Genome assembly of Thaumatotibia leucotreta, a major polyphagous pest of agriculture in sub-Saharan Africa.

The False Codling Moth (FCM) (Meyrick) (Thaumatotibia leucotreta; Lepidoptera: Tortricidae) is a highly polyphagous, major agricultural pest indigenous to sub-Saharan Africa. With growing international trade there is increasing concern about introducing this pest into other countries. In South Africa, FCM poses a risk to multiple crops, and is currently suppressed through a combination of chemical, microbial, cultural, augmentative biological control and the sterile insect technique. Compared to other lepidopteran agricultural pests, such as codling moth Cydia pomonella, genetic and other -omic resources for FCM have not been as well developed and/or not made publicly available to date. The need to develop genomic resources to address questions around insecticide resistance, chemosensory capabilities and, ultimately, develop novel control (e.g. gene editing) of this pest is highlighted. In this study, an adult male was sequenced using longread PacBio Sequel II reads and Illumina NextSeq short reads and assembled using a hybrid assembly pipeline and Pilon error correction. Using the chromosome-level genome assembly of C. pomonella we performed comparative analysis, and arranged FCM scaffolds to chromosomes, and investigated genetic variation related to insecticide resistance and chemosensory capabilities. This work provides a platform upon which to build future genomic research on this economically-important agricultural pest.