Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

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

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.

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

PROJECT SUMMARY:
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/).