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\begin{document}

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



\author[1]{Zachary Cohen}%
\author[2]{D J Hawthorne}%
\author[1]{Sean Schoville}%
\affil[1]{University of Wisconsin Madison}%
\affil[2]{University of Maryland}%


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  \date{May 26, 2024}


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\begin{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
\textgreater{}100-fold improvement of contiguity and include derived
pest and ancestral non-pest individuals. We identify
\textgreater{}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.%
\end{abstract}%



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