Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Nekemias from Vine Tea

Abstract

Abstract Nekemias grossedentata is a plant species that has been utilized for centuries as both a traditional medicine and food source due to its high levels of bioactive compounds. Specifically, the plant's young stems and leaves are used to make vine tea, which has been used to treat various ailments. While Nekemias cantoniensis and Nekemias megalophylla are also utilized for similar purposes in various regions, limited research on their chloroplast genomes and chromatography has significantly hindered the study of their evolutionary and phylogenetic relationships, as well as the market supply of these materials. In order to address these gaps in knowledge, this study used the Illumina sequencing platform to sequence the complete chloroplast (cp) genomes of three Nekemias species, which were then compared to that of Nekemias grossedentata. Additionally, high-performance liquid chromatography (HPLC) was utilized to construct chromatographic fingerprints of the three plants. The annotation results demonstrated that the three chloroplast genomes were typical quadripartite structures, with lengths of 162,147 bp (N. grossedentata), 161,981 bp (N. megalophylla), and 162,500 bp (N. cantoniensis), respectively. A total of 89 (N. grossedentata)/86 (N. megalophylla,N. cantoniensis) protein-coding genes, 37 tRNA genes, and 8 rRNA genes were annotated. The IR/SC boundary regions were relatively conserved across the three species, although three regions (rps19-rpl2, rpl32-trnL-UAG, ccsA-ndhD) exhibited nucleotide diversity values (Pi) of variable sites higher than 1%. Phylogenetic analysis indicated that N. grossedentata had a closer genetic relationship with N. megalophylla than N. cantoniensis. Moreover, the chromatographic fingerprints revealed that the functional components were highly similar to the genetic relatedness of the species. Overall, this study provides valuable information for species identification, phylogeny, quality assessment, and rational use of three medicinal plants of the genus Nekemias. Furthermore, the findings of this study will contribute to the standardization of vine tea raw materials and the optimization of product efficacy.