Dataset: Breviolum antillogorgium microsatellite loci

Name: Microsatellite loci for Breviolum antillogorgium cultures isolated from the octocoral Antillogorgia bipinnata and used in 2018 growth experiments to compare growth at 26 and 30 degrees C
Published: 2019-03-04
Keywords: Breviolum antillogorgium, symbiont diversity, biota, oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.756404.1

Spatial Extent: N:25.1326 E:-80.2635 S:25.1326 W:-80.2635

Temporal Extent: 2016 - 2016

Project:

RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs (Host Symbiont Temp Response)

Principal Investigator:

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

Co-Principal Investigator:

Casey terHorst (California State University Northridge, CSUN)

BCO-DMO Data Manager:

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

Version:

Version Date:

2019-03-04

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Microsatellite loci for Breviolum antillogorgium cultures isolated from the octocoral Antillogorgia bipinnata and used in 2018 growth experiments to compare growth at 26 and 30 degrees C

Abstract:

Microsatellite loci for Breviolum antillogorgium cultures isolated from the octocoral Antillogorgia bipinnata and used in 2018 growth experiments to compare growth at 26 and 30 degrees C

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2019-03-04	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.756404.1	2019-10-02

Description

This dataset includes the microsatellite locus allele size for Breviolum antillogorgium cultures isolated from the octocoral Antillogorgia bipinnata and used in 2018 growth experiments to compare growth at 26 and 30 degrees C.;

Methods & Sampling

Breviolum antillogorgium cultures were initially isolated from Antillogorgia bipinnata colonies collected at in the upper Florida Reef tract at Elbow Reef (N 25 07.956 W 80 15.810) in September 2016. Culture isolations and cell growth experimentation occurred in the Coffroth lab, University at Buffalo.

DNA was extracted from symbiont cells following Coffroth et al. (1992) and re-suspended in TE buffer (5-15µl, diluted to a concentration of 5ng/µl). Symbionts were characterized using six polymorphic microsatellite loci, B7SYM4, B7SYM8, B7Sym34, B7Sym36, CA6.38 and GV-1C following the protocols of Pettay and LaJeunesse (2007), Andras et al (2009) and Santos et al (2003b).

Data Processing Description

BCO-DMO Processing notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- converted latitude and longitude to decimal degrees

Data Files

File
microsat_Bant.csv (Comma Separated Values (.csv), 1.21 KB) MD5:91e7fb33fb38c5c1f5dae6074f505afc Primary data file for dataset ID 756404

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1559286

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: I-COR 4200 NEN® Global IR2 DNA sequencing system (LI-COR Biosciences)

Supplied Description:

Fragment analysis of the PCR product of the microsatellite loci were run a on a 25 cm long, 0.25 mm thick, 6.5% non-denaturing polyacrylamide gel on an automated LI-COR 4200 NEN Global IR2 DNA sequencing system (LI-COR Biosciences).

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.

Thermal Cycler

Supplied Name: a PTC-100 MJ Research Inc. thermal cycler or a BioRad T100-Thermal Cycler

Supplied Description:

Used to amplify microsatellite loci.

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
Culture_ID	Identification of sample given as culture name (16-0587)	Unitless	sample
Incubation_Temperature	Temperature at which the culture is maintained	Degree Celsius	temp_inc
Host	Octocoral from which the symbiont was isolated. Note - In the vast majority of cases the culture is NOT representative of the host symbiont population (Santos et al 2001)	Unitless	species
Putative_Species	Putative species based on sequence analysis of B7 SYM15 flanking region (LaJeunesse et al 2012; Parkinson et al 2015)	Unitless	species
Location	collection location	Unitless	region
Latitude	latitude; north is positive	decimal degrees	lat
Longitude	longitude; east is positive	decimal degrees	lon
State_Country	collection state and country	unitless	region
Ocean	ocean or sea of collection	unitless	region
Host_stage	growth stage of host	unitless	stage
Axenic	culture is free from other living organisms	unitless	sample_descrip
Isolated_by	person who isolated sample	unitless	person
Year_isolated	the year the culture was isolated	unitless	year
ITS2_type	Classification based on sequence of ITS2 following LaJeunesse et al (2012) and Parkinson et al (2015)	Unitless	no_bcodmo_term
cp_type	Fragment length of the hypervariable region of Domain V of symbiont 23S rDNA (Santos et al 2003a)	base pairs (bp)	no_bcodmo_term
GV_1C	Microsatellite locus allele size	base pairs (bp)	no_bcodmo_term
B7SYM34	Microsatellite locus allele size	base pairs (bp)	no_bcodmo_term
BYSYM36	Microsatellite locus allele size	base pairs (bp)	no_bcodmo_term
CA6_38	Microsatellite locus allele size	base pairs (bp)	no_bcodmo_term
B7SYM4	Microsatellite locus allele size	base pairs (bp)	no_bcodmo_term
B7SYM8	Microsatellite locus allele size	base pairs (bp)	no_bcodmo_term