Preliminary phylogenetic analysis of plastid‐encoded genes from an anomalously pigmented dinoflagellate Gymnodinium mikimotoi (Gymnodiniales, Dinophyta)

SUMMARY We cloned and sequenced three plastid‐encoded genes, psbA (encoding D1 protein), psaA (encoding P700 chlorophyll a apoprotein) and the small‐subunit ribo‐somal RNA (pl‐SSU rRNA) from an anomalously pigmented dinoflagellate, Gymnodinium mikimotoi Miyake et Kominami ex Oda, with a plastid containing 19′‐hexanoyloxyfucoxanthin, 19′‐butanoyloxyfucoxanthin and fucoxanthin instead of peridinin as the major carot‐enoids. Molecular phylogenetic trees based on the deduced amino acid sequences of D1 and P700 chlorophyll a apoprotein and nucleotide sequence of pl‐SSU rRNA were then constructed separately. In the D1 tree, G. mikimotoi and typically pigmented dinofl age Nates harboring a peridinin type plastid were monophyletic and G. mikimotoi was positioned most basally within the dinoflagellate lineage. The dinoflagellate lineage was the sister group of heterokonts and the dinoflagellates/heterokonts lineage was clustered with the rhodophytes/cryptophyte lineage. In the P700 chlorophyll a apoprotein phylogenetic tree, G. mikimotoi was clustered with a rhodo‐phyte, a cryptophyte and a heterokont. In the pl‐SSU rRNA tree, G. mikimotoi and haptophytes constituted a monophyletic group associated with rhodophytes and heterokonts. These results, derived from the three phylogenetic analyses, support the hypothesis that the plastid of G. mikimotoi belongs to the rhodoplast lineage. Although we have previously demonstrated that D1 from peridinin type dinofl age Nates lacks a ‘C‐terminus extension’ (which should be removed by proteolytic cleavage from the D1 precursor), the D1 from G. mikimotoi revealed a C‐terminus extension that is different from those of other photosynthetic organisms with respect to the length of the amino acid residues.