Ishii Yuu, Kanamori Shunsuke, Deguchi Ryusaku, Kawata Masakado, Maruyama Shinichiro, Yoshida Takashi, Kamikawa Ryoma
Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
Genome Biol Evol. 2025 Jul 3;17(7). doi: 10.1093/gbe/evaf133.
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.
共生是物种通过生物体间相互作用实现多样化的基础。在热带和亚热带海洋中，属于共生藻科的甲藻共生体，包括共生藻属，支持着包括珊瑚在内的刺胞动物宿主的繁荣，从而通过它们光合产物的碳转移维持了贫营养海洋的生态。虽然共生藻属包括自由生活和共生的物种，但其生活方式差异的详细遗传背景仍不清楚。在本研究中，我们通过检测在共生和自由生活方式多样化过程中经历正选择的基因，鉴定了共生藻属中参与共生进化获得或维持的候选基因。利用多个共生藻基因组检测正选择，共鉴定出35个基因，包括一个编码可溶性淀粉合酶SSY1的基因和与代谢物分泌相关的基因，这些基因可能更适合共生生活方式。特别是，我们的计算机分析表明，SSY1基因家族在一个祖先甲藻中经历了广泛的基因复制，并且检测到的作为正选择的突变发生在其中一个同源物的内在无序区域。与分子进化一致，当在不同的pH值和氮条件下培养时，共生藻的共生和自由生活物种在细胞内淀粉合成/积累的表型上存在差异。这些结果为共生藻与珊瑚的关系提供了分子和表型方面的见解。
