Complete chloroplast genome and phylogenetic relationship of Nymphaea nouchali (Nymphaeaceae), a rare species of water lily in China

•The complete chloroplast genome of Nymphaea nouchali was reported for the first time.•The chloroplast genomes of N. nouchali and other related species were compared and analyzed.•Five highly variable sites of N. nouchali were identified as potential DNA markers.•Phylogenetic analysis showed a close relationship between N. nouchali and N. ampla. Nymphaea nouchali is a native species of Chinese water lily with important ornamental, economical, and medicinal purposes. However, due to the serious disturbance by alien biological invasion and human factors, N. nouchali is in an endangered state in China and urgently needs to be protected. Here, we reported the complete chloroplast genome of N. nouchali for the first time, and we found that its plastome is 159 978 bp long, comprising large and small single copies and two inverted repeats (90 001, 19 603, and 50 374 bp, respectively), indicating a typical tetrad structure. In total, 130 genes were identified, including 85 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. Additionally, 136 simple sequence repeat sites were identified, composed mainly of single nucleotide (46.32%) and trinucleotide (47.05%) sequences. Five highly variable sites (psaI, rps19, ndhF, rps15, and ycf1) with a high Pi value were identified as potential molecular markers. Phylogenetic analysis showed that N. nouchali and N. ampla are closely related, and further validated previous water lily classification results based on morphological characteristics, which divided water lilies into five subgenera: Nymphaea, Brachyceras, Anecphya, Hydrocallis, and Lotos. These results are valuable for the identification and the formulation of protection strategies of N. nouchali, as well as contributing to understanding the evolutionary relationships among Nymphaeaceae species.