Single-molecule long-read transcriptome profiling of Platysternon megacephalum mitochondrial genome with gene rearrangement and control region duplication

Abstract

Platysternon megacephalum is the sole living representative of the poorly studied turtle lineage Platysternidae. Their mitochondrial genome has been subject to gene rearrangement and control region duplication, resulting in a unique mitochondrial gene order in vertebrates. In this study, we sequenced the first full-length turtle (P. megacephalum) liver transcriptome using single-molecule real-time sequencing to study the transcriptional mechanisms of its mitochondrial genome. ND5 and ND6 anti-sense (ND6AS) forms a single transcript with the same expression in the human mitochondrial genome, but here we demonstrated differential expression of the rearranged ND5 and ND6AS genes in P. megacephalum. And some polycistronic transcripts were also reported in this study. Notably, we detected some novel long non-coding RNAs with alternative polyadenylation from the duplicated control region, and a novel ND6AS transcript composed of a long non-coding sequence, ND6AS, and tRNA-GluAS. These results provide the first description of a mtDNA transcriptome with gene rearrangement and control region duplication. These findings further our understanding of the fundamental concepts of mitochondrial gene transcription and RNA processing, and provide a new insight into the mechanism of transcription regulation of the mitochondrial genome.

Keywords: CR duplication; Platysternon megacephalum; full-length transcriptome; gene rearrangement; mtDNA.

Figure 1.

Comparison of mitochondrial gene arrangements between typical vertebrates (A) and P. megacephalum (B). ND1–6, and ND4L: subunits 1–6 and 4L of nicotine amid adenine dinucleotide dehydrogenase; A 6 and 8: ATP synthase F0 subunits 6 and 8; CO1–3: cytochrome c oxidase subunits 1–3; 12S and 16S: 12 and 16S rRNA. CR I and II: control region I and II; NC1–3: non-coding spacers 1–3; ØT: pseudo T; OL represents the replication origin of L strand [2].

Figure 2.

The quantitative transcription map of P. megacephalum mitochondrial genomes. Alignments of transcripts on Heavy strand in red color were piled along the positive y-axis. Alignments of transcripts on Light strand in Green color were piled along the negative y-axis. tRNAs were not represented.

Figure 3.

Transcript structures of LncRNAs pm-MDL2-1, pm-MDL2-2, pm-MDL2-3. Arrows represented the alternative polyadenylation sites.

Figure 4.

Comparison of transcription of pm-MDL1 and pm-MDL2. Prepresents tRNA-pro, F represents tRNA-Phe, Q represents tRNA-Gln, ⋆ represents the LncRNA of tRNA-ProAS/CRII/tRNA-GlnAS.

Figure 5.

Models of processing COI to COIII. ⋆ represents putative transcripts, which were not obtained in this study.