| Summary: | 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.
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