Dataset: Krill barcodes

Name: Euphausiid DNA barcode metadata and accession numbers collected from cruises in the Red Sea, the western North Atlantic, the Sargasso Sea, the Southeast North Atlantic Ocean, and Arabian Sea (Red Sea Krill project)
Published: 2016-05-04
Keywords: genomics, Euphausiid, biota, oceans

Cite This Dataset

Spatial Extent: N:39.692 E:65 S:-37.54 W:-135.073

Project:

Red Sea Krill (Red Sea Krill)

Principal Investigator:

Peter H. Wiebe (Woods Hole Oceanographic Institution, WHOI)

Scientist:

Ann Bucklin (University of Connecticut, UConn - Avery Point)

BCO-DMO Data Manager:

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

Version:

Version Date:

2016-05-04

Restricted:

Validated:

Yes

Current State:

Preliminary and in progress

Euphausiid DNA barcode metadata and accession numbers collected from cruises in the Red Sea, the western North Atlantic, the Sargasso Sea, the Southeast North Atlantic Ocean, and Arabian Sea (Red Sea Krill project)

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Description

Euphausiid DNA barcode metadata and accession numbers for DNA sequences for mitochondrial cytochrome oxidase I (COI) barcode regions. Specimens were collected in the Red Sea, Atlantic and Pacific Oceans.

Methods & Sampling

Specimens of each of the five euphausiid species identified from the alcohol-preserved samples were prepared for PCR amplification and DNA sequencing. DNA sequences for the COI barcode region were determined for Euphausia diomedeae (4 individuals); E. sanzoi (2); E. sibogae (4); Stylocheiron abbreviatum (3); and S. affine (4). The designated GenBank Accession Numbers can be used to access the GenBank records, which include data and metadata for all specimens (Table 2). Additional specimens of each species (except Euphausia sanzoi) were identified from archived samples from cruises in the NE Pacific; NW, NE, and SE Atlantic; and Arabian Sea (Fig. 4), and were analyzed using the same methods.

DNA was purified from individual euphausiids using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) using standard protocols, except that elution volumes were reduced usually to 100-200 µL. A ~708 base-pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene was amplified using consensus primers (Folmer et al., 1994) and published PCR amplification protocols (Bucklin et al., 2010b). The PCR products were run on 2% agarose gels and purified using the QIAquick Gel Extraction Kit (QIAGEN) following the manufacturer’s instructions, with an elution volume of 35 µL. DNA sequencing was done using a commercial service (Eurofins MWG Operon, Louisville, KY) following all protocols and instructions provided.

See "Related Datasets" for data that can be joined to this dataset using the column "tow."

Data Processing Description

DNA sequences were manually checked for accurate machine reading using the Molecular Evolutionary Genetics Analysis (MEGA, Ver. 6) software package (Tamura et al., 2013). DNA sequences to be analyzed were aligned and forward and reverse reads were reconciled using CLUSTAL-W, as implemented in MEGA (Thompson et al., 1997). MegaBLAST searches were conducted in GenBank to confirm the accuracy and validity of the sequences. DNA sequences that could not be verified and validated, including aberrant or highly divergent sequences, were omitted from the dataset. Published DNA sequences for the COI barcode region were obtained from GenBank (see e.g., Bucklin et al., 2007) and included in the sequence alignment for comparative analysis. Both the original alignment and an alignment trimmed to a 500 bp region in common among all sequences were used. In the latter case, any sequence shorter than the target 500 bp region was removed from further analysis, with the exception of several shorter sequences for Red Sea specimens.

A pairwise distance matrix showing within and between species differences (p-distances) for all sequences was determined and mean and standard deviations for within and between species were calculated. Pairwise p-distances were visually displayed as heat maps. A Neighbor Joining tree analysis was carried out in MEGA Ver.6 (Tamura et al., 2013) with Kimura-2-Parameter distances (a = 0.5). Node support was obtained after 1,000 bootstraps.

