The complete chloroplast genome of the medicinal plant Lysimachia mauritiana (Lamarck, 1792)

Abstract

Lysimachia mauritiana Lam. (Primulaceae) is known as a medicinal plant with anti-tumor and anti-viral effects. In this study, we reported the first complete chloroplast genome sequence of L. mauritiana. The total length of the complete chloroplast genome was 152,691 bp, comprising a small-single copy region (SSC) of 17,928 bp, a large-single copy region of 83,811 bp, and a pair of inverted repeat regions of 25,476 bp. It contained 114 genes comprising 80 protein-coding genes, four rRNA, and 30 tRNA genes. The phylogenetic analysis showed that a chloroplast genome of L. mauritiana was a sister to a monophyletic clade, including L. christinae, L. congestiflora, L. hemsleyana. Our study will help to provide basic information for further studies on phylogenetics and population genetics.

Keywords:

• Lysimachia mauritiana
• Primulaceae
• chloroplast genome
• phylogenetic analysis

Lysimachia mauritiana (Lamarck, 1792) is a medicinal plant belonging to the genus Lysimachia (Primulaceae). The plant extract of this species has known as a good source with anti-tumor and anti-viral effects (Yasukawa and Takido 1987; Bae and Song 2017). The plant is a biennial herb distributing coastlines in East Asia, the Philippines, Micronesia, Polynesia, and the Indian Ocean islands (Iwatsuki et al. 1993; Hu and Kelso 1996; Kono et al. 2013). Until recently, the chloroplast genome of this species has not been reported. In this study, we determined the complete chloroplast genome of L. mauritiana and investigated its phylogenetic position in the family Primulaceae.

Fresh leaves of L. mauritiana was collected from Byeonsan-myeon, Buan-gun, Jeollabuk-do in Korea (N 35°39′22", E 126°29′41") and the voucher specimen (voucher number KRIB0088806, Jin-Hyub Paik, [email protected]) was deposited in International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience & Biotechnology (KRIBB). L. mauritiana is not an endangered or protected species, and we did not collected from private or protected area that required permission. Ethics approval for this study was obtained from the Institutional Bioethics Committee of KRIBB.

The total genomic DNA of this plant was extracted using modified CTAB methods (Healey et al. 2014) and sequenced by Illumina HiseqXten platform (San Diego, CA). The raw data were filtered using Trimmomatic v.0.36 (Bolger et al. 2014), and the filtered data were assembled using the chloroplast genome of L. coreana (NC_026197.1) as the reference with Geneious Prime (v.2021.1.1; Kearse et al. 2012). Finally, the chloroplast genome was annotated using Geneious Prime (v.2021.1.1; Kearse et al. 2012) and GeSeq (Tillich et al. 2017) based on the chloroplast genome of L. coreana (NC_026197.1), and the complete chloroplast genome of L. mauritiana was submitted to GenBank (accession number: OK491633).

The complete chloroplast genome of L. mauritiana determined in this study has 152,691 bp in length, which contains a large-single copy region (LSC) of 83,811 bp, a small-single copy region (SSC) of 17,928 bp, and a pair of inverted repeat regions (IRs) of 25,476 bp. The chloroplast genome includes a total of 114 genes comprising 80 protein-coding genes, four rRNA, and 30 tRNA genes.

The phylogenetic analysis was performed with 14 accessions of Primulaceae deposited on Genbank, including a chloroplast genome of L. mauritiana determined in this study and an outgroup taxa from the genus Myrsine (MN167883.1 and MN177700.1). The sequences of these chloroplast genomes were aligned using MAFFT alignment v.7 (Katoh and Standley 2013; http://mafft.cbrc.jp/alignment/server/index.html). We selected TVM + F + I + G4 as the best model using ModelFinder module (Kalyaanamoorthy et al. 2017) in IQ-tree v.1.6.3 (Nguyen et al. 2015), and the maximum likelihood phylogenetic tree was reconstructed using in IQ-tree v.1.6.3 (Nguyen et al., 2015) with 1000 bootstrap replicates.

A Maximum-likelihood tree (Figure 1) shows that each genus is a highly supported monophyletic group (bootstrap support value = 100%). A chloroplast genome of L. mauritiana is a sister to a monophyletic clade including L. christinae, L. congestiflora, and L. hemsleyana with a high bootstrap value (bootstrap support value = 100%). Our study will provide basic information to understand the evolution and diversification of L. mauritiana.

Figure 1. A Maximum-likelihood tree using 15 chloroplast genomes from Primulaceae, including a chloroplast genome of Lysimachia mauritiana determined in this study and an outgroup taxon (Myrsine stolonifera). The numbers near the nodes indicate bootstrap values.

Author contributions

Conceptualization: YL, SC, JP; Resources: NY, JK, SC, JP; Performed the experiments: YL, JK; Formal analysis: YL, NY, JK; Writing: 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. OK491633. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA791132, SRR17284494, and SAMN24255752 respectively.

Additional information

Funding

This work was supported by the KRIBB Initiative Program [KGM4582221] of the Republic of Korea.