Molecular phylogeny of symbiotic dinoflagellates inferred from partial chloroplast large subunit (23S)-rDNA sequences

Symbiotic associations between invertebrates and dinoflagellates of the genus Symbiodinium are a common occurrence in marine environments. However, despite our extensive knowledge concerning the physiological contributions of these algae to their symbiotic partners, our understanding of zooxanthella phylogenetics is still in its early stages. In the past 10 years, studies of Symbiodinium phylogenetics have relied solely on nuclear ribosomal (rDNA) genes. To date, organellar DNA sequences have not been employed to infer phylogenies for this genus of symbiotic dinoflagellates. We address this by presenting the first Symbiodinium phylogeny based on chloroplast (cp) large subunit (23S)-rDNA sequences. Cp23S-rDNA Domain V sequences were determined for 35 dinoflagellate cultures isolated from a range of invertebrate host species and geographical locations. Symbiodinium phylogenies inferred from cp23S-rDNA produced topologies that were not statistically different from those generated from nuclear rDNA, providing the first independent evidence supporting the published major clades of Symbiodinium. In addition, comparisons of sequence dissimilarity indicated that cp23S-rDNA Domain V evolves 9-30 times faster than the V1-V4 regions of nuclear small subunit (n18S)-rDNA, 1-7 times as fast as the D1-D3 regions of nuclear large subunit (n28S)-rDNA, and 0.27-2.25 times that of the internal transcribed spacer (ITS)-rDNA region. Our data suggested that cp23S-rDNA Domain V will prove to be a useful molecule for exploring Symbiodinium phylogenetics.