Dataset: picoeukaryote accession numbers
Deployment: OC374

Links to Accessions for 18S rDNA , chloroplast and metagenomics data

Principal Investigator:

Dr Alexandra Z. Worden (Monterey Bay Aquarium Research Institute, MBARI)

BCO-DMO Data Manager:

Stephen R. Gegg (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Unveiling the contributions and regulation of picoeukaryotic phytoplankton in oceanic environments (PHYTO_GENOME)

Current State:

Final no updates expected

Version:

18 January 2011

Version Date:

2011-01-18

Data URL:

https://www.bco-dmo.org/dataset-deployment/453389/data

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Description

Accessions for 18S rDNA , chloroplast and metagenomics data

Biliphyte sequences from this study have been deposited in GenBank under Accession No. EU368003-EU368039

Cuvelier ML, Ortiz A, Kim E, Moehlig H, Richardson DE, Heidelberg JF, Archibald JM, Worden AZ (2008).
Widespread distribution of a unique marine protistan lineage. Environmental Microbiology. Vol. 10:1621-1634.

Prymnesiophyte sequences from this study have been deposited in GenBank under Accession Nos.
HM581528-HM581638 and HM565909-HM565914. Other scaffolds with predicted genes from this Whole
Genome Shotgun/454 project have been deposited at DNA Data Bank of Japan/European Molecular Biology
Laboratory/GenBank under the accession no. AEAR00000000. The version described in this paper is
the first version, AEAR01000000.

Cuvelier ML, Allen* AE, Monier* A, McCrow JP, Messie M, Tringe SG, Woyke T, Welsh RM, Ishoey T,
Lee JH, Binder BJ, DuPont CL, Latasa M, Guigand C, Buck KR, Hilton J, Thiagarajan M, Caler E,
Read B, Lasken RS, Chavez FP & AZ Worden (2010). Targeted metagenomics and ecology of globally
important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences USA.

Alveolate sequences from this study have been deposited in GenBank under:
EU818567-EU818691, EU836584-EU836597, EU818578-EU818566, EU817966-EU818077,
EU836613-EU836615; EU817882-EU817965; EU836616-EU816617

Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, Massana R, Scanlan DJ and AZ Worden (2008).
Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata).
Environmental Microbiology. DOI: 10.1111/j.1462-2920.2008.01731.x

Methods & Sampling

Dataset acquisition description

Samples were typically taken at the surface and deep chlorophyll maximum using a niskin rosette, all contextual data available (typically temperature and salinity) was deposited with the GenBank Submission for each sequence.

Field sites and sample collection
Five cruises were conducted, two transects from coastal New England to the BATS site (R/V Endeavor cruise EN351 and R/V Oceanus cruise OC413) and three transects across the Florida Straits (R/V Walton Smith cruises WS0503, WS0518, WS0528) with characteristics as in Table 1. Samples were collected in surface and DCM waters using a Sea-Bird Niskin Rosette equipped with standard CTD and PAR detectors (see also below). For DNA extraction samples, 1 l of seawater was gravity filtered through 2 um pore size filters (GE Osmonics, Minnetonka, MN, USA) and then onto a 0.45 um pore size (2001) or 0.2 um pore size (2005) Supor filter (Pall Gelman, Ann Arbor, MI, USA) using vacuum. For FISH samples whole seawater (no size fractionation) was preserved with 1% paraformaldahyde (final concentration) for at least 1 h in the dark at 4°C. For each replicate, volumes of 180 ml or more of seawater were gently filtered onto a 25 mm, 0.2 um Anodisc filter (Whatman, Maidstone, England). The filters were then subjected to an ethanol dehydration series at 50%, 80%, 100% (diluted in sterile, 18.2 ° H2O) for 3 min each and stored at -80°C. Flow cytometry samples were preserved with 0.25% (final concentration) fresh electron microscopy grade glutaraldehyde (Tousimis, Rockville, MD, USA), flash frozen in liquid nitrogen and moved to -80°C for long-term storage.

Data Processing Description

Dataset Processing Description

PCR, cloning and Sanger sequencing for all 18S rDNA
sequences; metagenomic data was produced by multiple
displacement amplification of flow cytometrically sorted
cells with subsequent Sanger and 454-FLX sequencing. See
Cuvelier et al. 2008 and Cuvelier et al. 2010 for greater
detail if desired.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0623928	NSF Division of Ocean Sciences
OCE-0836721	NSF Division of Ocean Sciences

Instruments

CTD Sea-Bird

Supplied Description:

Instrument Type

Generic Name: CTD Sea-Bird

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.

Niskin bottle

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Photosynthetically Available Radiation Sensor

Supplied Description:

Instrument Type

Generic Name: Photosynthetically Available Radiation Sensor

Acronym: PAR sensor

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/122/

Generic Description:

A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Sequence	Environmental DNA sequencing type	text	no_bcodmo_term
Accession_Number_Series	GenBank Start-End accession numbers of sequence	text	accession_number
Accession_Number_Link	Link to accession number at GenBank	text	accession_number

Database

Contribute Data

Dataset: picoeukaryote accession numbers
Deployment: OC374

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: picoeukaryote accession numbersDeployment: OC374

Dataset acquisition description

Dataset Processing Description

Dataset: picoeukaryote accession numbers
Deployment: OC374