Blood orange (BO) is a rare red-fleshed sweet orange (SWO) with a high anthocyanin content and is associated with numerous health-related benefits. Here, we reported a high-quality chromosome-scale genome assembly for Neixiu (NX) BO, reaching 336.63 Mb in length with contig and scaffold N50 values of 30.6 Mb. Furthermore, 96% of the assembled sequences were successfully anchored to 9 pseudo-chromosomes. The genome assembly also revealed the presence of 37.87% transposon elements and 7.64% tandem repeats, and the annotation of 30,395 protein-coding genes. A high level of genome synteny was observed between BO and SWO, further supporting their genetic similarity. The speciation event that gave rise to the Citrus species predated the duplication event found within them. The genome-wide variation between NX and SWO was also compared. This first high-quality BO genome will serve as a fundamental basis for future studies on functional genomics and genome evolution.

血橙 (BO) 是一种稀有的红肉甜橙 (SWO)，花青素含量高，具有许多与健康相关的益处。在这里，我们报道了 Neixiu (NX) BO 的高质量染色体规模基因组组装，长度达到 336.63 Mb，重叠群和支架 N50 值为 30.6 Mb。此外，96% 的组装序列成功锚定到 9 条假染色体上。基因组组装还揭示了 37.87% 转座子元件和 7.64% 串联重复的存在，以及 30,395 个蛋白质编码基因的注释。在 BO 和 SWO 之间观察到高水平的基因组同线性，进一步支持了它们的遗传相似性。产生柑橘属物种的物种形成事件早于柑橘属物种内发现的复制事件。还比较了 NX 和 SWO 之间的全基因组变异。这个第一个高质量的BO基因组将作为未来功能基因组学和基因组进化研究的基础。