Dataset: McIlroy_2016: Symbionts genotypes in Orbicella faveolata

Collection of Orbicella faveolata larvae was made at Alligator Reef (24°48.7710 N, 80°40.1670 W) and Looe Key (24°32.6930 N, 81°24.5620 W) in 2011. Initial rearing was done at Keys Marine Laboratory (KML), Long Key, FL. Settled corals were then maintained at University of Miami Experimental Hatchery (Virginia Key, Miami, FL). Symbiodinium cultures originated from highly concentrated, isoclonal reference cultures maintained at the University at Buffalo – SUNY (BURR Culture Collection: http://www.nsm.buffalo.edu/Bio/burr/). The cultures used in the experiments were maintained at the Keys Marine Lab (Florida) in f/2 medium (Guillard 1975), at ~27°C, under a 14:10 h light:dark regime.

Samples were preserved in 95% ethanol for subsequent DNA extraction following a 29 Cetyl trimethyl ammonium bromide protocol for Symbiodinium DNA isolation (Coffroth et al. 1992). This protocol was slightly modified by the addition of a "bead-beating" step in which a 50-100 lL volume of glass beads (size: 425-600 lm; Sigma, Sigma-Aldrich, St. Louis, MO, USA) per tube were added and shaken on high on a Vortex Genie (Scientific Industries, Inc., Bohemia, New York, USA) on the highest setting for 5 min to rupture the symbiont cell wall (Goulet and Coffroth 1997, Yuan et al. 2015). Symbiont species were distinguished via length heteroplasmy in domain V of cp23S ribosomal DNA (Santos et al. 2003). The cp-23S gene was amplified by polymerase chain reaction (PCR) and the PCR product was then run on a 6.5% Long Ranger acrylamide gel using LI-COR’s Long ReadIR 4200 DNA Sequencer along with size standards for fragment size analysis. PCR for each sample was repeated at least twice for scoring. In rare cases, replicates differed in their banding patterns and were repeated a third time. Very faint bands were excluded if they occurred only once in three replicates, otherwise, all bands from all replicates were included in the analysis.