DOI: 10.5061/dryad.9kd51c5hj
title: The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

description: 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 &gt;100-fold improvement of contiguity and include derived
 pest and ancestral non-pest individuals. We identify &gt;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.
description: 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.
description: # The role of structural variants in pest adaptation and genome evolution
 of the Colorado potato beetle, Leptinotarsa decemlineata (Say)
 [https://doi.org/10.5061/dryad.9kd51c5hj](https://doi.org/10.5061/dryad.9kd51c5hj) ## Description of the data and file structure This is a reference-based pangenome assembly that was generated using both minigraph v0.14-r425-dirty (Li et al., [2020](https://onlinelibrary.wiley.com/doi/full/10.1111/mec.16838#mec16838-bib-0048)) and variant graph suite: vg 1.31.0 (Hickey et al., [2020](https://onlinelibrary.wiley.com/doi/full/10.1111/mec.16838#mec16838-bib-0039)). It is comprised of four Colorado potato beetle, *Leptinotarsa decemlineata*, individuals: the existing reference CPB genome (SAMN02376991) (Schoville et al., [2018) ](https://onlinelibrary.wiley.com/doi/full/10.1111/mec.16838#mec16838-bib-0066), Maryland Sire I, Colorado Dam I (reference assembly for pangenome), and Oregon Dam II.  Sharing/Access information Links to other publicly accessible locations of the data: * [Generic sample from Leptinotarsa decemlineata - BioSample - NCBI (nih.gov)](https://ncbi.nlm.nih.gov/biosample/SAMN02376991) ## Code/Software \#minigraph v0.14-r425-dirty  ``` ./minigraph/minigraph -xggs -t4 F_KSCO_60.fasta F_Oregon_60.fasta Ldec_2018LI_60.fasta M_MD_contigs2.fasta &gt; CPB_Mar18.gfa ``` ``` ./gfatools/gfatools gfa2fa -s CPB_Mar18.gfa &gt; CPB_Mar18_linear.fa ``` \#vg 1.31.0 ``` ./vg convert -g CPB_Mar18.gfa -v &gt; CPB_Mar18.vg ./vg prune -r -p -t 32 CPB_Mar18.vg &gt; CPB_Mar18.pruned.vg ```