To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published reference genome, T2T-G42, by adding 399.2 Mb and 11,225 genes. Comparative analysis has unveiled gene variants and structural variations (SVs), shedding light on watermelon evolution and domestication processes that enhanced attributes such as bitterness and sugar content while compromising disease resistance. Multidisease-resistant loci from Citrullus amarus and Citrullus mucosospermus were successfully introduced into cultivated Citrullus lanatus. The SVs identified in C. lanatus have not only been inherited from cordophanus but also from C. mucosospermus, suggesting additional ancestors beyond cordophanus in the lineage of cultivated watermelon. Our investigation substantially improves the comprehension of watermelon genome diversity, furnishing comprehensive reference genomes for all Citrullus species. This advancement aids in the exploration and genetic enhancement of watermelon using its wild relatives.

为了破译葫芦属西瓜属内的遗传多样性，我们生成了 27 个不同基因型的端粒到端粒 (T2T) 组合，涵盖了所有七种西瓜属物种。该 T2T 超级泛基因组通过添加 399.2 Mb 和 11,225 个基因扩展了之前发布的参考基因组 T2T-G42。比较分析揭示了基因变异和结构变异（SV），揭示了西瓜的进化和驯化过程，这些过程增强了苦味和糖含量等属性，同时损害了抗病性。苦瓜和粘子西瓜的多重抗病基因座已成功导入栽培西瓜中。在C. lanatus中鉴定出的 SV 不仅遗传自Cordophanus ，而且还遗传自C. mucosospermus ，这表明在栽培西瓜谱系中除了Cordophanus之外还有其他祖先。我们的研究极大地提高了对西瓜基因组多样性的理解，为所有西瓜属物种提供了全面的参考基因组。这一进步有助于利用西瓜的野生近缘种来探索和遗传增强西瓜。