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Dinoflagellates belong to one of the most strongly supported macrolineages among the protists, the superphylum/kingdom Alveolata. This superphylum contains three phyla, the Dinoflagellata, the Apicomplexa and the Ciliata, all of which have cortical alveoli and micropores. As more taxa have been added to the molecular analyses and/or more genes have been used, our understanding of phylogenetic relationships within the dinoflagellates has changed and this is also true at the species level. Notwithstanding the fact that most analyses have focused at the genus level, cryptic species have been uncovered in some cases at the species level. Below species level however, microsatellites have shown immense spatial fragmentation in dinoflagellate populations. Expressed sequence tags (EST) libraries have been constructed for several species to try to understand toxin gene expression in relationship to stress conditions. Initial annotation results indicated that a low percentage of the genes could be annotated. Recent advances have pushed this level to nearly 29% of ESTs. Some common responses to stress conditions have been noted. Toxin genes been only been identified in EST libraries that have been screened by 454 sequencing Illumina. The complete genome of Heterocapsa circularisquama is near completion.

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