Global-Scale Diversity and Distribution Characteristics of Reef-Associated Symbiodiniaceae via the Cluster-Based Parsimony of Internal Transcribed Spacer 2 Sequences

Photosynthetic species belonging to Symbiodiniaceae play important ecological roles in coral reef ecosystems. Nine phylogenetically supported Symbiodiniaceae clades(each containing multiple genetically distinct molecular types) have been detected in reef-associated animals and in seawater or sediments near coral reef areas. Although major advances in research on Symbiodiniaceae diversity have been made, information on the global-scale diversity and distribution characteristics of Symbiodiniaceae clades/types is still limited or must be expanded because most studies on Symbiodiniaceae have mainly focused on a limited number of hosts associated with Symbiodiniaceae or coral reef areas. Here, the diversity and distribution characteristics of Symbiodiniaceae data derived from reef-associated animals and seawater or sediments near coral reef areas were analyzed using 3899 qualified Symbiodiniaceae internal transcribed spacer 2(ITS2) sequences retrieved from the GenBank database in May 2017. These sequences were annotated as Symbiodiniaceae ITS2 types via sequence alignment against database of Symbiodiniaceae ITS2 types. Results showed that photosynthetic Symbiodiniaceae ITS2 sequences could be annotated as 119 Symbiodiniaceae ITS2 types within nine clades(A–I), and Symbiodiniaceae ITS2 types mainly inhabited coral reefs between 30?N and 30?S. Symbiodiniaceae ITS2 types could be associated with multiple host taxa. Interestingly, these results implied that the distribution of Symbiodiniaceae ITS2 types was distinct in the Atlantic Ocean, the Red Sea, the Mediterranean Sea, and the Indo-Pacific Ocean. Although future field research should be performed to verify our results, this study provided a broad perspective of the diversity of Symbiodiniaceae clades/types on a global scale.

Genotype and Phylogenetic Diversity of Symbiodinium ITS2 Sequences Within Clade C in Three Typical Coral Species from Luhuitou Fringing Reef of the South China Sea

Dinoflagellates in the genus Symbiodinium, including nine clades(A–I), mainly form mutualistic symbioses with corals. More than 100 Symbiodinium molecular types have been identified by the ITS2-based genotype method within any given clade, and specifically within Symbiodinium clade C. However, the genotype identification method using the ITS2 sequence is likely to lead to high diversity estimates due to the intra-genomic variations in the ITS2 space; thus, further validation is essential for a correct identification. In this study, the molecular diversity of Symbiodinium ITS2 sequences cloned from two stone corals, Acropora sp. SY-01 and Pocillopora sp. SY-05, and one soft coral, Sarcophyton sp. SY-07, living in the northern part of South China Sea(SCS), were analyzed and compared using the ITS2-based genotype identification method, coupled with ITS2-based secondary structural and phylogenetic analyses. As the result, 12 Symbiodinium ITS2 genotypes were identified, while only six and three Symbiodinium ITS2 genotypes were supported by ITS2-based secondary structural and phylogenetic analyses, respectively. In addition, no shared Symbiodinium ITS2 genotypes were observed among the three coral species, suggesting coral species-dependent Symbiodinium genotypes were within clade C. In summary, the present study provides a theoretical basis for validating the molecular diversity of Symbiodinium ITS2 genotypes in corals.