The complete chloroplast genome of Elsholtzia fruticosa (D. Don) Rehd. (Labiatae), an ornamental plant with high medicinal value

Abstract

Elsholtzia fruticosa is an ornamental plant with high medicinal value. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of the species. The complete cp sequence is 151,550 bp, including the large single-copy (LSC) region of 82,778 bp, the small single-copy (SSC) region of 17,492 bp, and a pair of invert repeats (IRs) regions of 25,640 bp. It encodes 132 unique genes in total, including 87 protein-coding genes, 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). The comparative analysis of complete cp genomes showed that the genomic structure and gene order of E. fruticosa cps were conserved. The sequences of rps15, rps19, ycf1, ycf3, ycf15, psbL, psaI, trnG-UCC, trnS-GCU, trnR-UCU, trnL-UAG, trnP-UG, and trnL-UAA serve as hotspots for developing the DNA barcoding of Elsholtzia species. There are 49 SSR loci in the cp genome of E. fruticosa, among which the repeat numbers of mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotides SSR are 37, 9, 3, 0, and 0, respectively. A total of 50 repeats were detected, including 15 forward repeats, seven reverse repeats, 26 palindromic repeats, and two complementary repeats. Phylogenetic analysis based on the complete cp genome and protein-coding DNA sequences of 26 plants indicates that E. fruticosa has a dose relationship with E. splendens and E. byeonsanensis.

Keywords: Elsholtzia fruticosa; chloroplast genome; phylogenetic analysis.

Figure 1.

Plant morphological characteristics of Elsholtzia fruticosa. (A) The leaves of this species are lanceolate or elliptic lanceolate, and the base is narrow cuneate. (B) The flowers of E. fruticosa are cylindrical spikes, terminal or axillary. The photos of E. fruticosa were taken by the authors in Hutiaoxia Town, Shangri La City, Yunnan Province, China (coordinates: 99°59′33.11″E, 27°16′7.56″N).

Figure 2.

Gene map of the Elsholtzia fruticosa plastid genome. Genes drawn inside the circle are transcribed clockwise, and those outside are transcribed counterclockwise. Genes belonging to different functional groups are color coded. The darker gray in the inner circle corresponds to DNA G + C content, while the lighter gray corresponds to A + T content. LSC: large single-copy; SSC: small single-copy; IR: inverted repeat.

Figure 3.

The best maximum-likelihood (ML) phylogenetic tree reconstructed by RAxML ver. 8.0.0 based on complete chloroplast genome (A) and the chloroplast protein-coding DNA sequences (B) of 24 species of Labiatae, including five Elsholtzia species, Thunbergia erecta and Barleria prionitis as outgroups. The numbers on branches are bootstrap support values from 1000 replicates. The following sequences were used: Salvia japonica MW381778.1 (Li et al. 2021), Salvia miltiorrhiza f. alba MT012420.1 (Lin et al. 2022), Salvia nanchuanensis NC 058851.1 (Li et al. 2021), Salvia honania NC 058852.1 (Wang et al. 2022), Salvia prattii MK944407.1 (Xia et al. 2022), Salvia plebeia NC 050929.1 (Paje et al. 2022), Salvia chanroenica MW381777.1 (Cui et al. 2021), Rosmarinus officinalis NC 027259.1 (Gonçalves et al. 2022), Salvia yangii MT537168.1 (Kozłowska et al. 2022), Siphocranion flavidum MT473778.1 (Chen et al. 2019), Siphocranion macranthum MT473779.1 (Feng et al. 2021), Elsholtzia densa MN793319.1 (Liang et al. 2021), Elsholtzia splendens MW900173.1 (Huang et al. 2022), Elsholtzia byeonsanensis ON040655.1 (Chen et al. 2022), Elsholtzia rugulosa MT473758.1 (Liu et al. 2022), Perilla frutescens var. crispa cultivar atropurpurea KT220688.1 (Salachna et al. 2021), Perilla frutescens var. hirtella NC 030757.1 (Salachna et al. 2021), Perilla frutescens cultivar viridis NC 030755.1 (Salachna et al. 2021), Perilla frutescens var. acuta KT220685.1 (Salachna et al. 2021), Perilla frutescens f. crispidiscolor KT220686.1 (Salachna et al. 2021), Perilla frutescens var. frutescens KT220689.1 (Salachna et al. 2021), Leucosceptrum canum NC 051966.1 (Yan et al. 2022), Thunbergia erecta MZ555773.1 (Zakaria et al. 2022), and Barleria prionitis MK548575.1 (Comito et al. 2022).