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The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)
  • Zachary Cohen,
  • D J Hawthorne,
  • Sean Schoville
Zachary Cohen
University of Wisconsin Madison

Corresponding Author:[email protected]

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D J Hawthorne
University of Maryland
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Sean Schoville
University of Wisconsin Madison
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Abstract

Structural variations (SVs) have 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 SVs in pesticide resistance evolution of the agricultural super-pest, the Colorado potato beetle, Leptinotarsa decemlineata. By employing a trio-binning procedure, we develop near chromosomal 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. SVs intersect exons for genes associated with insecticide resistance, development, and transcription, most notably cytochrome P450 (CYP) genes. To understand the role that SVs might play in adaptation, we incorporate an additional 66 genomes among pest and non-pest populations of North America into the SV graph. Single nucleotide polymorphisms (SNPs) and SVs have a similar proportion in coding and non-coding regions of the genome, but there is a deficit of SNPs in SVs, suggesting SVs may be under selection. Using multiple lines of evidence, we identify 28 positively selected genes that include 337 SVs and 442 outlier SNPs. Among these, there are four associated with insecticide resistance. Two of these genes (CYP4g15 and glycosyltransferase-13) are physically linked by a structural variant and have previously been shown to be co-induced during insecticide exposure.
28 Jul 2021Submitted to Molecular Ecology
29 Jul 2021Submission Checks Completed
29 Jul 2021Assigned to Editor
08 Sep 2021Reviewer(s) Assigned
22 Sep 2021Review(s) Completed, Editorial Evaluation Pending
27 Sep 2021Editorial Decision: Revise Minor
06 Dec 2021Review(s) Completed, Editorial Evaluation Pending
06 Dec 20211st Revision Received
16 Dec 2021Reviewer(s) Assigned
03 Feb 2022Editorial Decision: Revise Minor
18 Mar 2022Review(s) Completed, Editorial Evaluation Pending
18 Mar 20222nd Revision Received
02 Apr 2022Reviewer(s) Assigned
09 Jun 2022Editorial Decision: Revise Minor
10 Jul 2022Review(s) Completed, Editorial Evaluation Pending
10 Jul 20223rd Revision Received
08 Aug 2022Editorial Decision: Revise Minor
12 Aug 2022Review(s) Completed, Editorial Evaluation Pending
12 Aug 20224th Revision Received
05 Sep 2022Editorial Decision: Revise Minor
05 Oct 2022Review(s) Completed, Editorial Evaluation Pending
05 Oct 20225th Revision Received
01 Nov 2022Editorial Decision: Revise Minor
30 Nov 2022Review(s) Completed, Editorial Evaluation Pending
30 Nov 20226th Revision Received
15 Dec 2022Editorial Decision: Accept
Mar 2023Published in Molecular Ecology volume 32 issue 6 on pages 1425-1440. 10.1111/mec.16838