Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element

Background: Annotation of mitochondrial (mt) genomes is indispensable for fundamental research in many fields, including mt biochemistry, physiology, and the molecular phylogenetics and evolution of animals. Moreover, high-resolution annotation of animal mt genomes can be used to investigate RNA processing, maturation, degradation, and even the regulation of gene expression. In this study, we used long-PCR amplification combined with Next-Generation Sequencing (NGS) to obtain complete mt genomes of individual ticks and performed precise annotation of these mt genomes. We aimed to: (1) develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal containing miniscule DNA; (2) provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) use these mt genomes containing two Control Regions (CRs) to confirm our previous findings from those containing one CR. Results: Based on these mt genome annotations, most of our findings were consistent with those from previous studies. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human. All the detected DNA variations within a single human cell were CNV of STRs, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and could produce deleterious proteins. Conclusions: We proposed that the accumulation of CNV of STRs in mitochondria causes aging or diseases. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.