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

Website: https://www.bco-dmo.org/dataset/882086
Data Type: experimental, Other Field Results
Version: 1
Version Date: 2022-10-10

» Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective (SymBioSys)
Coffroth, Mary AliceState University of New York at Buffalo (SUNY Buffalo)Principal Investigator, Contact
Miller, Margaret W.NOAA Southeast Fisheries Science Center (NOAA SEFSC)Co-Principal Investigator
Sheets, DavidCanisius CollegeCo-Principal Investigator
Leigh, Noel J.State University of New York at Buffalo (SUNY Buffalo)Student
McIlroy, Shelby E.State University of New York at Buffalo (SUNY Buffalo)Student
Newman, SawyerWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

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.


Spatial Extent: N:25.1167 E:-80.2833 S:24.5449 W:-81.4094
Temporal Extent: 2009 - 2011

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)



Coral Garden

Cheeca Rocks

East Turtle

Grecian Rocks

Looe Key

Sand Island



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 

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Data Files

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

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Related Publications

Coffroth, M. A., Lasker, H. R., Diamond, M. E., Bruenn, J. A., & Bermingham, E. (1992). DNA fingerprints of a gorgonian coral: a method for detecting clonal structure in a vegetative species. Marine Biology, 114(2), 317–325. doi:10.1007/bf00349534 https://doi.org/10.1007/BF00349534
Coffroth, M. A., Leigh, N. J., McIlroy, S. E., Miller, M. W., & Sheets, H. D. (2022). Genetic structure of dinoflagellate symbionts in coral recruits differs from that of parental or local adults. Ecology and Evolution, 12(9). Portico. https://doi.org/10.1002/ece3.9312
Correa, A. M. S., Brandt, M. E., Smith, T. B., Thornhill, D. J., & Baker, A. C. (2009). Symbiodinium associations with diseased and healthy scleractinian corals. Coral Reefs, 28(2), 437–448. https://doi.org/10.1007/s00338-008-0464-6
Santos, S. R., Gutierrez-Rodriguez, C., & Coffroth, M. A. (2003). Phylogenetic identification of symbiotic dinoflagellates via length heteroplasmy in Domain V of chloroplast Large Subunit (cp23S)-Ribosomal DNA Sequences. Marine Biotechnology, 5(2), 130–140. doi:10.1007/s10126-002-0076-z

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Sample_IDIdentification of tissue sample collected from adult Orbicella faveolata colonies. unitless
YearYear in which sample was collected. unitless
SiteReef where sample was collected� see abbreviation key above. unitless
Latitude_decimal_degreesLatitude of reef where samples were taken in decimal degrees. A positive value indicates a Northern coordinate value. decimal degrees
Longitude_decimal_degreesLongitude of reef where samples were taken in decimal degrees. A negative value indicatres a Western coordinate value. decimal degrees
B7Sym34Fragment 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
B7Sym36Fragment 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
Colony_NumberIdentification number for colony. unitless
Location_in_colonyLocation within the colony where the sample as taken; T: Top, M: Middle, B: Bottom. unitless
Depth_mDepth where sample was taken. meters (m)
CA_6_38Fragment 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
Assigned_GenotypeGenotype assigned based on the combination of microsatellite alleles at the three loci. Numbering is arbitrary. unitless
CP_typeFragment size of the hypervariable region of domain B of chloroplast large subunit rDNA (cp23S) allele. unitless

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Project Information

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

Coverage: Florida Keys, Bahamas, Panama, Mexico

The symbiosis between corals (Cnidaria:Hexacorallia:Scleractinia) and photosynthetic dinoflagellate symbionts (Alveolata: Dinophycea: Symbiodinium) provides the foundation and structure of the coral reef ecosystem, as well as significant contributions to global carbon and biogeochemical cycles. Given the importance of this symbiosis to the coral-algal holobiont and the reef ecosystem, understanding the mechanisms governing the establishment and long term maintenance of this symbiosis is essential. The overall aim of this project is to identify the mechanisms and selective processes that lead to the final assemblage of symbionts harbored by adult hosts. This question will be approached from two perspectives, ecologic and genomic, with the specific aims of determining (1) if different Symbiodinium strains differentially affect fitness of corals as the adult settles into a mature symbiosis (2) if competition among symbionts or environmental conditions contribute to the final host-symbiont pairing and (3) how host/symbiont transcriptomes varying as the symbiont community within a host is winnowed to the final assemblage found in the adult host. Traits that directly affect coral fitness (i.e. growth, survivorship, energy production) will be measured under different environmental conditions over the ontogeny of coral recruits that are experimentally infected with different types of Symbiodinium. Concurrently, high throughput gene expression profiling will be used to follow changes in gene expression between host and symbiont. Together, these data will be used to validate or falsify the hypotheses that the final symbiont assemblage found in the adult host is determined by (a) host selection (b) competition among symbionts and/or (c) environmental condition.

This study pools the expertise of two labs that have focused on these aspects of the symbiosis. The Coffroth lab pioneered the studies on early ontogeny of the symbiosis and symbiont diversity and will continue to take the lead in the ecological studies. The Medina lab is at the forefront in the development and utilization of genomic technology to study transcriptomic changes during the establishment and breakdown of the symbiosis. Furthermore, the Medina lab has the coral microarrays to be used in this study and in 2009 will also have oligo arrays for two Symbiodinium species based on 454 EST data. Although several groups have initial studies of the host transcriptome, none have combined an approach that examines the host and the symbiont in a single experiment. This will be a powerful approach as it will allow the investigators to track complementary changes in gene expression between host and symbiont and relate those to turnover in the symbiont community as the final symbiont complement is established.

The data resulting form the study will bridge an important gap in our understanding of the establishment and maintenance of coral-Symbiodinium symbiosis. Understanding the mechanism(s) regulating the establishment of the symbiosis will broaden our knowledge and help to predict the response of this symbiosis to future climate conditions. As in the past, the genomic tools (arrays, ESTs) will be made readily available to researchers via array distribution at cost, microarray analysis training, or sequence data, providing valuable resources to continue exploring these systems.

In conjunction the Aquarium of Niagara, Coffroth will develop educational and outreach programs to train and disseminate information on coral reefs to local area teachers and the general public. The Medina lab will continue to produce science and environment podcasts in multiple languages (English, Spanish and Hmong) with undergraduate students at UC Merced and will continue to collaborate with the California Academy of Sciences (CAS) in their coral reef outreach efforts. Additionally, this work will result in the training and mentoring of a postdoctoral fellow, at least one graduate student and at least 2 undergraduates. Through this project these students will have the opportunity to participate in research in both a lab and field setting, learning a range of ecological, molecular and algal culturing techniques. The extensive culture collection housed at the University at Buffalo is an important resource that is available to researchers worldwide which the proposed funding will help to maintain. Our EST annotations are publicly available through our EST database (http://montastraea.psu.edu/SymBioSys/).

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Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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