Genome Evolution of Coral Reef Symbionts as Intracellular Residents

Coral reefs are sustained by symbioses between corals and symbiodiniacean dinoflagellates. These symbioses vary in the extent of their permanence in and specificity to the host. Although dinoflagellates are primarily free-living, Symbiodiniaceae diversified mainly as symbiotic lineages. Their genomes reveal conserved symbiosis-related gene functions and high sequence divergence. However, the evolutionary mechanisms that underpin the transition from the free-living lifestyle to symbiosis remain poorly understood. Here, we discuss the genome evolution of Symbiodiniaceae in diverse ecological niches across the broad spectrum of symbiotic associations, from free-living to putative obligate symbionts. We pose key questions regarding genome evolution vis-à-vis the transition of dinoflagellates from free-living to symbiotic and propose strategies for future research to better understand coral–dinoflagellate and other eukaryote–eukaryote symbioses. Coral reefs are sustained by long-term symbiosis between coral animals and dinoflagellate algae of the family Symbiodiniaceae.Genomic studies have shed light on the molecular basis of the coral–dinoflagellate symbiosis.Evolutionary mechanisms that underpin the transition of dinoflagellates in the family Symbiodiniaceae from free-living to symbiotic remain largely unknown.Symbiodiniacean dinoflagellates are expected to share common evolutionary trajectories with other intracellular symbionts and parasites.Comparison of the genome features of Symbiodiniaceae with those of other intracellular residents will improve our understanding of their evolutionary history and of other eukaryote–eukaryote symbioses.