Dataset: GenBank accessions for 18S rRNA gene amplicons from swab specimens collected in the Caribbean and Réunion (France) from May 2022 to Dec 2024

Surface swab specimens were collected between May 2022 and December 2024. Samples were collected from sites affected (i.e. sites which bore DaSc-affected urchins) at the time of sampling or those which were previously affected; sites that were never affected (i.e. reference sites); and ports/marinas. Swab specimens were collected by snorkelers at depths of ~1–4 m. Polyester swabs (Dry Transport Systems, Puritan Medical Products) were transported to the survey site sealed in an air-filled transport tube and withdrawn into the water immediately adjacent to the swabbed surface. The swab was gently rubbed for 10 s across a ~2 cm2 surface before retrieval into the air-filled transport tube. Live swabbed surfaces, chosen haphazardly, were photographed to confirm the identity of invertebrate or plant species (seagrass and macroalgae).  At some sites, identity of swabbed surfaces could not be determined (i.e. unidentifiable surface swabs), and in some cases, the taxonomy of swabbed specimens was unclear (e.g. macroalgae; n = 11), so they were assigned to higher taxonomy. Swabs were transported at ambient temperature to shore, where the swab tips were cut off with clean scissors into cryovials containing RNAlater Solution (Invitrogen).

DNA was extracted from swab tips were extracted using the Quick-DNA Insect/Tissue kit (Zymo Research). The manufacturer’s extraction protocol (v.2.21) was followed with these exceptions: we did not add beta-mercaptoethanol to the lysis buffer, bead bashing was shortened to 2 min, and DNA was eluted into nuclease-free sterile water instead of elution buffer. Specimens were subjected to PCR employing pan-Ciliophora 18S rRNA gene primers 384F (5’-YTB GAT GGT AGT GTA TTG GA-3’) and 1147R (5’-GAC GGT ATC TRA TCG TCT TT-3’) (Dopheide et al. 2008). PCR was performed in 50 μl reactions comprising 1× PCR buffer, 2.5 mM MgCl2, 0.2 mM deoxynucleoside triphosphates (Promega PCR Nucleotide Mix), 200 pmol forward and reverse primers, 1 μl of 2 ng ml–1 BSA (Sigma), 5U Taq DNA polymerase (Invitrogen), and 2 μl of pooled DNA extracts. Thermal cycling was preceded by an initial heating step for 3 min at 95°C, followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 54°C for 30 s, and extension at 72°C for 30 s, followed by a final extension at 72°C for 5 min in a BioRad MyCycler.

The PCR amplicons (5 μl) were then visualized on a 1 % agarose gel in 1× Tris-borate-EDTA after electrophoresis at 85 V for 45 min and staining with SYBR Gold. PCR products were cleaned up using the Zymo Clean & Concentrator-5 kit and subject to dye terminator (Sanger) sequencing at the Biotechnology Resource Center at Cornell University.