Dataset: Bleached octocoral genotypes

Name: Genotypes of symbionts in Muricea atlantica, M. elongata, and Plexaurella dichotoma across the 2015 Bleaching event (May 2015-August 2017) in the Florida Keys
Published: 2023-06-05
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.896886.1

Spatial Extent: N:24.8246 E:-80.6864 S:24.7451 W:-80.7799

Temporal Extent: 2015-05 - 2017-08

Project:

RAPID: Variations in symbiont diversity in octocoral across seasons and a predicted bleaching event (Octocoral symbiont diversity)

Principal Investigator:

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

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-06-05

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Genotypes of symbionts in Muricea atlantica, M. elongata, and Plexaurella dichotoma across the 2015 Bleaching event (May 2015-August 2017) in the Florida Keys

Abstract:

Alleles at four microsatellite loci, genotype based on these, fragment size of hypervariable region of the chloroplast 23S rDNA and genus of symbionts in Muricea atlantica, M. elongata, and Plexaurella dichotoma across the 2015 Bleaching event (May 2015-August 2017).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2023-06-05	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.896886.1	2023-07-18

Methods & Sampling

Methodology by organism type:

M.elongata:
Tagged colonies were sampled in May 2015 (before bleaching), September 2015 (during bleaching), and after bleaching - November 2015, March 2016, May 2016, September 2016, November 2016, March 2017 and August 2017. Tissue was preserved in 95% ethanol. 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 four polymorphic microsatellite loci, B7SYM15, B7SYM34, B7Sym8, and SYM 155 following the protocols of Pettay and LaJeunesse (2007) and Andras et al (2009). Cp-type were determined following the protocols outline in Santos et al (2003). Putative species identity was based on cp-type or Breviolum microsatellites as noted above.

P. dichotoma:
Tagged colonies were sampled in May 2015 (before bleaching), September 2015 (during bleaching), and after bleaching - November 2015, March 2016, May 2016, September 2016, November 2016, March 2017 and August 2017. Tissue was preserved in 95% ethanol. 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 four polymorphic microsatellite loci, B7SYM15, B7SYM36, B7Sym9, and CA6.38 following the protocols of Pettay and LaJeunesse (2007), Andras et al (2009) and Santos et al (2003a) Cp-type were determined following the protocols outline in Santos et al (2003b). Putative species identity was based on cp-type were available.

M. atlantica:
Tagged colonies were sampled in September 2015 (during bleaching), and after bleaching - November 2015, March 2016, May 2016, September 2016, November 2016, March 2017 and August 2017 and tissue preserved in 95% ethanol. 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 four polymorphic microsatellite loci, B7SYM15, B7SYM34, B7Sym8, and SYM 155 following the protocols of Pettay and LaJeunesse (2007) and Andras et al (2009). Cp-type were determined following the protocols outline in Santos et al (2003). Putative species identity was based on cp-type or Breviolum microsatellites as noted above.

Location:
Two patch reefs in the vicinity of Long Key in the Florida Keys (CMF-N24.44.704, W 80 46.793 and SC2- N24 49.478 W80 41.187)

Coral taxonomic identifiers (Genus species, LSID):
Muricea atlantica, urn:lsid:marinespecies.org:taxname:287554
Muricea elongata, urn:lsid:marinespecies.org:taxname:287559
Plexaurella dichotoma, urn:lsid:marinespecies.org:taxname:290812

Endosymbiont taxonomic identifiers (Genus species, LSID):
Breviolum, urn:lsid:marinespecies.org:taxname:1391356
Cladocopium, urn:lsid:marinespecies.org:taxname:1491877

Data Processing Description

BCO-DMO Processing Notes:
* File ALL_BleachOcto_genotype_BCO-DMO_REVISED.xlsx that were submitted 2023-06-22 was imported data into the bco-dmo data system.
* lat lon in decimal degree columns extracted from degrees decimal minutes provided within text of "site" column.
* rounded lat and lon to 5 decimal places

Data Files

File
bleached-genotypes.csv (Comma Separated Values (.csv), 67.58 KB) MD5:30fb5a492ccca055a5d4cde873ac677b This is the primary data table for dataset 896886.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1552949

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: LI-COR NEN Global IR2

Supplied Description:

Fragment analysis was performed on a LI-COR NEN Global IR2 DNA Sequencer.

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: BioRad T100 thermal cycler

Supplied Description:

DNA amplifications were performed on a BioRad T100 thermal cycler.

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	Species of each octocoral host monitored in the study	unitless	species
Sample_ID	Identification of the octocoral colony that was sampled across the study	unitless	sample
Month	Month in which the sample was collected	unitless	month
Year	Year in which the sample was collected Format: %Y	unitless	year
SITE	Latitude and longitude where were sample collected	unitless	site
lat	Latitude where were sample collected	decimal degrees	lat
lon	Longitude where were sample collected	decimal degrees	lon
Comment	"DEAD" indicates colony missing or skeleton located but dead. "no sample" indicates colony was not sampled.	unitless	comment
B7SYM15	Microsatellite locus allele size. Base pairs (bp). Format examples ("248" "252+248" "248, 256" "219+(229)"). Allele sizes in parentheses indicate a weak band and an allele size followed by "st?" indicates that the second band may be the result of stutter.	unitless	no_bcodmo_term
B7SYM34	Microsatellite locus allele size. Base pairs (bp). Format examples ("248" "252+248" "248, 256" "219+(229)"). Allele sizes in parentheses indicate a weak band and an allele size followed by "st?" indicates that the second band may be the result of stutter.	unitless	no_bcodmo_term
B7SYM8	Microsatellite locus allele size. Base pairs (bp). Format examples ("248" "252+248" "248, 256" "219+(229)"). Allele sizes in parentheses indicate a weak band and an allele size followed by "st?" indicates that the second band may be the result of stutter.	unitless	no_bcodmo_term
SYM155	Microsatellite locus allele size. Base pairs (bp). Format examples ("248" "252+248" "248, 256" "219+(229)"). Allele sizes in parentheses indicate a weak band and an allele size followed by "st?" indicates that the second band may be the result of stutter.	unitless	no_bcodmo_term
Assigned_Genotype	Multilocus genotype assigned based on the allele(s) present at each locus	unitless	no_bcodmo_term
CP_type	Fragment length of the hypervariable region of Domain V of symbiont 23S rDNA (Santos et al 2003a) or in cases where cp-type not available, based on the ability to amplify sample with Breviolum microsatellites. NA= No amplification after three attempts.	unitless	no_bcodmo_term
Genus	Symbiont genus based on cp-type (comma delimited if more than one Genus)	unitless	genus

Database

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Dataset: Bleached octocoral genotypes