The Genome of Symbiodinium kawagutii Illuminates Dinoflagellate Gene Expression and Coral Symbiosis

Coral reefs, and the biological diversity they foster, ultimately depend on symbiotic dinoflagellates belonging to the genus Symbiodinium. Unfortunately, attempts to understand this symbiosis have been hampered by the paucity of genome sequence for the dinoflagellate partner. Here we report the analysis of a 935 Mbp high-quality assembly derived from the 1.18 Gbp genome of Symbiodinium kawagutii. We annotated 36,850 protein-coding genes including 11,833 S. kawagutii-specific novel gene families. The genome shows active (retro)transposition and expansion of some gene families, in particular those regulating DNA modification, N and P nutrient (including phosphonate) uptake mechanisms, metabolite transporters, and stress response machinery. These later represent key adaptations for survival in both oligotrophic and symbiotic environments. Importantly, we find extensive complementarity between the S. kawagutii genome and that of the anthozoan Acropora, presumably a result of host-symbiont co-evolution. This study provides an essential genomic resource for elucidating the basic molecular biology of the dinoflagellates and for understanding coral-Symbiodinium symbiosis.