Expression of fragmented ribosomal RNA from the mitochondrial genome of Eimeria tenella

Highly fragmented ribosomal RNA-coding sequences are characteristic of mitogenomes of protozoan parasites of the phylum Apicomplexa. Identification of ribosomal RNA encoding sequences in apicomplexan mitogenomes has largely relied on sequence similarity with several apicomplexan species for which expression of these genes has been demonstrated. The present study applied Next-Gen sequencing to investigate the expression of fragmented putative mitochondrial rRNAs in Eimeria tenella, a coccidian parasite of poultry. Expression of 18 of 19 putative rDNA fragments included in the original published E. tenella mitogenome was confirmed. Sequence comparison with Plasmodium falciparum and NGS identified 14 additional putative fragments. Two small RNAs were identified that did not share sequence similarities with other known rDNA sequences. Eight sRNAs were identified that represented smaller chunks of putative rDNA fragments and three were observed that represented two putative rDNA fragments (i.e., polycistronic transcripts). Relative abundances of each sRNA species ranged across three orders of magnitude. Twenty-five of the 45 distinct sRNAs expressed from the mitogenome were polyadenylated in more than 50% of instances. The identification of unique sRNAs without significant homology to known sequences and the observation of polycistronic transcripts highlight the complexity of regulation of expression of the E. tenella mitogenome. The varied relative abundances, presence of shorter RNAs expressed from longer putative rDNA fragments, and variable polyadenylation of these sRNAs highlight additional areas for future work towards better understanding the expression of the mitogenome in this important poultry pathogen. More generally, these findings expand our wider understanding of evolution of apicomplexan mitogenomes.