Lotus (family: Nelumbonaceae) are perennial aquatic plants that represent one of the most ancient basal dicots. In the present study, we resequenced 296 lotus accessions from various geographical locations and germplasms to explore their genomic diversity and population structure. This germplasm set consisted of four accessions of American wild lotus and 292 accessions of Asian lotus, which were divided into four subgroups: wild, rhizome, flower and seed. Total single nucleotide polymorphisms (SNPs) suggested that the wild lotus had the highest variant number (7 191 010). Population structure and genome diversity analysis indicated that the American wild lotus demonstrated a distant genetic relationship with the Asian lotus. Furthermore, the seed and rhizome lotus groups had not originated from a single source but rather had a more complex multisource origin. Besides that, the seed lotus showed higher genetic diversity, which might have been due to the gene flow from the flower lotus to seed lotus by artificial crossing, and the rhizome lotus showed a much lower genetic diversity than the other groups. The present study provides SNP markers for lotus genomic diversity analysis, which will be useful for guiding lotus breeding.

中文翻译：

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对296种栽培和野生荷花种的重新测序揭示了其进化和育种历史

莲花（科：莲科）是多年生水生植物，代表最古老的基础双子叶植物之一。在本研究中，我们对来自不同地理位置和种质的296个荷花种质进行了重新排序，以探索其基因组多样性和种群结构。该种质集由美国野生荷花的四份种和亚洲荷花的292份组成，分为四个亚类：野生，根茎，花和种子。总的单核苷酸多态性（SNPs）表明，野生莲具有最高的变异数（7 191 010）。种群结构和基因组多样性分析表明，美洲野莲与亚洲莲具有远缘的遗传关系。此外，种子和根茎莲花群并非起源于单一来源，而是具有更为复杂的多重来源。除此之外，莲子的遗传多样性更高，这可能是由于通过人工杂交从莲子到莲子的基因流动所致，而根茎莲的遗传多样性却比其他群体低。本研究为莲花基因组多样性分析提供了SNP标记，对指导莲花育种很有帮助。