Implications for evolution, adaptation, and coral biodiversity from the genomic landscape of deep-sea corals

Deep-sea corals are marine invertebrates vital for the biodiversity of coral ecosystems, but their genomes remain understudied. Here, we present 11 newly-sequenced deep-sea coral genomes, including four Hexacorallia and seven Octocorallia species, and contribute new genomic information to three orders. Exploring rapid coral speciation and global temperature changes highlights the diversity of coral reef ecosystems. We also identified 126 horizontal gene transfer (HGT) genes from symbiotic microorganisms in coral genomes and several of these HGT genes are involved in phosphorus and cholesterol metabolisms within corals, indicating that HGT potentially may serve as an adaptive survival strategy for the coral holobiont. Interesting, given our discovery of HGT from zooxanthellae in the common ancestor of corals, it is plausible to suggest that corals may have originated in shallow-sea. In addition, we also observed the loss of key rhythm genes (e.g., clock and cry) in deep-sea corals. Based on a comprehensive genomic analysis, our study provides the first genetic evidence for a shallow-sea origin of the Anthozoa. At the same time, newly sequenced deep-sea coral genomes contribute to a better understanding of the evolution, biodiversity, and adaptation of deep-sea corals. Furthermore, it provides a genetic foundation for the conservation and sustainable management of coral reefs.