RAD-seq of Porites cf. lobata coral colony from Palau
Between 2011-18, we collected tissue from Porites cf. lobata colonies using a hammer and chisel while on SCUBA. Tissue was preserved in RNAlater (Invitrogen, Waltham, MA), incubated overnight at 4C, and frozen at -20C (N=329), or frozen directly at -80C (N=20), or preserved in 95% ethanol and frozen at -20C (N=194) until DNA extraction. A thawed ~1 mm2 piece of coral was homogenized into a fine powder using a new standard safety razor blade sterilized with ethyl alcohol and flamed. The homogenate was processed using the Qiagen DNeasy Blood and Tissue DNA extraction kit according to the manufacturer instructions, with a modified Proteinase K incubation of at least 24 hours. Genomic DNA concentrations were standardized using a Qubit 2.0 fluorometer (Invitrogen) to 20 ng/ul. A total of 50 ul per sample was sent to Floragenex (Portland, Oregon) for single enzyme RAD library preparation with PstI enzyme digestion. Each sample was identified by a unique 10 nucleotide barcode. Samples (N=185) were sequenced as 100 base pair single end reads across 6 lanes of an Illumina Hiseq 4000 using v4 chemistry at the University of Oregon Genomics Core facility.