Structural variation has been associated with genetic diversity and adaptation in diverse taxa. Despite these observations, it is not yet clear what their relative importance is for microevolution, especially with respect to known drivers of diversity, e.g., nucleotide substitutions, in rapidly adapting species. Here we examine the significance of structural variants (SVs) in pesticide resistance evolution of the agricultural super-pest, the Colorado potato beetle, Leptinotarsa decemlineata. By employing a parent offspring trio sequencing procedure, we develop highly contiguous reference genomes to characterize structural variation within this species. These updated assemblies represent >100-fold improvement of contiguity and include derived pest and ancestral non-pest individuals. We identify >200,000 SVs, which appear to be non-randomly distributed across the genome as they co-occur with transposable elements and genes. SVs intersect exons for a large proportion of gene annotations (~20%) and are associated with insecticide resistance, development, and transcription, most notably cytochrome P450 (CYP) genes. To understand the role that SVs might play in adaptation we measure allele frequencies of SVs for an additional 57 individuals, using whole genome resequencing data, representing pest and non-pest populations of North America. Incorporating multiple independent tests of significance using SNP data, we identify 14 positively selected genes that include SVs and SNPs of elevated frequency within the sampled pest lineages. Among these, four are associated with insecticide resistance. One of these genes, glycosyltransferase-13, is a duplicated gene enclosed within a structural variant that resides inside the CYP4g15 genic region. Both gene products have been observed to be co-induced during insecticide exposure. These results demonstrate the significance of structural variations as a genomic feature to describe species history, genetic diversity, and adaptation.

A combination of long and short read whole genome sequencing, using SPAdes and Canu assemblers, followed by quality curation and multiple whole genome sequence alignment in minigraph.