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BackgroundThe marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential component of marine ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, and one of the reported differences among phenotypes is their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, the genetic basis for this difference in synthetic capacity is unknown. To understand genetics underlying Symbiodinium diversity, we report two draft genomes, one from clade A, presumed to have been the earliest branching clade, and the other from clade C, in the terminal branch.ResultsThe nuclear genome of Symbiodinium clade A (SymA) has more gene families than that of clade C, with larger numbers of organelle-related genes, including mitochondrial transcription terminal factor (mTERF) and Rubisco. While clade C (SymC) has fewer gene families, it displays specific expansions of repeat domain-containing genes, such as leucine-rich repeats (LRRs) and retrovirus-related dUTPases. Interestingly, the SymA genome encodes a gene cluster for MAA biosynthesis, potentially transferred from an endosymbiotic red alga (probably of bacterial origin), while SymC has completely lost these genes.ConclusionsOur analysis demonstrates that SymC appears to have evolved by losing gene families, such as the MAA biosynthesis gene cluster. In contrast to the conservation of genes related to photosynthetic ability, the terminal clade has suffered more gene family losses than other clades, suggesting a possible adaptation to symbiosis. Overall, this study implies that Symbiodinium ecology drives acquisition and loss of gene families.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4857-9) contains supplementary material, which is available to authorized users.

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Mutualisms are often viewed as reciprocal exploitations that nonetheless provide net benefits to each partner. While the benefits of symbiosis with dinoflagellates of the genus Symbiodinium (zooxanthellae) for corals are well understood, the costs of the association, particularly when under stress, remain a focus of much research. One of the primary impediments to exploring the costs of symbiosis in zooxanthellate corals is that it is impossible to examine the animal host in isolation. Evidence for a cost of symbiosis with zooxanthellae includes the fact that direct transmission of zooxanthellae between generations is rare, particularly in broadcast spawning corals. Fortuitously, the absence of zooxanthellae in oocytes of many species and the ability to readily infect larvae with zooxanthellae provide an opportunity to compare individuals with and without these symbionts. Here, we use this larval model to show that individuals with zooxanthellae have lower survival than those lacking zooxanthellae when exposed to high temperature. Higher activity of anti-oxidant defenses and higher levels of oxidative cellular damage in larvae with zooxanthellae suggest that oxidative stress originating in the symbionts is a cause of tissue damage in the host under heat stress. We hypothesize that this may be one reason for the absence of direct transmission of zooxanthellae in most broadcast spawning corals whose propagules must spend at least 1 d on the ocean surface.