Dataset: RNAseq data from apparently healthy and Stony Coral Tissue Loss Disease-affected Montastraea cavernosa coral collected from St. Thomas, US Virgin Islands in 2020

Golf ball-sized coral fragments were collected by divers on SCUBA with hammers and chisels from two reefs in St. Thomas, United States Virgin Islands (USVI) showing signs of active SCTLD in February of 2020: Buck Island (18.27883˚, –64.89833˚) and Black Point (18.3445˚, –64.98595˚). Black Point, a nearshore reef, first exhibited SCTLD cases between December 2018 and January 2019, as documented in Brandt et al. (2021). Buck Island, situated near an offshore undeveloped island, recorded its first cases of SCTLD in October 2019, also documented in Brandt et al. (2021). Current environments at both sites are similar. SCTLD-affected corals were identified based on displaying acute multifocal lesions consistent with the SCTLD case definition at the time (SCTLD Case Definition, 2018). Lesions were bright white where the skeleton had recently been denuded of tissue, with no visible algal colonization at the skeletal/tissue boundary, indicating actively expanding lesions.  

At both sites, one coral fragment was collected from each apparently healthy colony (Buck Island, n=3; Black Point, n=3), termed apparently healthy tissue on an apparently healthy colony (HH). Two fragments were collected from each diseased colony: one immediately adjacent to the SCTLD lesion line (Buck Island, n=3; Black Point, n=5), termed lesion tissue on a diseased colony (LD), and one as far away from the lesion line as possible (approximately 10 cm from the lesion line) (Buck Island, n=3; Black Point, n=5), termed apparently healthy tissue on a diseased colony (HD). The sampling scheme aimed to capture the variability in gene expression across different tissue health states while ensuring consistency in sampling methodology. Coral fragments were placed in individual bags that were sealed and transported to land on ice before being flash-frozen at -80˚C.

Total RNA was extracted from all 22 coral fragments following the protocol outlined in Beavers et al. (2023) using the RNAqueous-4PCR Total RNA Isolation Kit from Invitrogen (Life Technologies AM1914). About one gram of frozen coral tissue was scraped off each fragment into a 2 mL microcentrifuge tube using a sterilized bone cutter. Lysis buffer was added to each microcentrifuge tube followed by mechanical disruption using a refrigerated Qiagen Tissuelyser II at 30 oscillations/s for 60 s. Elution was performed in two 30 µL steps at a time. After combining elutions, contaminating DNA and chromatin were removed using the Ambion DNase I kit from Invitrogen (Life Technologies AM 2222). Resulting total RNA samples were sent to Novogene Co., LTD (Beijing, China) for quality assessment using an Agilent Bioanalyzer 2100. All 22 samples passed quality assessment with RNA integrity (RIN) values ≥ 7 and were preprocessed for mRNA enrichment using polyA tail capture. cDNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit from Illumina and sequenced on the Illumina NovaSeq 6000 for 150 bp, paired-end sequencing. Sample and data analysis was performed in January 2024.