Positive selection of a starch synthesis gene and phenotypic differentiation of starch accumulation in symbiotic and free-living coral symbiont dinoflagellate species

Abstract

Symbiosis is a basis for species diversification through interactions between organisms. In tropical and subtropical oceans, dinoflagellate symbionts belonging to the family Symbiodiniaceae, including the genus Symbiodinium, support the flourishment of cnidarian hosts, including corals, and thereby the ecology of oligotrophic oceans through their photosynthate carbon transfers. Although the genus Symbiodinium includes both free-living and symbiotic species, the detailed genetic background of their lifestyle differences remains unclear. In this study, we identified candidate genes involved in the evolutionary acquisition or maintenance of symbiosis in Symbiodinium spp. by detecting genes that have undergone positive selection during symbiotic and free-living lifestyle diversification. Using multiple Symbiodinium genomes to detect positive selection, 35 genes were identified, including a gene encoding soluble starch synthase SSY1 and genes related to metabolite secretion, which may be preferred for symbiotic lifestyles. In particular, our in silico analyses revealed that the SSY1 gene family has undergone extensive gene duplications in an ancestral dinoflagellate, and that the mutations detected as positive selection have occurred in the intrinsically disordered region of one of the homologs. Consistent with molecular evolution, the phenotypes of intracellular starch synthesis/accumulation were distinct between the symbiotic and free-living species of Symbiodinium when cultured under different pH and nitrogen conditions. These results provide molecular and phenotypic insights into symbiotic Symbiodinium-coral relationships. Significance statementClarifying how coral symbiont algae of the family Symbiodiniaceae are functionally diversified is crucial for understanding the molecular mechanisms of symbiotic relationships and interactions in animal-algal symbioses. However, gene-level molecular evolution that contributes to symbiotic relationships remains unclear. Our genome-wide single-gene analyses of the genus Symbiodinium, comprising both symbiotic and free-living species, successfully detected several dozen protein-coding genes that underwent symbiont-specific positive selection after divergence from the free-living species in the genus. Furthermore, our cultivation experiments demonstrated differences in photosynthate-related phenotypes between the symbiotic and free-living species. Our findings provide a key to illuminating the molecular evolution involved in phenotypic changes that potentially contribute to symbiotic lifestyles in Symbiodinium.