Long-read sequencing reveals that the mitochondrial genome of an individual <i>Ixodiphagus hookeri</i> is a mixture of structural variants with an invariable core region and heterogeneous repeat regions

The encyrtid wasp <i>Ixodiphagus hookeri</i> (Hymenoptera: Encyrtidae) predates on a broad range of tick species, including the important disease vectors of the <i>Ixodes ricinus</i> complex. This wasp is a promising candidate for the biological control of tick populations. To support future studies on the biological interaction between ticks and tick wasps, the complete genome sequence of <i>I. hookeri</i> was determined using nanopore long-read technology. This work presents the complete mitochondrial genome of a singular <i>I. hookeri</i>. In-depth annotation of multiple nanopore long reads revealed that the mtDNA genome is a mixture of structural variants. It consists of an invariable ∼15.2-kb core flanked by variable regions. Together, this variable region contains tens of copies of a 92-bp repeat unit, two copies of a ∼340-bp repeat unit, and up to more than 1500 copies of a TA-dinucleotide. Parts of the mtDNA core sequence and the repeat region have integrated a few hundred times into the nuclear genome of <i>I. hookeri</i>. Our study shows that long-read DNA sequencing is essential for reliable <i>de novo</i> assembly of insect mtDNA genomes.