Characterization of the complete mitochondrial genome of Dendroctonus valens and elimination of nuclear mitochondrial pseudogene interference

Abstract Nuclear mitochondrial pseudogenes (numts) are short, nonfunctional DNA sequences resulting from mitochondrial gene transfer to the nuclear genome; these sequences seriously affect the accuracy of mitochondrial gene for population genetic and phylogenetic analyses. The nuclear genome of Dendroctonus valens (Coleoptera: Curculionidae: Scolytidae), a major forest quarantine pest that seriously threatens the ecological security of pine forests, contains a large number of numts, and these interfere with analyses of genetic variation based on the mitochondrial cox1 gene. To eliminate interference by numts, we sequenced, assembled and analysed the complete mitochondrial genome of D. valens . The mitogenome is a circular molecule of 16,547 bp and shows typical gene content and arrangement. We identified its codon preference, tRNA secondary structure and nucleotide evolution rate. Furthermore, we designed primers for long fragment amplification to eliminate numts in the mitochondrial cox1 gene. Finally, amplified products were sequenced with universal primers, and cox1 gene sequences (464 bp) without numts were successfully obtained. The Heilihe Nature Reserve (harbouring Pinus tabulaeformis ) in Inner Mongolia, is in the early stage of D. valens northward invasion, with a high population genetic diversity. We hypothesized that the high genetic diversity was related to human activities around the reserve and the reproductive characteristics in the early stage of D. valens invasion. The newly developed method resolves the issue of numt interference and lays a foundation for the analyses of genetic diversity in D. valens populations in the region as well as its invasion routes.