Comparative analysis of whole chloroplast genomes of three common species of Nekemias from vine tea.

ABSTRACT

Nekemias grossedentata (N. grossedentata) is a medicinal and edible plant. The young leaves and tender stems are specifically utilized to manufacture vine tea, which is traditionally employed in the treatment of conditions such as the common cold fever, sore throat, jaundice hepatitis, and other ailments. The morphologically of N. grossedentata similar to Nekemias cantoniensis (N. cantoniensis) and Nekemias megalophylla (N. megalophylla), which lead to a chaotic market supply. Numerious studies have confirmed that chloroplast genomes and chromatography play important role in plant classification. Here, the whole chloroplast (cp) genomes of the three Nekemias species were sequenced in Illumina sequencing platform. Meanwhile, their chromatographic fingerprints have constructed using high-performance liquid chromatography (HPLC). 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 and N. cantoniensis) protein-coding genes, 37 tRNA gene 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 that of N. cantoniensis. Moreover, the chromatographic fingerprints revealed that the main functional components and genetic relatedness of three species were highly similar with their morphological results. In conclusion, N. grossedentata and N. megalophylla can be consider as the origin plants of vine tea. This study provides appropriate information for species identification, phylogeny, quality assessment of three medicinal plants of the genus Nekemias and will contribute to the standardization of vine tea raw materials.