Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) numerous TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.

中文翻译：

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转座因子对番茄多样性的影响

尽管遗传库很窄，但番茄仍具有多种形状和风味。在这里，我们利用可用于602个栽培种和野生种的全基因组重测序数据来确定转座因子（TEs）对番茄多样性的贡献。我们确定了6,906个TE插入多态性（TIP），这是由337个不同的TE家族的动员导致的。大多数TIP是低频变体，不成比例地位于与环境反应有关的基因内或附近。此外，我们表明基因TE插入往往具有很强的转录作用，并且可以显着导致多种转录异构体的产生。通过全基因组关联研究（GWAS），我们还发现了许多与主要农艺性状或次生代谢产物极端变异相关的TIP。重要的，这些TIP倾向于影响与SNP标记的基因座不同的基因座。总的来说，我们的发现表明TE动员在番茄多样化中具有独特而重要的作用，对未来的育种具有重要意义。