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

Huihui Zhang; Yu Si; Runan Zhao; Qianqian Sheng; Zunling Zhu

doi:10.1016/j.gene.2022.147139

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

Gene. 2023 Mar 30:858:147139. doi: 10.1016/j.gene.2022.147139. Epub 2023 Jan 5.

Authors

Huihui Zhang¹, Yu Si², Runan Zhao³, Qianqian Sheng⁴, Zunling Zhu⁵

Affiliations

¹ College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China. Electronic address: zhanghuihui@njfu.edu.cn.
² College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China. Electronic address: siyu_njfu@outlook.com.
³ College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
⁴ College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China. Electronic address: qqs@njfu.edu.cn.
⁵ College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; College of Art & Design, Nanjing Forestry University, Nanjing 210037, China. Electronic address: zhuzunling@njfu.edu.cn.

PMID: 36621658
DOI: 10.1016/j.gene.2022.147139

Abstract

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.

Keywords: Chloroplast genome; Comparative analysis; Nymphaea nouchali; Phylogeny; Water lily.

MeSH terms

China
Endangered Species
Genome, Chloroplast*
Nymphaea* / genetics
Nymphaeaceae* / genetics
Phylogeny