Sequencing the genome and transcriptome of false codling moth, Thaumatotibia leucotreta, for pest management

The development of novel control methods for false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) is an urgent priority for several fruit to maintain market access. Here we aimed to develop a new genomic and transcriptomic toolkit for FCM in order to support novel population control methods and better understand the rapid evolution of, and constraints on, pesticide resistance and environmental stress adaptation.

Here we used PacBio Sequel II long reads and Illumina NextSeq short reads to sequence the genome of an adult FCM male and assembled the genome using a hybrid assembly pipeline and Pilon error correction. Our final assembly was evaluated using BUSCO and compared to that of codling moth to investigate genetic variation in chemosensory ability and insecticide resistance.

The FCM draft genome is 1,283.41Mb in size, similar to other lepidopteran pests. We obtained 35,050 contigs and a scaffold N50 of 54,511bp. The number of complete genes amounts to 95.7% of the conserved genes present in the Lepidopteran database. We found evidence of potential novel odorant receptors in our assembly and a variant in the Octopamine receptor gene associated with insecticide resistance.

This work provides a platform upon which to build future genomic research of this agricultural pest, specifically for the development and optimisation of attractants and potential screening of insecticide resistance in field populations of FCM. Future work should focus on investigating the effect of the identified genes on FCM behaviour and biology in the field.

A high quality draft genome of FCM has been completed. This genomic data will provide a foundational platform and toolkit for innovative pest control programmes, while leading to novel insights into the species’ biology.