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. 2022 Dec 12;7(12):2025–2026. doi: 10.1080/23802359.2022.2149248

The complete chloroplast genome of Elsholtzia byeonsanensis M. Kim, an endemic species in Korea

Yun-Chang Jeon a, Jin-Hyub Paik b, Narae Yun b, Sangho Choi b, Yoonkyung Lee b,*,✉
PMCID: PMC9754010  PMID: 36530458

Abstract

Elsholtzia byeonsanensis M. Kim. is an endemic species in Korea, and its leaves are distinguished from other taxa of Elsholtzia by the leathery texture. In this study, we first presented the complete chloroplast genome of E. byeonsanensis. The complete chloroplast genome was 150,628 bp, including a large-single copy region (LSC) of 82,738 bp, a small-single copy region (SSC) of 17,492 bp, and a pair of inverted repeat regions (IRs) of 25,199 bp. It contained 112 genes including 78 protein-coding genes, four rRNA, and 30 tRNA genes. The phylogenetic analysis indicated that E. byeonsanensis and E. splendens formed a monophyletic clade and showed a close relationship. The complete chloroplast genome of E. byeonsanensis will provide useful information for phylogenetic and evolutionary studies.

Keywords: Elsholtzia byeonsanensis, Endemic species, Lamiaceae, Chloroplast genome, Phylogenetic analysis

The genus Elsholtzia Willd. (Lamiaceae) is primarily distributed in the temperate regions of the Northern hemisphere (Harley et al. 2004), the center of the greatest diversity in the genus is in eastern Asia, particularly China, Korea, and Japan, with approximately 40 species (Li and Hedge 1994, Govaerts et al. 2022). Elsholtzia byeonsanensis M. Kim 2012, an endemic species in Korea, is distinguished from other species in Elsholtzia by several characteristics; coriaceous leaf textures, petioles glabrous, the adaxial surface of leaf blade glabrous, bract surface glabrous, and coastal habitat (Choi et al. 2012). Here, we report the complete chloroplast genome of E. byeonsanensis and investigated its phylogenetic position with the related taxa in the family Lamiaceae.

The genomic DNA used for the analysis was extracted from fresh leaves of E. byeonsanensis (35° 39′ 22.09″N, 126° 29′ 41.14″E; Byeonsan-myeon, Buan-gun, Jeollabuk-do, Korea) using modified CTAB method (Healey et al. 2014). The voucher specimen (voucher number KRIB 0090053, Jin-Hyub Paik, jpaik@kribb.re.kr) was deposited in the International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience & Biotechnology (KRIBB). E. byeonsanensis is not an endangered or protected species, and not required specific permission to collect this species. Additionally, ethics approval for this study was obtained by KRIBB Initiative Program (no. KGM4582221). The raw reads were obtained by Illumina HiseqXten platform (San Diego, CA), and were filtered on Trimmomatic v.0.36 (Bolger et al. 2014). The filtered reads were assembled and mapped to a reference chloroplast genome of E. densa (accession number: MN793319) using Geneious Prime (v.2021.1.1; Kearse et al. 2012). The chloroplast genome was annotated using Geneious Prime (v.2021.1.1; Kearse et al. 2012) and GeSeq (Tillich et al. 2017) with a chloroplast genome of E. densa as a reference. Finally, the complete chloroplast genome of E. byeonsanensis has beensubmitted GenBank with accession number: ON040655.

The total length of the complete chloroplast genome of E. byeonsanensis in this study has 150,628 bp, which contains a large-single copy region (LSC) of 82,738 bp, a small-single copy region (SSC) of 17,492 bp, and a pair of inverted repeat regions (IRs) of 25,199 bp. The chloroplast genome has 112 genes, including 78 protein-coding genes, four rRNA, and 30 tRNA genes.

The phylogenetic analysis included 15 representative taxa of Lamiaceae based on a previous study (Li et al. 2017), and these sequences were obtained from GenBank. Caryopteris forrestii and Lamium galeobdolon were selected as outgroup taxa, and all sequences including E. byeonsanensis determined in this study were aligned using MAFFT alignment v.7 (Katoh & Standley 2013; http://mafft.cbrc.jp/alignment/server/index.html). The best model TVM + F + I + G4 was calculated by ModelFinder module (Kalyaanamoorthy et al. 2017) in IQ-tree v.1.6.3 (Nguyen et al. 2015), and IQ-tree v.1.6.3 (Nguyen et al. 2015) was used to construct the maximum likelihood (ML) tree.

A ML tree (Figure 1) indicated that five taxa (E. rugulosa, E. byeonsanensis, E. splendens, E. densa and E. densa var. ianthina) of Elsholtzia formed a monophyletic clade with 87% bootstrap support value (BS). E. byeonsanensis and E. splendens formed a monophyletic clade with a highly supported value (BS = 100%), and these species showed a close relationship. Elsholtzia was sister to a monophyletic clade of Perilla at the intergeneric level (BS = 100%), and the tribe Elsholtzieae including both genera formed a monophyletic clade (BS = 100%). In this study, we first report the complete chloroplast genome of E. byeonsanensis, as an endemic taxon in Korea. The results contribute to the conservation of this species and the phylogenetic study of Elsholtzia.

Figure 1.

Figure 1.

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A maximum likelihood tree based on a chloroplast genome of Elsholtzia byeonsanensis and related taxa in Lamiaceae. The numbers near the nodes indicate bootstrap support values.

Funding Statement

This work was supported by the KRIBB Initiative Program (KGM4582221) of the Republic of Korea.

Author contributions

Conceptualization: YJ, JP, SC, YL; Resources: JP, NY, SC, YL; Performed the experiments: NY, YL; Formal analysis: YJ, YL; Writing: YJ, YL; All authors reviewed the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov] under the accession no. ON040655. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA791132, SRR18450390, and SAMN26865087 respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov] under the accession no. ON040655. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA791132, SRR18450390, and SAMN26865087 respectively.

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