Comparative mitochondrial genome and transcriptome analyses reveal strain-specific features of RNA editing in Trypanosoma brucei

Trypanosoma brucei, a kinetoplastid parasite, cycles between a tsetse fly vector and a mammalian host, undergoing profound changes in cell architecture and metabolism. Central to these transitions are modifications in mitochondrial structure, volume, and energy production. The parasite’s mitochondrial genome is highly complex, comprising a few maxicircles that encode proteins and rRNAs, and thousands of minicircles that encode guide RNAs (gRNAs). Most messenger RNAs (mRNAs) sustain gRNA-directed U-insertion/deletion editing to acquire functional protein-coding sequences. Although the minicircle repertoire varies among isolates and environmental conditions, the extent and biological significance of this variability in commonly used laboratory strains remain unclear. Here, we analyzed mitochondrial genomes and transcriptomes of the developmentally competent AnTat1.1 strain, the differentiation-incapable Lister 427 strain, and transgenic derivatives of Lister 427. While maxicircle sequences are broadly conserved and stable, minicircles differ markedly in sequence complexity, relative abundance, and gRNA gene content. These variations likely affect the efficiency and accuracy of mRNA editing. Compared with Lister 427, the AnTat1.1 strain retains greater minicircle diversity, longer predicted gRNA–mRNA duplexes, and higher editing fidelity. By examining cell lines with distinct developmental capacities and cultivation histories, our findings reveal how mitochondrial genomes evolve in response to changing environmental contexts.