Dataset: Host genome and microbiome sequencing data for Porites cryptic lineages in classic and extreme reefs in Palau in November 2021

Colonies resembling the gross morphology of Porites lobata Dana, 1846 were tagged at six sites, at the Rock Islands of Palau, in November 2021 in a transect along the shoreline (N=15 per site, 90 colonies total). All colonies were sampled using a hammer and chisel between 1 and 6 meters (m) depth, with the majority between 3 and 4 m. All selected colonies were at least 1-5 m apart to reduce the risk of sampling clone mates while maximizing the probability that the colonies were exposed to similar conditions within a site. Targeted colonies were also relatively small in size (30-50 centimeters (cm)) to facilitate transportation to aquarium facilities for further analyses and experiments. The total area over which corals were collected was 250-500 square meters (m²) per site. Tissue samples were taken from the center of each colony, immediately fixed in ethanol, and stored at -20 degrees Celsius (°C) (2 × 2 cm samples).

Tissue samples from all coral colonies were crushed with a sterile razor blade, and DNeasy Blood and Tissue kits (Qiagen) were used to isolate DNA from the resulting homogenate according to the manufacturer's instructions, with one modification: the lysis step was conducted overnight. Isolated DNA was then cleaned with a Zymo Clean and Concentrator kit (Zymo Research, CA). DNA was quantified using a Qubit fluorometer (Invitrogen), standardized to 25 nanograms per microliter (ng μL⁻¹), prepared for 2b-RAD sequencing according to (Wang et al., 2012), and sequenced across one lane of Illumina HiSeq 2500 using single-end 50 bp sequencing at the Tufts University Core Facility (TUCF) Genomics. Five technical replicates were included in the library preparation to aid the downstream identification of clonemates.

Photobiont communities were characterized in samples through sequencing of the internal transcribed spacer region 2 (ITS2) region using SYM_VAR_5.8S2 and SYM_VAR_REV primers (Hume et al., 2015, 2018). The PCR profile included 26 cycles of 95 °C for 40 seconds, 59 °C for 2 minutes, 72 °C for 1 minute and a final extension of 72 °C for 7 minutes. A negative control was included in the initial amplification but failed to amplify, so it was not included in downstream library preparations. Successful amplifications were cleaned using the GeneJET PCR Purification kit (ThermoFisher Scientific) and a second PCR was conducted to attach Illumina MiSeq dual barcodes to the PCR product before samples were pooled. Volumes for pooling were based on the visualization of barcoded sample band intensity on a 1% agarose gel. This pool was cleaned using the GeneJET PCR Purification kit, gel extracted, and submitted for sequencing as described below.

To characterize bacterial communities, the V4 region of the 16S rRNA gene was amplified from the same samples via PCR using Hyb515f (Parada et al., 2016) and Hyb806R (Apprill et al., 2015) primers and the following PCR profile: 35 cycles of 95 °C for 40 seconds, 65 °C for 2 minutes, 72 °C for 1 minute and a final extension of 7 minutes. Subsequent PCR amplification, cleaning, dual-barcoding, and gel extraction followed the same protocol described for ITS2 with the inclusion of three negative controls, which were also submitted for sequencing. ITS2 and 16S pools were quantified and combined in a 1:3 ratio, respectively. Libraries were sequenced together on Illumina MiSeq (paired-end 250 bp) at Tufts University Core Facility (TUCF) Genomics.