Significance: Kinetoplastids are a group of protists with unique morphology and molecular features. Many have developed a parasitic lifestyle and are economically and medically important causative agents of serious crop, animal, and human diseases. Evolutionarily, Paratrypanosoma confusum sits between parasitic trypanosomatids and free-living bodonids and therefore is uniquely informative for study of the emergence of parasitism. It is morphologically very flexible, as it forms three distinct life stages that can be studied separately. Particularly interesting is the haptomonad stage in which it rebuilds its flagellum into an extensive adhesive plaque. As an adaptation to parasitism, Paratrypanosoma lost a plethora of enzymes involved in breakdown of macromolecules and the capacity of receptor-mediated endocytosis but has gained surface proteins and membrane transporters to obtain nutrients from the host.

In this study, we describe the mitochondrial genome of the excavate flagellate Euglena gracilis . Its gene complement is reduced as compared with the well-studied sister groups Diplonemea and Kinetoplastea. We have identified seven protein-coding genes: Three subunits of respiratory complex I ( nad1 , nad4 , and nad5 ), one subunit of complex III ( cob ), and three subunits of complex IV ( cox1 , cox2 , and a highly divergent cox3 ) . Moreover, fragments of ribosomal RNA genes have also been identified. Genes encoding subunits of complex V, ribosomal proteins and tRNAs were missing, and are likely located in the nuclear genome. Although mitochondrial genomes of diplonemids and kinetoplastids possess the most complex RNA processing machineries known, including trans -splicing and editing of the uridine insertion/deletion type, respectively, our transcriptomic data suggest their total absence in E. gracilis . This finding supports a scenario in which the complex mitochondrial processing machineries of both sister groups evolved relatively late in evolution from a streamlined genome and transcriptome of their common predecessor.