Dataset: Coral 16s rRNA

Location: Brewer’s Bay (18.34403, -64.98435), St. Thomas, The U.S. Virgin Islands

Processing of fragments included freezing the coral tissue in liquid nitrogen and storing at -80˚C for 16S rRNA analysis. DNA from the coral samples were extracted at the University of Texas at Arlington (UTA) using DNeasy Powersoil Isolation kits (MO BIO Laboratories, Carlsbad, CA).  Roughly 0.25g of tissue was removed from each of the coral fragments. Tissue from healthy-state fragments (“control”) was extracted from the center of the fragment. Tissue was extracted in a similar manner from fragments exposed to WPD that did not display lesions by the end of the experiment (“disease-exposed”). For fragments that developed a lesion(s) (“disease-infected”), tissue was extracted approximately 2 to 3mm horizontally from the lesion margin.  

Tissue samples were sent to MR DNA Molecular Research LP (Shallowater, TX) for 16S rRNA gene amplification using 515F and 806R primers for the V4 region and sequenced on an Illumina MiSeq 2x250bp PE reads. Before sequencing, coral DNA was amplified using 515F and 806R primers through 30 PCR cycles using HotStarTaq Plus Master Mix Kit (Qiagen, USA) under the following conditions: 94°C for 3 minutes, followed by 30-35 cycles of 94°C for 30 seconds, 53°C for 40 seconds and 72°C for 1 minute, after which a final elongation step at 72°C for 5 minutes was performed. PCR products were checked for amplification intensity and integrity on a 2% agarose gel and then bands of similar weight were pooled, purified using Ampure XP beads and used for illumina DNA library prep. Libraries were sequenced at MR DNA on an illumina MiSeq and then bioinformatically processed to combine homologous sequences, depleted barcodes, sequences <150bp removed, and sequences with ambiguous base calls removed using the MR DNA analysis pipeline (MR DNA, Shallowater, TX, USA). 

Libraries were sequenced at MR DNA on an illumina MiSeq and then bioinformatically processed to combine homologous sequences, depleted barcodes, sequences <150bp removed, and sequences with ambiguous base calls removed using the MR DNA analysis pipeline (MR DNA, Shallowater, TX, USA). Sequences were grouped into operational taxonomic units (OTU’s) with a 3% tolerated divergence (97% similarity) and taxonomically annotated using BLASTn against the NCBI database.
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Instruments: 
DNeasy Powersoil Isolation kits (MO BIO Laboratories, Carlsbad, CA)
Illumina MiSeq 2x250bp PE reads
HotStarTaq Plus Master Mix Kit (Qiagen, USA)
MR DNA analysis pipeline (MR DNA, Shallowater, TX, USA)
Taxonomically annotated using BLASTn against the NCBI database

Coral species list in this dataset:

ScientificName,AphiaID
Colpophyllia natans,289697
Montastraea cavernosa,287962
Orbicella annularis,758260
Orbicella faveolata,758261
Porites astreoides,288889
Porites porites,207238
Siderastrea siderea,207516