Dataset: Symbiont accession numbers
Deployment: Coffroth_2010

Accession numbers of symbiotic algae in coral

Principal Investigator:

Mary Alice Coffroth (State University of New York at Buffalo, SUNY Buffalo)

BCO-DMO Data Manager:

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

Project:

Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective (SymBioSys)

Current State:

Final no updates expected

Version:

2015-01-15

Version Date:

2015-01-15

Data URL:

https://www.bco-dmo.org/dataset-deployment/546130/data

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Description

Links to GenBank accession numbers of symbiotic algae in Eunicea flexuosa coral.

Related Reference:

Coffroth MA, Poland DM, Petrou EL, Brazeau DA, Holmberg JC (2010) Environmental Symbiont Acquisition May Not Be the Solution to Warming Seas for Reef-Building Corals. PLoS ONE 5(10): e13258. doi:10.1371/journal.pone.0013258. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013258

Methods & Sampling

Dataset acquisition description

Samples from host, Eunicea flexuosa,were amplified and sequenced following (Prada & Hellberg 2013). We amplified and sequenced Symbiodinium samples from Eunicea flexuosa, following earlier protocols [(LaJeunesse 2002) for ITS2; [(Moore et al. 2003) for psbA; (Santos et al. 2002) for cp23s-rDNA]. We also sequenced a subset of samples (42) from all populations (three locations and two depths) using the flanking region of the microsatellite B7SYM15, following previous procedures (Pettay & La- Jeunesse 2007). Amplicons were directly sequenced in both directions (except B7SYM15, forward only) in an ABI 3100 using BigDye chemistry v 3.1 and both amplification primers. The COI region from Symbiodinium from a western Pacific Cassiopea (obtained from Shedd Aquarium, Chicago, IL) was amplified and sequenced following Holland et al (2004).

References:

Drummond AJ, Ashton B, Cheung M et al. (2009) GENEIOUS v4.5.4. Available from http://www.geneious.com.

Holland, B.S., Dawson, M.N., Crow, G.L., Hofmann, D.K., 2004. Global phylogeography of Cassiopea (Scyphozoa: Rhizostomeae): molecular evidence for cryptic species and multiple invasions of the Hawaiian Islands. Mar. Biol. 145 (6), 1119–1128.

LaJeunesse TC (2002) Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs. Marine Biology, 141, 387–400.

Moore RB, Ferguson KM, Loh WKW, Hoegh-Guldberg O, Carter DA (2003) Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium. International Journal of Systematic and Evolutionary Microbiology, 53, 1725–1734.

Pettay DT, LaJeunesse TC (2007) Microsatellites from clade B Symbiodinium spp. specialized for Caribbean corals in the genus Madracis. Molecular Ecology Notes, 7, 1271–1274.

Prada C, Hellberg ME (2013) Long pre-reproductive selection and divergence by depth in a Caribbean candelabrum coral. Proceedings of the National Academy of Sciences of the USA, 119, 53–60.

Santos SR, Taylor DJ, Kinzie RA, Hidaka M, Sakai K, Coffroth MA (2002) Molecular phylogeny of symbiotic dinoflagellates inferred from partial chloroplast large subunit 23sr DNA sequences. Molecular Phylogeetics and Evolution, 23, 97–111.

Data Processing Description

Dataset Processing Description

All sequences were edited and assembled using GENEIOUS v4.5.5 (Drummond et al. 2009).

BCO-DMO Processing:

- original file: Coffroth_Links to GenBank submissions.xlsx
- added conventional header with dataset name, PI name, version date, reference information
- changed parameter names to be BCO-DMO compatible
- replaced spaces with underscores

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0926822	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Automated Sequencer

Supplied Description:

LI-COR 4200 NENH Global IR2 DNA sequencing system (LI-COR Biosciences, Lincoln, NE,USA)

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.

Spectrophotometer

Supplied Description:

Nano-Drop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE)

Instrument Type

Generic Name: Spectrophotometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic Description:

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

Thermal Cycler

Supplied Description:

Stratagene Mx3005P QPCR System (Stratagene, La Jolla, CA.)

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

Supplied Name	Supplied description	Supplied Units	Standard Name
lab	laboratory identification; for mapping puposes	unitless	laboratory
lat	latitude of lab; north is positive	decimal degrees	lat
lon	londitude of lab; east is positive	decimal degrees	lon
description	sequenced organism and gene	unitless	no_bcodmo_term
reference_paper	citation of published sequence reference	unitless	reference_paper
Genbank_accession_num	GenBank accession number	unitless	accession_number
accession_link	GenBank accession number url link	unitless	no_bcodmo_term

Database

Contribute Data

Dataset: Symbiont accession numbers
Deployment: Coffroth_2010

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Symbiont accession numbersDeployment: Coffroth_2010

Dataset acquisition description

Dataset Processing Description

Dataset: Symbiont accession numbers
Deployment: Coffroth_2010