Corals comprise a biomineralizing cnidarian, dinoflagellate algal symbionts, and associated microbiome of</p><p>prokaryotes and viruses. Ongoing efforts to conserve coral reefs by identifying the major stress response</p><p>pathways and thereby laying the foundation to select resistant genotypes rely on a robust genomic foundation.</p><p>Here we generated and analyzed a high quality long-read based ~886 Mbp nuclear genome assembly and</p><p>transcriptome data from the dominant rice coral, Montipora capitata from Hawai’i. Our work provides insights</p><p>into the architecture of coral genomes and shows how they differ in size and gene inventory, putatively due to</p><p>population size variation. We describe a recent example of foreign gene acquisition via a bacterial gene</p><p>transfer agent and illustrate the major pathways of stress response that can be used to predict regulatory</p><p>components of the transcriptional networks in M. capitata. These genomic resources provide insights into the</p><p>adaptive potential of these sessile, long-lived species in both natural and human influenced environments and</p><p>facilitate functional and population genomic studies aimed at Hawaiian reef restoration and conservation.
