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

The encyrtid wasp Ixodiphagus hookeri (Hymenoptera: Encyrtidae) predates on a broad range of tick species, including the important disease vectors of the Ixodes ricinus 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. hookeri was determined using nanopore long-read technology. This work presents the complete mitochondrial genome of a singular I. hookeri . 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. hookeri . Our study shows that long-read DNA sequencing is essential for reliable de novo assembly of insect mtDNA genomes. • The mitogenome of Ixodiphagus hookeri consists of an invariable core and a heterogeneous repeat region. • Long-read sequencing is essential for reliable de novo assembly of insect mitogenomes. • The nuclear genome of Ixodiphagus hookeri contains hundreds of nuclear mitochondrial DNA segments.