Sequencing, assembly and annotation of the whole-insect genome of Lymantria dispar dispar, the European gypsy moth

Abstract

The European gypsy moth, Lymantria dispar dispar (LDD), is an invasive insect and a threat to urban trees, forests and forest-related industries in North America. For use as a comparator with a previously published genome based on the LD652 pupal ovary-derived cell line, as well as whole-insect genome sequences obtained from the Asian gypsy moth subspecies L. dispar asiatica and L. dispar japonica, the whole-insect LDD genome was sequenced, assembled and annotated. The resulting assembly was 998 Mb in size, with a contig N50 of 662 Kb and a GC content of 38.8%. Long interspersed nuclear elements constitute 25.4% of the whole-insect genome, and a total of 11,901 genes predicted by automated gene finding encoded proteins exhibiting homology with reference sequences in the NCBI NR and/or UniProtKB databases at the most stringent similarity cutoff level (i.e., the gold tier). These results will be especially useful in developing a better understanding of the biology and population genetics of L. dispar and the genetic features underlying Lepidoptera in general.

Keywords: European gypsy moth; Illumina short-read polishing; Lepidoptera; PacBio long-read assembly; automated gene finding; gypsy moth genomics; whole-genome sequencing.

Figure 1

L. dispar dispar genome assembly and annotation pipeline. The automated pipeline used to assemble the European gypsy moth genome, as well as annotate repetitive content and nuclear protein coding genes, is a modified version of the methods used for annotating the Asian gypsy moth genomes, L. dispar asiatica and L. dispar japonica (Hebert et al. 2019). (The Bombyx mori image is copyright Freepik 2018 and reproduced here with permission.)