Supplementary Material for: Chromosome Nomenclature and Cytological Characterization of Sacred Lotus

Sacred lotus is a basal eudicot plant that has been cultivated in Asia for over 7,000 years for its agricultural, ornamental, religious, and medicinal importance. A notable characteristic of lotus is the seed longevity. Extensive endeavors have been devoted to dissect its genome assembly, including the variety China Antique, which germinated from a 1,300-year-old seed. Here, cytogenetic markers representing the 10 largest megascaffolds, which constitute approximately 70% of the lotus genome assembly, were developed. These 10 megascaffolds were then anchored to the corresponding lotus chromosomes by fluorescence in situ hybridization using these cytogenetic markers, and a set of chromosome-specific cytogenetic markers that could unambiguously identify each of the 8 chromosomes was generated. Karyotyping was conducted, and a nomenclature based on chromosomal length was established for the 8 chromosomes of China Antique. Comparative karyotyping revealed relatively conserved chromosomal structures between China Antique and 3 modern cultivars. Interestingly, significant variations in the copy number of 45S rDNA were detected between China Antique and modern cultivars. Our results provide a comprehensive view on the chromosomal structure of sacred lotus and will facilitate further studies and the genome assembly of lotus.圣莲（Sacred lotus）是一类基部真双子叶植物（basal eudicot），在亚洲已有7000余年的栽培历史，因其兼具农业、观赏、宗教与药用价值而被广泛种植。莲的显著特征之一为超长种子寿命。学界已针对其基因组组装开展了大量解析工作，其中便涵盖了对‘中国古莲’（China Antique）这一品种的研究——该品种的植株可由1300年历史的古莲子萌发而来。 本研究开发了代表10个最大巨型支架（megascaffolds）的细胞遗传标记，这10个巨型支架约占莲基因组组装序列的70%。随后，研究人员借助这些细胞遗传标记，通过荧光原位杂交（fluorescence in situ hybridization, FISH）技术将上述10个巨型支架锚定至对应的莲染色体，并构建了一套可明确区分莲全部8条染色体的染色体特异性细胞遗传标记。研究人员完成了核型分析，并基于染色体长度为‘中国古莲’的8条染色体建立了标准化命名体系。 比较核型分析结果显示，‘中国古莲’与3个现代栽培品种的染色体结构相对保守。值得关注的是，‘中国古莲’与现代栽培品种之间的45S核糖体DNA（45S rDNA）拷贝数存在显著差异。本研究结果全面阐明了圣莲的染色体结构特征，将为莲的后续研究及基因组组装工作提供重要支撑。