the 3 protein-coding genes map to a linear, tandem repeat with rRNA fragments interspersed (Feagin, 2000). In dinoflagellates, the same coding regions are present, but the organization is much more complex. Here, multiple copies of each gene are found in various orientations on linear chromosomes of varying size. In some species, all possible permutations of 3 genes are adjacent, whereas in others chromosomes seem to contain copies of only 1 gene. Chromosomes also contain rRNA fragments, and substantial noncoding regions, and some have been shown to have structurally complex ends characterized by families of repeats (Jackson et al., 2007; Slamovits et al., 2007; Nash et al., 2008).
In kinetoplastids, the evolution of the complex genome organization is tightly linked to how genes are expressed, and specifically to RNA editing. The genes, such as they are, are encoded on the maxicircles and expressed as polycistronic mRNAs, but after processing into monocistrons these messages are then massively altered by the insertion and deletion of uridine residues (up to 553 insertions and 89 deletions in a single mRNA). Editing is mediated by hundreds of small guide (g) RNAs in an elaborate process involving numerous multisubunit protein complexes (Lukeš et al., 2005; Hashimi et al., 2008). The gRNAs that contain the information that directs editing are encoded on the minicircles, so the breakup of the genome into 2 chromosome types is likely linked to the evolution of editing.
In dinoflagellates, RNA editing has also been found to be widespread, but the process is mechanistically different and in no way related to the breakdown of the genome structure. Here, transcripts are edited at ≈2% of their positions via substitutional editing, as opposed to insertion/deletion editing (Lin et al., 2002; Nash et al., 2008; Zhang and Lin, 2008). Although A to G is the most common substitution, several others have been observed (U → C, G → C, G → A, A → C, and C → U), suggesting a highly flexible and sophisticated editing mechanism (Nash et al., 2008; Zhang and Lin, 2008). Fragments of edited gene sequences have been found in dinoflagellate mitochondrial genomes, prompting the suggestion that they employ gRNAs similar to that of kinetoplastids (Nash et al., 2007). However, the genomes are prone to recombination, so the significance of these fragments remains unclear; overall, there is no direct evidence for any particular editing mechanism at present. It is worth noting that mitochondrial transcripts in dinoflagellates have substantial polyadenylated tails, a feature linked to the editing process in kinetoplastids (Etheridge et al., 2008), and generally very rare in organelles.
The limited data further indicate that uridine insertion type of RNA editing might even coexist with trans-splicing in diplonemids (Marande and Burger, 2007). We predict that the extreme diversity of editing types documented in the dinoflagellate mitochondrion (Zhang and Lin, 2008) also requires poorly understood albeit complex protein machinery that is