Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for >1000 Arabidopsis (Arabidopsis thaliana) accessions focused on small variations and did not include CNVs. Here, we performed genome-wide analysis and identified large indels (50 to 499 bp) and CNVs (500 bp and larger) in these accessions. The CNVs fully overlap with 18.3% of protein-coding genes, with enrichment for evolutionarily young genes and genes involved in stress and defense. By combining analysis of both genes and transposable elements (TEs) affected by CNVs, we revealed that the variation statuses of genes and TEs are tightly linked and jointly contribute to the unequal distribution of these elements in the genome. We also determined the gene copy numbers in a set of 1060 accessions and experimentally validated the accuracy of our predictions by multiplex ligation-dependent probe amplification assays. We then successfully used the CNVs as markers to analyze population structure and migration patterns. Finally, we examined the impact of gene dosage variation triggered by a CNV spanning the SEC10 gene on SEC10 expression at both the transcript and protein levels. The catalog of CNVs, CNV-overlapping genes, and their genotypes in a top model dicot will stimulate the exploration of the genetic basis of phenotypic variation.

拷贝数变异（CNV）极大地促进了种内遗传多态性和表型多样性。> 1000拟南芥（Arabidopsis thaliana）测序数据的最新分析）登录集中在较小的变化上，不包括CNV。在这里，我们进行了全基因组分析，并在这些种质中鉴定出大插入缺失（50至499 bp）和CNV（500 bp或更大）。CNV与蛋白质编码基因的18.3％完全重叠，富含进化中的年轻基因以及与压力和防御有关的基因。通过对基因和受CNV影响的转座因子（TEs）的分析相结合，我们发现基因和TEs的变异状态紧密相连，共同导致这些元素在基因组中的分布不均。我们还确定了一组1060份保藏号中的基因拷贝数，并通过多重连接依赖性探针扩增分析实验性地验证了我们预测的准确性。然后，我们成功地使用CNV作为标记来分析种群结构和迁移模式。最后，我们研究了跨越CNV的CNV触发的基因剂量变化的影响SEC10基因在转录本和蛋白质水平上都与SEC10表达有关。顶级模型双子叶植物中CNV，CNV重叠基因及其基因型的目录将刺激对表型变异的遗传基础的探索。