Dataset: NCBI Sequence Read Archive (SRA) accession numbers for raw fastq sequence files of ITS-2 amplicons collected from healthy and SCTLD-affected tissues of nine coral species in Florida, U.S.A. and the U.S. Virgin Islands from 2018-2020

For samples collected from the Florida Keys, U.S.A., sterile, 10 milliliter (mL) syringes were used to scrape/remove tissue from Montastraea cavernosa, Orbicella faveolata, Colpophyllia natans, Meandrina meandrites, and Pseudodiploria strigosa corals. For Siderastrea siderea corals collected from the Florida Keys, U.S.A., a sterile corer was used to scrape tissue off, which was captured in a sterile syringe. Coral tissues were transferred from the syringes to plastic tubes before transport on ice to the South Florida Regional Laboratory of the Florida Fish & Wildlife Conservation Commission's Fish and Wildlife Research Institute. There, coral tissues were flash frozen with liquid nitrogen before storage at -80 degrees Celsius (°C). DNA was extracted from samples using DNeasy PowerSoil Kits (QIAGEN, Germantown, MD, USA). 6 mL of coral tissue/mucus slurries were used for S. siderea, but 2 mL were used for all other species. Each slurry was centrifuged, and the supernatant was discarded to isolate a pellet of coral tissue/mucus. These methods are described by Clark et al. (2021).

For samples collected from the United States Virgin Islands, diseased and apparently healthy Porites astreoides, M. cavernosa, Orbicella annularis, S. siderea, C. natans, Diploria labyrinthiformis, M. meandrites, and P. strigosa corals were collected by divers on SCUBA via hammer and chisel. Fragments were stored in individual, sterile whirlpaks before being flash frozen in a charged liquid nitrogen dry shipper on the boat and subsequently stored at -80°C. All in situ samples (i.e., from both Florida, U.S.A., and the U.S. Virgin Islands) were sampled as sets of stony coral tissue loss disease-affected and apparently healthy conspecifics. Two samples were collected from each diseased coral: one adjacent to the gross tissue loss lesion and one from apparently healthy tissue on the same coral. One sample was collected from a nearby conspecific coral that was apparently healthy. Coral tissue was airbrushed from the flash-frozen fragments using phosphate buffered saline. Then, coral tissue slurry was centrifuged, and the supernatant was discarded to isolate a pellet of coral tissue/mucus. No more than 0.040 grams (g) of coral tissue was used for a DNA extraction using the ZymoBIOMICS DNA/RNA Miniprep Kit (ZymoResearch, Irvine, CA, USA).

Apparently healthy corals (C. natans, M. cavernosa, O. annularis, P. astreoides, P. strigosa, and S. siderea) for the stony coral tissue loss disease transmission experiment were originally collected from Rupert's Rock by divers on SCUBA via hammer and chisel. Corals were placed in separate, sealed bags before transport to the Center for Marine and Environmental Sciences in coolers with seawater. There, corals were halved with a sterilized chop saw or bandsaw and placed into shaded raceways for at least one week prior to the start of the experiment. One day before the start of the transmission experiment, healthy and diseased Diploria labyrinthiformis corals were collected from Rupert's Rock and Flat Cay, respectively, via hammer and chisel. These D. labyrinthiformis corals were placed in separate gallon bags and transported to the Center for Marine and Environmental Sciences. For the control treatment, one fragment each of C. natans, M. cavernosa, O. annularis, P. astreoides, P. strigosa, and S. siderea were randomly arranged around a central apparently healthy D. labyrinthiformis coral. For the disease treatment, corresponding fragments of each genet were randomly arranged around a central diseased D. labyrinthiformis coral. This was replicated eight times. Corals were examined twice daily. If a lesion was observed to actively expand for at least 12 hours, the fragment was removed from the experimental container and flash frozen in a charged dry shipper. After eight days, all remaining fragments were flash frozen. Methods for the transmission experiment are reported by Meiling et al. (2021), and DNA was extracted according to the in situ samples collected from the U.S. Virgin Islands, as described above.

The internal transcribed spacer-2 (ITS-2) region of Symbiodiniaceae rDNA was amplified from all extracted DNA using the SYM_Var primer pair (Hume et al., 2018): SYM_VAR_5.8SII (5'-GAATTGCAGAACTCCGTGAACC-3') and SYM_REV (5'-CGGGTTCWCTTGTYTGACTTCATGC-3'). PCR reagents included 2 microliters (µL) of DNA, 0.42 µL of forward and reverse primers, 15 µL of DNase/RNase-free water, and 17.5 µL of EconoTaq PLUS GREEN 2X Master Mix. After 10 minutes at 74°C, PCR conditions included 32 cycles of 94°C for 1 minute, 59°C for 1 minute, and 74°C for 2 minutes, followed by 74°C for 7 minutes. Sequencing was performed on an Illumina MiSeq PE300 platform at Oregon State University's Center for Quantitative Life Sciences (OSU CQLS, Corvallis, OR, USA). These methods are described by Karrick et al. (in review).