A molecular phylogeny of dinoflagellate protists (Pyrrhophyta) inferred from the sequence of 24S rRNA divergent domains D1 and D8

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Abstract
The sequence of two divergent domains (D1 and D8) from dinoflagellate 24S large subunit rRNA was determined by primer extension using total RNA as template. Nucleotide sequence alignments over 401 bases have been analyzed in order to investigate phylogenetic relationships within this highly divergent and taxonomically controversial group of protists of the division Pyrrhophyta. Data are provided confirming that dinoflagellates represent a monophyletic group. For 11 out of the 13 investigated laboratory grown species, an additional domain (D2) could not be completely sequenced by reverse transcription because of a hidden break located near its 3′-terminus. Two sets of sequence alignments were used to infer dinoflagellate phylogeny. The first [199 nucleotides (nt)] included conservative sequences flanking the D1 and D8 divergent domains. It was used to reconstruct a broad evolutionary tree for the dinoflagellates, which was rooted usingTetrahymena thermophila as the outgroup. To confirm the tree topology, and mainly the branchings leading to closely related species, a second alignment (401 nt) was considered, which included the D1 and D8 variable sequences in addition to the more conserved flanking regions. Species that showed sequence similarities with other species lower than 60% on average (Knuc values higher than 0.550) were removed from this analysis. A coherent and convincing evolutionary pattern was obtained for the dinoflagellates, also confirmed by the position of the hidden break within the D2 domain, which appears to be group specific. The reconstructed phylogeny indicates that the early emergence ofOxyrrhis marina preceded that of most Peridiniales, a large order of thecate species, whereas the unarmored Gymnodiniales appeared more recently, along with members of the Prorocentrales characterized by two thecal plates. In addition, the emergence of heterotrophic species preceded that of photosynthetic species. These results provide new perspectives on proposed evolutionary trees for the dinoflagellates based on morphology, biology, and fossil records.