At different points in their evolutionary history, both euglenids and dinoflagellates independently acquired photosynthesis via secondary endosymbiosis. Accordingly, some representatives of both groups contain at least 3 different genomes within 3 different cellular compartments: the nucleus, the plastid, and the mitochondrion. The general organization of the nucleus is a particularly notable feature that is shared by euglenids and dinoflagellates; both groups possess a conspicuous nucleus with a relatively large nucleolus and permanently condensed chromosomes (Fig. 4.2B and G). The plastids in both groups also share the unusual features of 3 envelope membranes and a tendency to have thylacoids in stacks of 3 (Fig. 4.2E and J) (Taylor, 1987). However, the analogous similarities between euglenozoans and dinoflagellates do not end at the ultrastructural level. As described in the next 3 sections, the molecular processes associated with the nucleus, plastid, and mitochondrion also reflect high levels of convergent evolution.

The nuclear genomes of kinetoplastids and dinoflagellates have both acquired a long list of unusual characteristics. Some of these are unique to one lineage and very different in the other. For example, dinoflagellates have among the largest nuclear genomes known, and these genomes have a very low gene density and permanently condensed chromosomes that lack nucleosomes (McEwan et al., 2008). Kinetoplastid genomes, however, are relatively small, are gene-dense, and remain uncondensed during the cell cycle (Berriman et al., 2005). Both genomes are notorious for their rich representation of modified nucleotides, but the nucleotides themselves are not the same: the hypermodified base J (β-D-glucopyranosyloxymethyluracil) is common in kinetoplastid telomeric regions, whereas dinoflagellates have a high proportion of 5-hydroxymethyluracil and 5-methylcytosine.

However, other dramatic alterations to these genomes have taken place convergently, and interestingly, several characteristics have been altered in the same way in both lineages, in particular relating to how genes are arranged and transcribed, and how transcripts are processed. The canonical, simplified view of eukaryotic gene expression involves a single gene transcribed, capped, polyadenylated, spliced (if introns are present), and exported to the cytosol. Both kinetoplastids and dinoflagellates deviate from this canonical view in 2 significant ways that impact the way expression may be controlled.

The first of these is trans-splicing. The spliceosome is a large multisubunit complex that normally recognizes GT-AG bounded spliceosomal