Silybum marianum (L.) Gaertn., commonly known as milk thistle, is a medicinal plant belonging to the Asteraceae family. This plant has been recognized for its medicinal properties for over 2,000 years. However, the genome of this plant remains largely undiscovered, having no reference genome at a chromosomal level. Here, we assembled the chromosome-level genome of S. marianum, allowing for the annotation of 53,552 genes and the identification of transposable elements comprising 58% of the genome. The genome assembly from this study showed 99.1% completeness as determined by BUSCO assessment, while the previous assembly (ASM154182v1) showed 36.7%. Functional annotation of the predicted genes showed 50,329 genes (94% of total genes) with known protein functions in public databases. Comparative genome analysis among Asteraceae plants revealed a striking conservation of collinearity between S. marianum and C. cardunculus. The genomic information generated from this study will be a valuable resource for milk thistle breeding and for use by the larger research community.

水飞蓟（Silybum marianum (L.) Gaertn.）俗称水飞蓟，是菊科的药用植物。 2000 多年来，这种植物因其药用特性而得到认可。然而，这种植物的基因组在很大程度上仍未被发现，在染色体水平上没有参考基因组。在这里，我们组装了S. marianum的染色体水平基因组，可以注释 53,552 个基因，并鉴定出占基因组 58% 的转座元件。根据 BUSCO 评估确定，本研究的基因组组装完整性为 99.1%，而之前的组装 (ASM154182v1) 完整性为 36.7%。预测基因的功能注释显示，公共数据库中有 50,329 个基因（占基因总数的 94%）具有已知的蛋白质功能。菊科植物的比较基因组分析揭示了S. marianum和C. cardunculus之间显着的共线性保守性。这项研究产生的基因组信息将成为水飞蓟育种的宝贵资源，并可供更大的研究界使用。