The complete chloroplast genome of Lonicera similis Hemsl. and its phylogenetic analysis

Abstract

Lonicera similis Hemsl. belongs to the Caprifoliaceae family and used as a substitute for 'jin yin hua'. Recent years, it demonstrates great economic value because of its rich chemical composition. However, the phylogenetic relationship between L. similis and other family members remains unclear. In this paper, we assembled the cp genome of L. similis using the high-throughput Illumina pair-end sequencing data. The circular cp genome was 155,207 bp in size, including a large single-copy (LSC) region of 88994 bp and a small single-copy (SSC) region of 18,633 bp, which were separated by two inverted repeat (IR) regions (23,790 bp each). A total of 121 genes were predicted, including eight ribosomal RNAs (rRNAs), 36 transfer RNAs (tRNAs), and 77 protein-coding genes (PCGs). In addition, the result of phylogenetic analysis indicated that L. similis formed a close relationship from another congeneric species (Lonicera confusa). This study provides helpful information for future genetic study of L. similis.

A Comparative Analysis of the Chloroplast Genomes of Three Lonicera Medicinal Plants

“…The cp genomes of the three species ranged in length from 155,079 ( L. japonica ) to 155,330 bp ( L. acuminata ); they had a typical quadripartite structure, usually consisting of an LSC, an SSC, and two IR regions, which is consistent with highly conserved features of the cp genome of most angiosperms [ 25 ]. Compared with previous studies [ 33 , 51 , 52 ], chloroplast genomes of Lonicera plants differ little in terms of genome organization, number of genes, and types. In a comparative analysis of repeat sequences in the cp genomes, L. japonica (a total of 121 repeats, 72 tandem, 37 forward, 12 palindromic repeats) and L. similis (a total of 115 repeats, 66 tandem, 35 forward, 14 palindromic repeats) repeats were similar, while L. acuminata (a total of 99 repeats, 53 tandem, 33 forward, 13 palindromic repeats) had shorter fragment repeats.…”