The sacred lotus (Nelumbo nucifera) is widely cultured in East Asia for its horticultural, agricultural, and medicinal values. Although many molecular markers had been used to extrapolate population genetics of the sacred lotus, a study of large variations, such as copy number variation (CNV), are absent up to now. In this study, we applied whole-genome re-sequencing to 24 lotus accessions, and use read depth information to genotype and filter original CNV call. Totally 448 duplications and 4,267 deletions were identified in the final CNV set. Further analysis of population structure revealed that the population structure patterns revealed by CNV and SNP are largely consistent with each other. Our result indicated that deep sequencing followed by genotyping is a quick and straightforward way to mine out CNV from the population, and the CNV along with SNP could enable us to better comprehend the biology of the plant.

神圣的莲花（莲））因其园艺，农业和药用价值而在东亚被广泛养殖。尽管已使用许多分子标记来推断神圣莲花的种群遗传学，但迄今为止，尚未进行大的变异研究，例如拷贝数变异（CNV）。在这项研究中，我们对24个荷花种质进行了全基因组重测序，并使用读取的深度信息对基因型和原始CNV调用进行了基因分型和过滤。在最终的CNV集中共鉴定出448个重复和4267个缺失。人口结构的进一步分析表明，CNV和SNP揭示的人口结构模式在很大程度上是一致的。我们的结果表明，先进行深度测序再进行基因分型，是从人群中挖掘出CNV的快速直接的方法，