Comparison of phylogenies based on nuclear-encoded SSU rDNA and plastid-encoded psbA in the symbiotic dinoflagellate genus Symbiodinium

The genus Symbiodinium comprises mostly symbiotic dinoflagellates that form a mutual association with a wide variety of marine protists and invertebrates. It is widely believed that the taxa included in it are genetically diverse. In the present study, the messenger RNA of psbA (which encodes the D1 protein of photosystem II) was located within the Symbiodinium plastids by using in situ hybridization at the electron microscopic level, directly indicating that the psbA gene from this genus is plastid encoded. The psbA gene sequences of Symbiodinium strains, which had already been shown to belong to various clades based on the phylogeny of nuclear-encoded small-subunit ribosomal DNA (SSU rDNA), were determined by reverse transcription–polymerase chain reaction (RT-PCR), cloning and sequencing. Based on their sequence data, phylogenetic analyses were then performed. The topologies of the nuclear SSU rDNA and psbA trees were similar, suggesting that these two genes from different organelles (nucleus and plastid) had evolved in parallel in the genus Symbiodinium and that psbA would be useful for inferring the phylogenetic relationship within the genus. In Symbiodinium, the psbA gene evolves 1.2–18.2 times faster than nuclear SSU rDNA.