1. INTRODUCTION
Animal mitogenome is a highly encoded genome (>90%) since it contains no introns. It typically encodes 37 genes (22 tRNA, 13 PCG and 2 rRNA) functional in oxidative phosphorylation (OXPHOS) process which effects all mitochondrial function either directly or indirectly. Thus, mitochondrial transcription is key to maintain mitochondrial function, both in terms of the expression of oxidative phosphorylation subunits encoded from mitochondria and mtDNA replication. Although advances have been made with more than 40 years of work to elucidate mitochondrial transcription, there are still challenges and contradictions that need to be addressed (Shokolenko and Alexeyev, 2017).
In insect mitogenomes, these “formal” 37 genes are distributed almost equally in heavy (GC-rich) and light (GC-poor) chains, and the entire chains are transcribed as polycistronic units. Accordingly, almost half of each polycistronic unit is not converted into known RNA molecules (mRNA, tRNA or rRNA) after transcripts are processed post- transcriptionally (Figure 1).
Interestingly, novel protein coding genes which are encoded in the mitogenome and not functional in OXPHOS have recently been identified (Caricasole et al. , 2002; Lee, Yen and Cohen, 2013; Lee, Kim and Cohen, 2016). Not only protein coding genes but also novel non-coding RNAs have been found especially in human mitogenomes including lncRNAs (Mercer et al. , 2011; Rackham et al. , 2011; Antonickaet al. , 2013). Even, some non-coding intergenic regions have also been found to be present in the transcripts, especially in mRNAs ofDrosophila (Stewart and Beckenbach, 2009). Consequently, it has been hypothesized that the mitochondrial transcription capacity may be more complex and intense than previously assumed.
Polyadenylation of mitochondrial transcripts can be functionally different when compared to their nuclear counterparts. While it is known that polyadenylation ensures mRNA stability in nuclear transcription, mitochondrial polyadenylation can lead to the degradation of mRNAs (Bouda, Stapon and Garcia‐Diaz, 2019). Especially, non-polyadenylated forms of some mRNAs can induce relatively higher expression and be more stable than the polyadenylated forms, as in the case of humancox1 (Mercer et al. , 2011).
Even processes of the mitochondrial transcription and post-transcriptionally RNA maturation have been studied inDrosophila and sea-urchin, it also needs to be studied in different invertebrates due to the variation of transcription profiles (Cantatore et al. , 1990; Polosa et al. , 2007; Torres, Dolezal, Schlötterer and Ottenwälder, 2009). In this study, we predicted the polyadenylation pattern of the mitogenome of Apis melliferabioinformatically by conducting high-throughput RNA sequencing data. Additionally, we determined the transcription patterns of mitochondrial intergenic regions.