Holobiont transcriptomes for the critically endangered staghorn coral (Acropora cervicornis) from two environmentally distinct sites on Turneffe Atoll, Belize

Historically, staghorn coral ( Acropora cervicornis ) was a preeminent reef-builder in the Caribbean and Tropical Western Atlantic, where it constructed extensive thickets at 5-20 m depth that supported diverse ecosystems and provided coastal populations with food, storm protection, and income from tourism. In recent decades, A. cervicornis declined precipitously, up to 97% in some localities. To reverse its decline, widespread efforts are underway to characterize the phenotypic and genetic diversity of persisting populations with the goal of restoring them to historical levels by out-planting nursery grown specimens. To support this target, we developed transcriptomes for two A. cervicornis populations located in Turneffe Atoll Marine Reserve, Belize. These populations experience significantly different temperatures, light levels and water currents, and they harbor individuals that differ in key phenotypes. Because differentiating the gene activity of diverse taxa—i.e., coral host, algal photosymbiont, plus associated eukaryotes, bacteria, archaea, and viruses— is critical to understanding the function of the coral holobiont, we developed a pipeline for parsing transcripts by taxon. Separate transcriptomes for each population contain complete representatives for >96% of 978 conserved metazoan single copy orthologs. The taxonomic breakdown of transcripts differed between sites, with more bacterial transcripts recovered from Calabash Caye and more symbiont transcripts from Blackbird Caye. The assembled transcriptomes will facilitate gene expression studies and in silico cloning from this endangered coral.