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. 2018 Jul 17;1:95.
doi: 10.1038/s42003-018-0098-3. eCollection 2018.

Symbiodinium Genomes Reveal Adaptive Evolution of Functions Related to Coral-Dinoflagellate Symbiosis

Free PMC article

Symbiodinium Genomes Reveal Adaptive Evolution of Functions Related to Coral-Dinoflagellate Symbiosis

Huanle Liu et al. Commun Biol. .
Free PMC article

Erratum in


Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world's coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.

Conflict of interest statement

The authors declare no competing interests.


Fig. 1
Fig. 1
Comparison of Symbiodinium genomes. Number of recovered core eukaryote genes in each genome based on CEGMA, out of the 458 core genes
Fig. 2
Fig. 2
Genome duplication and evolution. a Percentage of genes that are implicated in syntenic collinear blocks within each genome as an indication of genome-fragment duplication. b The probability density of the dN/dS ratio for each pair of homologous genes found within syntenic collinear blocks in the genomes of S. microadriaticum (red: 1688 comparisons, mean 1.75, median 1.36), S. goreaui (yellow: 23499 comparisons, mean 2.04, median 1.65) and S. kawagutii (blue: 745 comparisons, mean 1.90, median 1.47). The S. minutum genome was excluded from this analysis due to incomplete data. Ratios between 0 and 6 are shown. The proportion of gene-pairs with dN/dS ratio >1 is 0.70–0.85 for these three genomes; the proportion of those with a ratio >6 is less than 0.02
Fig. 3
Fig. 3
Testing for positive selection acting on Symbiodinium genomes. a The reference 15-species tree of Symbiodinium, dinoflagellates and Perkinsus marinus (as outgroup) based on single-copy orthologous genes, reconstructed based on a concatenated protein alignment with partition-specific maximum-likelihood model testing using IQtree, following Price and Bhattacharya. Support based on 2000 rapid bootstraps is shown on each internal node, and the branch length is the number of substitutions per site. b Percentage of the 1069 positively selected gene sets in Symbiodinium that are annotated with GO (level 3) terms, shown for principal hierarchies Biological Process, Molecular Function and Cellular Component. The corresponding number of gene sets is shown on each bar
Fig. 4
Fig. 4
Recovery of genes in Symbiodinium. a Meiosis-related genes recovered in the genomes of S. microadriaticum (Clade A), S. minutum (Clade B), S. goreaui (Clade C) and S. kawagutii (Clade F). The first 11 genes are noted as meiosis-specific in Chi et al. b Scytonemin biosynthesis genes in Symbiodinium genomes relative to the coral Acropora digitifera, sea anemone Nematostella vectensis, hydra (Hydra magnipapillata) and the green plant Arabidopsis thaliana. The order of the 18-gene cluster (shown in green arrows) in the cyanobacteria Nostoc punctiforme is used as a reference, with presence (+) and absence (−) of a gene in each species are shown. Figure modified from Shinzato et al

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