Abstract

We created a dataset of dinoflagellate transcriptomes to resolve internal phylogenetic relationships of the group. We show that the dinoflagellate theca originated once, through a process that likely involved changes in the metabolism of cellulose, and suggest that a late origin of dinosterol in the group is at odds with dinoflagellates being the source of this important biomarker before the Mesozoic. We also show that nonphotosynthetic dinoflagellates have retained nonphotosynthetic plastids with vital metabolic functions, and propose that one of these may be the evolutionary source of dinoflagellate bioluminescence. Finally, we reconstruct major molecular and morphological transitions in dinoflagellates and highlight the role of horizontal gene transfer in the origin of their unique nuclear architecture.