The dinoflagellate is a member of the eukaryotes that belong to a diverged protist group, Alveolata. Because the nuclei show several unusual features not observed in other eukaryotes, the nucleus in the "core" or typical dinoflagellate is especially called a "dinokaryon". Chromosomes in the dinokaryon are condensed throughout the whole cell cycle and show a cholesteric liquid crystal organization. Its nucleosome lacks the "beads on a string" structure which is commonly observed in eukaryotic nuclei. Despite the existence of canonical histone protein-coding genes, those proteins are not found in the dinokaryon, while certain proteins showing amino acid sequences similar to bacterial or viral proteins are abundantly contained in the dinokaryon. The dinoflagellate genome carries some rare bases such as 5-hydroxymethyluracil, and TTTT repeats exist as a possible transcription initiator element instead of the TATA box. A comprehensive transcriptome analysis of the EST database using a variety of dinoflagellates including ancestral to divergent species showed that SL trans-splicing is required for transcript maturation.
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