Although there has been a long history of cultivation and research on Nymphaea, the taxonomic relationships and evolutionary relationships among Nymphaea species remain controversial. The chloroplast (cp) genome can provide a new method to determine species origin, evolution, and phylogenetic relationships of Nymphaea. The complete cp genomes of seven Nymphaea species were sequenced by high-throughput sequencing technology, and the structural characteristics and phylogenetic relationships of cp genomes were analyzed. The cp genomes of seven species of Nymphaea had rich variation in large single-copy (LSC) and small single-copy (SSC) regions. A comparative cp genomic analysis of seven Nymphaea species showed that the cp gene sequence of Nymphaea was consistent, with no signs of reverse rearrangement. Using N. colorata as the reference sequence, a total of 8,328 single nucleotide polymorphisms (SNPs) and 1,579 insertions/deletions were obtained. The degree of variation of the cp genome of the seven Nymphaea species in rpoA–rpl20, rbcL–ndhC, ndhD–ndhF, and trnN-GUU–ndhA regions was relatively high. The ycf2 gene was positively selected. The phylogenetic analysis showed that the genus Nymphaea can be further divided into five subgenera.

尽管睡莲的栽培和研究已有很长的历史，但睡莲物种之间的分类学关系和进化关系仍存在争议。叶绿体（CP）基因组可以提供一种新的方法来确定物种的起源，进化和亲缘关系的睡莲。利用高通量测序技术对七个睡莲物种的完整cp基因组进行了测序，并分析了cp基因组的结构特征和系统发育关系。睡莲的7个物种的cp基因组在大单拷贝（LSC）和小单拷贝（SSC）区域具有丰富的变异。七个睡莲的比较cp基因组分析物种表明星莲的cp基因序列是一致的，没有反向重排的迹象。使用N. colorata作为参考序列，共有8328个单核苷酸多态性（SNP）和1579个插入/获得缺失。七的CP基因组的变异程度睡莲种RPOA - rpl20，rbcL基因- ndhC，ndhD的- ndhF和TRNN-GUU - ndhA地区相对较高。该ycf2基因正选择。系统发育分析表明星云属 可以进一步分为五个亚属。