PacBio full-length transcriptome profiling of insect mitochondrial gene expression

Abstract

In this study, we sequenced the first full-length insect transcriptome using the Erthesina fullo Thunberg based on the PacBio platform. We constructed the first quantitative transcription map of animal mitochondrial genomes and built a straightforward and concise methodology to investigate mitochondrial gene transcription, RNA processing, mRNA maturation and several other related topics. Most of the results were consistent with the previous studies, while to the best of our knowledge some findings were reported for the first time in this study. The new findings included the high levels of mitochondrial gene expression, the 3 0 polyadenylation and possible 5 0 m 7 G caps of rRNAs, the isoform diversity of 12S rRNA, the polycistronic transcripts and natural antisense transcripts of mitochondrial genes et al. These findings could challenge and enrich fundamental concepts of mitochondrial gene transcription and RNA processing, particularly of the rRNA primary (sequence) structure. The methodology constructed in this study can also be used to study gene expression or RNA processing of nuclear genomes.

Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes using 5’ and 3’ end small RNAs

“…The mistakes with the previous annotations of mitochondrial coding genes were usually attributed to the irregularity of the start codons (e.g. TTG in Erthesina fullo [3]) and stop codons (e.g. TA and T) in their Coding Sequences (CDSs), which usually begin at the 5' ends by start codons ATG, ATA or ATT and end at the 3' ends by stop codons TAA, TA and T. However, TA and T are completed by polyadenylation to form TAA after RNA cleavage and are thus often ignored.…”

“…Blastx or structure-based covariance models) result in gaps and overlaps in the annotations of mitochondrial genomes and the annotation resolution is limited. In 2017, we constructed the first quantitative transcription map of animal mitochondrial genomes by sequencing the full-length transcriptome of the insect Erthesina fullo Thunberg [3] on the PacBio platform [4] and established a straightforward and concise methodology to improve genome annotation. In 2019, we used 5′ and 3′ end small RNAs (5′ and 3′ sRNAs) [1] to improve genome annotation at 1 bp resolution [5], which was later named as precise annotation.…”

Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region

“…As a result, all genes on both strands of the E. fullo mitochondrial genome were annotated ( Table 1) to update the previous version of annotations which were obtained using PacBio full-length transcripts [4].…”

“…The PacBio full-length transcriptome data was collected from our previous study [4]. The RNA-seq and sRNA-seq data were obtained by sequencing one and three libraries, respectively.…”

“…MITOS [3]), the annotation resolution is still limited because of the diversity in animal mitochondrial genomes, particularly the control regions. Gao et al constructed the first quantitative transcription map of animal mitochondrial genomes [4] by sequencing the full-length transcriptome of the insect Erthesina fullo Thunberg [5] on the PacBio platform and established a straightforward and concise methodology to improve genome annotation, resulting in several findings. These findings included the 3′ polyadenylation and possible 5′ m 7 G caps of rRNAs, the polycistronic transcripts, natural antisense transcripts of mitochondrial genes [5] and two novel lncRNAs in human mitochondrial DNA [2].…”