and cold seeps at ocean margins. Sentry is uniquely able to operate in extreme terrain, including volcano caldera and scarps. Sentry's navigation system uses a doppler velocity log and inertial navigation system, aided by acoustic navigation systems (USBL or LBL). The USBL system also provides acoustic communications, which can be used to obtain the vehicle state and sensor status as well as to retask the vehicle while on the bottom. In addition its standard sensors, Sentry has carried a variety of science-supplied sensors, including the Nakamura redox potential probe, ACFR 3-D imaging system, and the Tethys in-situ mass spectrometer.

Sentry can be used to locate and quantify hydrothermal fluxes. Sentry is also capable of a much wider range of oceanographic applications due to its superior sensing suite, increased speed and endurance, improved navigation, and acoustic communications. Sentry can be used as a stand alone vehicle or in tandem with Alvin or an ROV to increase the efficiency of deep-submergence investigations.

More information is available from the operator site at URL: http://www.whoi.edu/main/sentry

MOCNESS1

Supplied Name:

Supplied Description:

MOCNESS plankton system with 300 um mesh nets.

Instrument Type

Generic Name: MOCNESS1

Acronym: MOC1

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/

Generic Description:

The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003).

Thermal Cycler

Supplied Name: Bio-Rad C1000 Touch Thermal Cycler

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
larva_id	larval specimen identifier	unitless	sample
larval_type	morphotype based on gross larval morphology; BV = Bivalve	unitless	sample_descrip
species	closest species match to the tested sequence in GenBank	unitless	species
gene_id_pcent	gene(s) tested and how closely it matched the GenBank sequence	percent	no_bcodmo_term
cruise_id	cruise identifier	unitless	cruise_id
date_collected	date collected and preserved (formatted as yyyy-mm-dd)	unitless	date
site	collection site: BAP=Barbados Acretionary Prism; WAM=Western Atlantic Margin; GOM=Gulf of Mexico	unitless	site
depth_range	range of depths in which the larva was collected (formatted as yyyy-mm-dd)	meters	depth_range
date_extraction	date the DNA was extracted; purified; and amplified for each larva	unitless	date
comment	overall results for each larva	unitless	comment

Status message

Database

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Dataset: SEEPC Bivalve DNA Barcoding Results