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

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 annotati..., 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., , # 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. 

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结构变异（structural variation）已在多样类群中与遗传多样性及适应性演化建立关联。尽管已有此类发现，但目前仍不明其在微演化中的相对重要性，尤其是在快速适应性物种种群中，相较于已知的多样性驱动因子（如核苷酸替换）而言。
在此，我们针对农业超级害虫科罗拉多马铃薯甲虫（*Leptinotarsa decemlineata*）的抗药性演化过程，探究结构变异（SVs）的重要性。本研究采用亲子三代测序方案，构建了高连续性的参考基因组，以表征该物种体内的结构变异。这些更新后的组装结果在连续性上提升超100倍，样本涵盖衍生的害虫种群与祖先型非害虫个体。
本研究共鉴定出超20万个结构变异，其在基因组中的分布并非随机，而是与转座元件及基因存在共现现象。结构变异在大量基因注释的外显子区域发生重叠……
研究结合长读长与短读长全基因组测序方案，使用SPAdes与Canu组装软件进行基因组组装，随后开展质量校验，并通过minigraph完成多份全基因组序列比对。

# 科罗拉多马铃薯甲虫（*Leptinotarsa decemlineata* (Say)）的结构变异在害虫适应性与基因组演化中的作用
https://doi.org/10.5061/dryad.9kd51c5hj

## 数据与文件结构说明
本数据集为基于参考序列的泛基因组（pangenome）组装结果，通过minigraph v0.14-r425-dirty（Li等人，[2020](https://onlinelibrary.wiley.com/doi/full/10.1111/mec.16838#mec16838-bib-0048)）与变异图形套件vg 1.31.0（Hickey等人，[2020](https://onlinelibrary.wiley.com/doi/full/10.1111/mec.16838#mec16838-bib-0039)）共同构建完成。
该组装包含4只科罗拉多马铃薯甲虫（*Leptinotarsa decemlineata*）个体：现有CPB参考基因组（SAMN02376991，Schoville等人，[2018](https://onlinelibrary.wiley.com/doi/full/10.1111/mec.16838#mec16838-bib-0066)）、马里兰父本I（Maryland Sire I）、科罗拉多母本I（Colorado Dam I，泛基因组参考组装样本）以及俄勒冈母本II（Oregon Dam II）。

## 数据共享与获取说明
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