Genomic analysis of stony coral tissue loss disease resistance in restoration genotypes of Orbicella faveolata

Stony coral tissue loss disease (SCTLD) has devastated Florida's Coral Reef since 2014, affecting many endangered species of coral and particularly Orbicella faveolata. While there exists limited evidence of disease resistance in O. faveolata populations, no study to date has quantitatively assessed the potential for certain genotypes to survive the SCTLD epidemic. Previous efforts have focused on field experiments, which cannot standardize disease exposure potential and often have covarying impacts of environmental variability and non-disease-associated mortality. A collaborative team from Mote Marine Laboratory, University of Miami, and NOAA's Atlantic Oceanographic and Meteorological Laboratory conducted the largest coral disease transmission study on record (170 putative genotypes, 346 total fragments, 38% with >2 replicates) using O. faveolata genotypes from Mote's land-based nursery. This study also prioritized sampling of corals at multiple time points, including initial, pre-exposure, early exposure, initial lesion signs, and >10% tissue mortality to better understand disease responses and progression using multi-'omic analyses. A subset of the total samples (n=2,565) were processed and sequenced for population genomics, microbial genomics, transcriptomics, and resistance/susceptibility. This comprehensive sampling approach allows for the greatest possible examination of molecular responses for any coral disease. This repository contains raw sequences for 174 whole-genome sequencing (WGS) samples of experimental genotypes, as well as 173 restriction site-associated DNA sequencing (2bRAD) samples of nursery genotypes.