Dataset: Montastrea cavernosa coral viromes

Name: Viral metagenomes derived from an apparently healthy M. cavernosa coral and a heat-stressed M. cavernosa coral analyzed in the Vega Thurber lab at Florida International University, North Miami, FL (Coral Virus project)
Published: 2015-05-12
Keywords: oceans

View Data: Data not available yet

Cite This Dataset

Project:

Effects of Viruses on Coral Fitness (Coral Virus)

Principal Investigator:

Rebecca Vega Thurber (Oregon State University, OSU)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

12 May 2015

Version Date:

2015-05-12

Validated:

Current State:

Preliminary and in progress

Viral metagenomes derived from an apparently healthy M. cavernosa coral and a heat-stressed M. cavernosa coral analyzed in the Vega Thurber lab at Florida International University, North Miami, FL (Coral Virus project)

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Description

These two viral metagenomes were derived from 1) an apparently healthy Montastrea cavernosa coral maintained in 28.0 degrees C, and 2) a heat stressed M. cavernosa coral which was exposed to 31.5 degrees C for 12 hours.

The experiment was conducted in North Miami, Florida, USA, at Florida International University. Specimens were collected at Key West, FL, USA.

Status Note [ 12 May 2015 ]: These data are stored at the MG-RAST Server http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeSearch under ID numbers: 44551158.3 and 44551159.3. However, at this time, these data are not publicly available. Links will be provided here once the data are available online through MG-RAST.

Methods & Sampling

For complete details see Correa et al. (2012).

Following treatment, the tissue layer from each fragment was removed using an airbrush and 0.02 mm filtered viral-free 1_ PBS (pH 7.8). Coral and coral symbiont homogenates were collected in sterile tri-pour containers and pre-filtered with an 1-mm nucleopore filter (Whatman, Piscataway, NJ,USA). VLPs were concentrated from 27 ml of homogenate using ultracentrifugation of four-layer (1.2, 1.35, 1.5 and 1.7 g ml-1) cesium chloride density gradients (Vega Thurber et al., 2009). A gray band formed in the 1.2 g ml-1 density layer (Supplementary Figure 1a) and was harvested using an 18-gage needle and sterile syringe. Before and following a 0.22-mm Sterivex (Millipore, Billerica,MA, USA) filtration step (for details, see Vega Thurber et al. (2009)), this fraction was visualized using epifluorescence microscopy and SYBR Gold (Invitrogen, Carlsbad, CA, USA) staining (Noble and Fuhrman, 1998; Vega Thurber et al., 2009).

Related publications:
Correa, A.M., Welsh, R.M., and Vega Thurber, R.L. 2012. Unique nucleocytoplasmic dsDNA and +ssRNA viruses are associated with the dinoflagellate endosymbionts of corals. ISME J., 7(1): 13-27. doi:10.1038/ismej.2012.75

Data Processing Description

Approximately 2 ug of cDNA of each sample was pyrosequenced on a Roche Titanium 454 platform at the Broad Institute (Massachusetts Institute of Technology, Cambridge, MA, USA). SFF files were converted to FASTA and FASTAQ files, and each read was parsed and assigned an alphanumeric name. Reads were archived at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) (ID SRA052068), as well as at CAMERA (IDs CAM_SMPL_000711 and CAM_SMPL_000712) (Sun et al., 2011) and MG-RAST (IDs 4455158.3 and 4455159.3).

More Information about this dataset

Funding Sources