Full‐length transcriptome profiling of true bug mitochondrial genomes reveals the unique transcriptional regulation during insect evolution

Abstract Heteroptera (Insecta: Hemiptera) represents the most successful radiation of nonholometabolous insects. Most heteropterans have ancestral mitochondrial gene arrangement, while some exhibit rearrangements. To investigate the transcription and regulatory patterns of the mitochondrial genome (mitogenome) and explore the effects of gene arrangement on these patterns, we sequenced the full‐length transcriptomes of 11 representative heteropterans. The results show that mitogenomes were transcribed into complete primary polycistrons on both strands and that the dynamic up‐/down‐regulation of expression levels was common during Heteroptera evolution. In contrast to the strict transcription termination model, we found that the heteropteran mitochondrial transcription termination factor (HmTTF) functions as a bidirectional attenuator and binds to 2 conserved motifs located in the transcription termination regions. Variations in motifs or HmTTF correlate with the weakened transcription attenuation pattern in specific species, but the robust interaction between mitogenome motifs and HmTTF is constantly observed for all tested species, indicating the evolutionary constraint on maintaining a key‐and‐lock relationship between the mitochondrial DNA and its binding proteins. Finally, the mitogenome rearrangements in a few species had little effect on HmTTF‐DNA binding and the transcription mode regardless of the distance between the rearrangement site and transcription termination regions. Taken together, we discovered the unique mitogenome structure and its cis‐/trans‐ regulatory modes in Heteroptera, modifying the traditional transcription model. Our work also illuminated the functional regulation of nuclear‐mitochondrion interaction during insect evolution.