• cloning;
  • deletion;
  • holobiont;
  • Symbiodinium;
  • zoanthid;
  • Zoanthus;
  • zooxanthellae


We sequenced the internal transcribed spacer of ribosomal DNA (ITS-rDNA) of Symbiodinium spp. (Freudenthal) from conspecific Zoanthus sansibaricus (Carlgren) colonies along a latitudinal gradient in Japan. Phylogenetic analysis reveals that Zoanthus in the two northern sites of Kokubu and Sakurajima harbor exclusively Symbiodinium subclade C1, whereas Yakushima Zoanthus harbors Symbiodinium subclades C1 and C15, and southernmost Amami Zoanthus Symbiodinium subclades A1 and C1, indicating holobiont flexibility. Individual Zoanthus colonies associated exclusively with one single subclade, but unexpectedly there was small variation between Symbiodinium ITS-rDNA clone sequences obtained from within individual Zoanthus colonies. There was also a large deletion in the ITS-2/28S rDNA boundary region in one clone sequence, and another large deletion in the 5.8S rDNA region in another clone. Our intracolony sequence heterogeneity might be a result of the presence of multiple copies of the ITS-rDNA region within individual Symbiodinium genomes, or result from the possible presence of closely related Symbiodinium genotypes in the host.