Within the Euglenozoa as a whole, mitochondrial genomes are generally odd. The euglenid mitochondrial genomes are experimentally refractive and remain poorly known (M. W. Gray, personal communication). The mitochondrion of related diplonemids was recently shown to harbor genomes of unprecedented organization, with fragments of genes residing on minicircles, which are assembled in the correct order posttranscriptionally by means as yet unknown (Marande et al., 2005). Virtually nothing is known about the form or content of the giant kDNAs in bodonid flagellates, which are estimated to comprise millions of base pairs (Lukeš et al., 1998), whereas the kDNA networks of trypanosomatids are among the best studied and most complex mitochondrial genomes known. They are composed of circular DNA molecules that are relaxed and catenated into a single 3-dimensional network. These networks are composed of dozens of maxicircles, which are equivalents of classical mitochondrial genome, and thousands of minicircles (Lukeš et al., 2005) involved in editing, discussed below. The gene content of the maxicircle genome is not unusual, except for the complete absence of tRNA genes. tRNAs have been demonstrated to be imported from the cytosol into the tRNA-lacking organelle of T. brucei, so that the prokaryotic translation system of the mitochondrion must cope with imported eukaryotic tRNAs (Crausaz-Esseiva et al., 2004). The only exception is tRNAMet-i, the import of which is blocked because it cannot function in the prokaryotic system. Instead, tRNAMet formyl-transferase is present, which formylates the translation initiator tRNAMet-e upon import (Tan et al., 2002).
Within alveolates, mitochondrial genome evolution has also taken more than its share of strange turns. Although the circular mitochondrial genome of ciliates is undistinguished in both form and content, the genomes in apicomplexans and dinoflagellates are both highly reduced and often scrambled (Feagin, 2000; Slamovits et al., 2007; Nash et al., 2008). These lineages have the smallest mitochondrial genomes known, with most species examined with just 3 protein-coding genes: cox1, cox3, and cob (strictly speaking, the dinoflagellate Oxyrrhis has only 2 genes since cob and cox3 are expressed as a fusion) (Slamovits et al., 2007). The only other coding regions are small fragments of rRNAs. These do not amount to an entire copy of either large or small subunit rRNAs, so fragments are all thought to be important and the functional RNAs assembled by base pairing interactions. As with kinetoplastids, no tRNAs are encoded in these genomes, and they have been shown to be imported into apicomplexan mitochondria. Moreover, apicomplexans also block the import of tRNAMet-i, and use tRNAMet formyl-transferase to formylate the translation initiator tRNAMet-e. Indeed, kinetoplastids and apicomplexans have independently evolved very similar tRNA import mechanisms to cope with this unique lack of tRNAs (Bouzaidi-Tiali et al., 2007). In apicomplexans,