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The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

Cite this dataset

Cohen, Zachary; Schoville, Sean; Hawthorne, David (2024). The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say) [Dataset]. Dryad. https://doi.org/10.5061/dryad.9kd51c5hj

Abstract

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.

README: 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

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) and variant graph suite: vg 1.31.0 (Hickey et al., 2020). It is comprised of four Colorado potato beetle, Leptinotarsa decemlineata, individuals: the existing reference CPB genome (SAMN02376991) (Schoville et al., 2018) , 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:

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 > CPB_Mar18.gfa
./gfatools/gfatools gfa2fa -s CPB_Mar18.gfa > CPB_Mar18_linear.fa

#vg 1.31.0

./vg convert -g CPB_Mar18.gfa -v >  CPB_Mar18.vg
./vg prune -r -p -t 32 CPB_Mar18.vg > CPB_Mar18.pruned.vg

Methods

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.

Funding

Wisconsin Potato and Vegetable Growers Association