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In the protist Diplonema papillatum (Diplonemea, Euglenozoa), mitochondrial genes are systematically fragmented with each nonoverlapping piece (module) encoded individually on a distinct circular chromosome. Gene modules are transcribed separately, and precursor transcripts are assembled to mature mRNA by a trans-splicing process of yet unknown mechanism. Expression of the cox1 gene that consists of nine modules, also involves RNA editing by which six uridines are added between Modules 4 and 5. Here, we investigate whether the unusual features of cox1 are shared by all Diplonemea and what the mechanism of trans-splicing might be. We examine three additional species representing both Diplonemea genera, namely D. papillatum described before, and D. ambulator, Diplonema sp.2, and Rhynchopus euleeides and discover that in all Diplonemea, the cox1 gene is discontinuous and split …