Comparative genome and phylogenetic analysis revealed the complex mitochondrial genome and phylogenetic position of Conopomorpha sinensis Bradley.

Conopomorpha sinensis Bradley is a destructive pest that causes severe economic damage to litchi and longan. Previous C. sinensis research has focused on population life tables, oviposition selectivity, pest population prediction, and control technology. However, there are few studies on its mitogenome and phylogenetic evolution. In this study, we sequenced the whole mitogenome of C. sinensis by the third-generation sequencing, and analyzed the characteristics of its mitogenome by comparative genome. The complete mitogenome of C. sinensis is a typical circular and double-stranded structure. The ENC-plot analyses revealed that natural selection could affect the information of codon bias of the protein-coding genes in the mitogenome of C. sinensis in the evolutionary process. Compared with 12 other Tineoidea species, the trnA-trnF gene cluster of tRNA in the C. sinensis mitogenome appears to have a new arrangement pattern. This new arrangement has not been found in other Tineoidea or other Lepidoptera, which needs further exploration. Meanwhile, a long AT repeated sequence was inserted between trnR and trnA, trnE and trnF, ND1 and trnS in the mitogenome of C. sinensis, and the reason for this sequence remains to be further studied. Furthermore, the results of phylogenetic analysis showed that the litchi fruit borer belonged to Gracillariidae, and Gracillariidae was monophyletic. The results will contribute to an improved understanding of the complex mitogenome and phylogeny of C. sinensis. It also will provide a molecular basis for further research on the genetic diversity and population differentiation of C. sinensis.