Dataset: Breviolum Symbiont Genotypes in Orbicella faveolata Adults

Name: Microsatellite and chloroplast 23S genotypes of Breviolum sp. symbionts within Orbicella faveolata adults from reefs in the Florida Keys from 2009-2011 (SymBioSys project)
Published: 2022-10-10
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.882086.1

Spatial Extent: N:25.1167 E:-80.2833 S:24.5449 W:-81.4094

Temporal Extent: 2009 - 2011

Project:

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

Principal Investigator:

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

Co-Principal Investigator:

Margaret W. Miller (NOAA Southeast Fisheries Science Center, NOAA SEFSC)

David Sheets (Canisius College)

Student:

Noel J. Leigh (State University of New York at Buffalo, SUNY Buffalo)

Shelby E. McIlroy (State University of New York at Buffalo, SUNY Buffalo)

Contact:

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

BCO-DMO Data Manager:

Sawyer Newman (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-10-10

Restricted:

Release Date:

2022-11-09

Validated:

Yes

Current State:

Final no updates expected

Microsatellite and chloroplast 23S genotypes of Breviolum sp. symbionts within Orbicella faveolata adults from reefs in the Florida Keys from 2009-2011 (SymBioSys project)

Abstract:

Microsatellite genotypes and chloroplast 23S genotypes (based on length heteroplasmy in domain V of chloroplast large subunit (cp23S) ribosomal DNA sequences) of Breviolum sp. symbionts within Orbicella faveolata adults in the Florida Keys.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-10-10	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.882086.1	2023-05-24

Methods & Sampling

Sampling and Analytical Methodology

Tissue samples were collected from the top, middle and bottom portions of adult Orbicella faveolata colonies using the syringe method as described in Correa et al. (2009) and DNA extracted following Coffroth et al. (1992).

Genotypes of the algal symbionts within the genus Breviolum were characterized using three polymorphic microsatellite loci, B7Sym34, B7Sym36 and CA6.38, which were adapted for use with O. faveolata (Thornhill et al. 2009).

Cp-23S genotypes of the algal symbionts within the genus Breviolum were characterized following the protocol of Santos et al. (2003).

Locations in the Florida Keys (Table of reef abbreviations)

Reef
Abbreviation

Alligator
AR

Coral Garden
CG

Cheeca Rocks
CR

East Turtle
ET

Grecian Rocks
GR

Looe Key
LK

Sand Island
SI

Tennessee
TR

Data Processing Description

Processing Notes from Researcher:

For parameters B7Sym34, B7Sym36, CA6.38 (CA_6_38), Assigned_Genotype, and CP_type, NA indicates "no amp - did not amplify after multiple attempts," and ND indicates "not determined because one or more loci did not amplify."

BCO-DMO Processing Notes:

Special characters and spaces replaced by underscores ("_") in parameter names
Longitude and latitude are split into separate columns and converted to decimal degrees
Separate data tables related to Orbicella faveolata adults merged into one data table

Data Files

File
microsatellite_genotypes_adults-1.csv (Comma Separated Values (.csv), 42.51 KB) MD5:666becc6ca7babd3eb46b0ee7cd8b969 File processed with laminar pipeline "882086_v1_breviolum_symbiont_microsatellite_genotypes" at path 882086/1/data/microsatellite_genotypes_adults-1.csv

More Information about this dataset

Funding Sources

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

Deployments

None available yet

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_ID	Identification of tissue sample collected from adult Orbicella faveolata colonies.	unitless	sample
Year	Year in which sample was collected. Format: %Y	unitless	year
Site	Reef where sample was collected� see abbreviation key above.	unitless	site
Latitude_decimal_degrees	Latitude of reef where samples were taken in decimal degrees. A positive value indicates a Northern coordinate value.	decimal degrees	lat
Longitude_decimal_degrees	Longitude of reef where samples were taken in decimal degrees. A negative value indicatres a Western coordinate value.	decimal degrees	lon
B7Sym34	Fragment size of the B7Sym34 microsatellite allele. NA indicates "No Amp - did not amplify after multiple attempts", and ND indicates "Not Determined - because one or more loci did not amplify.	basepair	sample_descrip
B7Sym36	Fragment size of the B7Sym36 microsatellite allele. NA indicates "No Amp - did not amplify after multiple attempts", and ND indicates "Not Determined - because one or more loci did not amplify.	basepair	sample_descrip
Colony_Number	Identification number for colony.	unitless	site
Location_in_colony	Location within the colony where the sample as taken; T: Top, M: Middle, B: Bottom.	unitless	site_descrip
Depth_m	Depth where sample was taken.	meters (m)	depth
CA_6_38	Fragment size of the CA6.38 microsatellite allele. NA indicates "No Amp - did not amplify after multiple attempts", and ND indicates "Not Determined - because one or more loci did not amplify.	basepair	sample_descrip
Assigned_Genotype	Genotype assigned based on the combination of microsatellite alleles at the three loci. Numbering is arbitrary.	unitless	sample_descrip
CP_type	Fragment size of the hypervariable region of domain B of chloroplast large subunit rDNA (cp23S) allele.	unitless	sample_descrip

Database

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Dataset: Breviolum Symbiont Genotypes in Orbicella faveolata Adults