Phylogeny of ultra-rapidly evolving dinoflagellate chloroplast genes: A possible common origin for sporozoan and dinoflagellate plastids

Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotund ata, Amphidinium carterae, and Protocertium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heim ii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and ps bA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were cons tructed. Intersite rate variation and invariant sites were allowed fur with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA t rees they are related to those of chromists and red algae, In 23S rRNA tree s, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maxi mum likelihood analysis of Heterocapsa triqutera 16S rRNA also groups the d inoflagellate and sporozoan sequences, but the other methods were inconsist ent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes lit the idea that d inoflagellate chloroplasts originated from red algae by a secondary endosym biosis, possibly the same one as for chromists and Sporozoa. The marked dis agreement between 16S rRNA trees using different phylogenetic algorithms in dicates that this is a rather poor molecule fur elucidating overall chlorop last phylogeny. We discuss possible reasons why both plastid and mitochondr ial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rap id substitution rates and a proneness to unique genomic rearrangements.