Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, although the fragmented nature of most contemporary assemblies obscures them. To discover such mutations, we assembled the first new reference-quality genome of Drosophila melanogaster since its initial sequencing. By comparing this new genome to the existing D. melanogaster assembly, we created a structural variant map of unprecedented resolution and identified extensive genetic variation that has remained hidden until now. Many of these variants constitute candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that amplifies the expression of detoxification-related genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high-quality reference genomes are to deciphering phenotypes.

中文翻译：

---

隐藏的遗传变异塑造了果蝇功能元件的结构。


添加、减少、重新排列或以其他方式重塑基因组结构的突变通常会影响表型，尽管大多数当代组装体的碎片性质掩盖了它们。为了发现此类突变，我们组装了自最初测序以来果蝇的第一个新的参考质量基因组。通过将这个新基因组与现有的黑腹果蝇基因组进行比较，我们创建了一个前所未有的分辨率的结构变异图谱，并鉴定了迄今为止一直隐藏的广泛遗传变异。其中许多变异构成了表型变异的候选者，包括串联重复和转座元件插入，可放大与尼古丁抗性相关的解毒相关基因的表达。大量尚未被发现的重要遗传变异凸显了高质量参考基因组对于破译表型的重要性。