Millepora spp are a group of calcifying hydrocorals that have an important role in the construction of the coral reef framework. They can be found in diverse shallow subtropical/tropical regions around the world, being nearly ubiquitous in the Indo-Pacific and the Caribbean-Atlantic regions. As one of the first cnidarians to lose their microalgal symbionts during bleaching events, Millepora serves as an important indicator of reef health. Okinawa experiences the inflow of warm waters from the Coral Triangle by the Kuroshio Current resulting in a region characterized by exceptional biodiversity. Despite the critical role of symbiotic relationships in coral ecosystems, limited research has focused on the biodiversity of Symbiodiniaceae in Millepora and no such study has been conducted in this region. Our work aims to address this research gap by examining the endosymbiont biodiversity of Millepora specimens previously characterized by Takama et al. 2018 by employing the Internal Transcribed Spacer 2 region (ITS2) from ribosomal internal transcribed spacer (ITS-rDNA). Through the analysis of this genetic marker, we recovered two distinct Symbiodiniaceae clades in our Millepora specimens, corresponding to Symbiodinium (formerly clade A) and Cladocopium (formerly clade C). While genetic analyses of corals or symbionts have been conducted separately in the past, the integration of both components in the Millepora-Symbiodiniaceae association has received limited attention. These insights might have implications for coral reef conservation and management, highlighting the need for further investigations into the genetic dynamics of the Millepora-Symbiodiniaceae association.
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