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

These data include NCBI Sequence Read Archive (SRA) accession numbers for raw fastq files of internal transcribed spacer-2 (ITS-2) amplicons from 491 apparently healthy and stony coral tissue loss disease (SCTLD)-affected corals in Florida, U.S.A., and the United States Virgin Islands (USVI), representing nine coral species sampled in situ or during an SCTLD transmission experiment. From Florida, 215 samples were collected in situ from six epidemic sites in 2018. From the USVI, 110 samples were collected in situ from four reef sites in 2019-2020. Of the total samples, 325 were sampled in situ as sets of SCTLD-affected and apparently healthy conspecifics: two samples were collected from each diseased coral, one from tissue adjacent to the gross tissue loss lesion and one from apparently healthy tissue on the same coral; one sample was then collected from a nearby conspecific coral that was apparently healthy. The 166 remaining samples were originally collected from Rupert's Rock in the USVI, and samples were taken from these corals during a wet lab-based SCTLD transmission experiment. Understanding whether Symbiodiniaceae composition is predictive of disease state is crucial for managing SCTLD outbreaks, and these data permit investigations of how Symbiodiniaceae lineage-level dynamics may underlie variation in holobiont disease response. Florida samples were collected by Kerry Maxwell, Lindsay Huebner, Dr. Erinn M. Muller, and their teams at the Florida Fish & Wildlife Research Institute and Mote Marine Laboratory. USVI samples were collected by Dr. Marilyn Brandt, Sonora Meiling, Dr. Alex Veglia, Dr. Daniel Holstein, Dr. Laura Mydlarz, Dr. Amy Apprill, Dr. Adrienne Correa, and their teams. Danielle Lasseigne, Adam Glahn, Amanda Long, Bradley Arrington, Daniel Mele, Kathryn Cobleigh, Alexandra Gutting, Joseph Townsend, Naomi Huntley, Kelsey Beavers, Paul Barbera, Nate Berkebile, Tiffany Boisvert, Michael Bollinger, Katy Cummings, Amanda Ellis, Kristine Fisher, John Hart, Lauri Maclaughlin, Brian Reckenbeil, and Jennifer Stein assisted with field collections.