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- replaced space with underscore

2016-04-27 revision: [replaces version: 2015-10-28]
- added live links to NCBI GenBank, columns for cruise_id, station, tow, and net

2016-05-04: added links to MOC-CTD data from other BCO-DMO datasets, where available

Data Files

File
krill_barcodes_v3.csv (Comma Separated Values (.csv), 16.19 KB) MD5:337ae03e5daadf41b4ad5488086a34a3 Primary data file for dataset ID 622522

More Information about this dataset

Funding Sources

Funding Source	Award Number
King Abdullah University of Science and Technology	KAUST-Kaartvedt-2014

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AKES-2		2008-02-19	R/V GO_Sars	Dr Webjørn Melle (Chief Scientist)	data info
ANT-XXIV_1	PS24_1	2007-10-26	R/V Polarstern	Dr Sigi Schiel (Chief Scientist)	data info
NH1208		2012-08-09	R/V New Horizon	Gareth Lawson (Chief Scientist)	data info
OC473		2011-08-07	R/V Oceanus	Gareth Lawson (Chief Scientist) Zhaohui Aleck Wang (Co-Principal Investigator) Peter H. Wiebe (Co-Principal Investigator) Ms Dicky Allison (BCO-DMO Data Manager)	data info
RHB0603		2006-04-10	NOAA Ship Ronald H. Brown	Peter H. Wiebe (Chief Scientist)	data info
Thuwal-2014-01		2014-01-07	R/V Thuwal	Peter H. Wiebe (Scientist)	data info
TT045	TTN045 TN045 TTN-045	1995-03-14	R/V Thomas G. Thompson	John F. Marra (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name:

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.

Midwater Trawl

Supplied Name:

Supplied Description:

a Krill trawl with a 38 m2 mouth area, and with a Multisampler unit attached to the rear end. The Multisampler unit has five nets mounted on a frame, similar to the MOCNESS, and is also remotely controlled. Also called a "Macroplankton Trawl".

Heino, M., Porteiro, F.M., Sutton, T.T., Falkenhaug, T., Godø, O.R., and Piatkowski, U. (2011) Catchability of pelagic trawls for sampling deep-living nekton in the mid-North Atlantic. ICES Journal of Marine Science 68, 377–389.

Krafft, B.A., Melle, W., Knutsen, T., Bagøien, E., Broms, C., Ellertsen, B., Siegel, V., (2010) Distribution and demography of Antarctic krill in the Southeast Atlantic sector of the Southern Ocean during the austral summer 2008. Polar Biology 33, 957–968.

Instrument Type

Generic Name: Midwater Trawl

Acronym: TrawlMid

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/23/

Generic Description:

A mid-water or pelagic trawl is a net towed at a chosen depth in the water column to catch schooling fish such as herring and mackerel. Midwater trawl nets have very large front openings to herd schooling fish toward the back end where they become trapped in the narrow "broiler". The sides of the deployed net are spread horizontally with two large metal foils, called "doors," positioned in front of the net. As the trawler moves forward, the doors, and therefore the net, are forced outward, keeping the net open.
This instrument designation is used when specific make and model are not known.

MOCNESS.25

Supplied Name: MOC-25

Supplied Description:

Instrument Type

Generic Name: MOCNESS.25

Acronym: MOC.25

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-1/4 carries nine 1/4-m2 nets usually of 64 micrometer mesh and is used to sample the larger micro-zooplankton.

MOCNESS1

Supplied Name: MOC-1

Supplied Description:

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).

Reeve Net

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Reeve Net

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0147/

Generic Description:

A Reeve Net is a conventional ring net with a very large acrylic cylindrical cod-end (30 liters) designed to collect fragile gelatinous animals. The net is lowered to a particular depth and then hauled slowly back to the surface (5-10 m/min). Reeve (1981) also described a double net system with no bridle and flotation at the net mouth that is attached to a roller mechanism that rides on a tow wire.
The roller system is locked in place by a pressure release device. Once below a set pressure, the roller
and nets are released and they float slowly up the wire, gently collecting the zooplankton, without being
influenced by the motion of the vessel and associated vertical wire movements. (from Wiebe and Benfield, 2003)

Thermal Cycler

Supplied Name:

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
species	Euphausiid species name	unitless	species
voucher_num	Bucklin lab specimen voucher number	unitless	sample
NCBI_accession	GenBank accession number	unitless	accession_number
region	geographical area of collection	unitless	region
date	date collected	yyyy-mm-dd	date
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
depth_range	depth range sampled	meters	depth_range
cruise_id	cruise identification	unitless	cruise_id
station	sequential station	unitless	station
tow	tow identification	unitless	tow
net	net number	unitless	net
comment	comments	unitless	comment
inst	type of gear used to sample zooplankton: MOC-1 = MOCNESS-1meter; MOC-25 = MOCNESS-1/4 meter;		instrument

Status message

Database

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Dataset: Krill barcodes