The genus Maesa Forssk. (Myrsinaceae) comprises approximately 200 species of woody shrubs, trees, scramblers, or lianas that are mainly distributed in the tropics, from southern Africa to east Asia (Sumanon et al., 2021; Li et al., 2022; Larson et al., 2023). Among them, Maesa japonica (Thunb.) Moritzi ex Zoll. is distributed in Vietnam, China, Taiwan, Japan, and Korea; notably, in Korea, this species is found only on Jejudo Island (Kim and Kim, 2011). Maesa japonica can be distinguished from related taxa by their leaf blade, which is lanceolate, oblong, rarely ovate, smooth, and flat, with subentire to distally serrate margins (Chen and Pipoly, 1996).

The chloroplast (cp) is an intracellular organelle that plays an essential role in photosynthesis and other primary and secondary metabolic processes (Shinozaki et al., 1986; Brunkard et al., 2015). Chloroplasts have their genetic replication mechanisms and are inherited maternally in most angiosperms and gymnosperms; however, they are paternally inherited in some gymnosperms (Yang et al., 2021). Typically, most cp genomes are circular 120–170 kb long DNA molecules with a quadripartite structure and consist of 120–130 genes, including a large single-copy (LSC, 80–90 kb), a small single-copy (SSC, 16–27 kb), and a pair of inverted repeats (IRs) (Chumley et al., 2006; Cui et al., 2019; Yoo et al., 2021). Owing to its highly conserved sequence and structure, the cp genome is useful for phylogenetic and evolutionary studies of plants (Palmer et al., 1988; Kwon et al., 2022). Recently, whole plastid genomes have been widely used in phylogenetic studies to analyze groups of plants whose evolutionary relationships remain unresolved (Gitzendanner et al., 2018).

In this study, we determined the complete cp genome sequences of an M. japonica individual from Korea and investigated the phylogenetic position of M. japonica within Myrsinaceae by analyzing our novel cp genome information with previously reported cp genomes of species in the family.

A specimen of M. japonica was sampled from Cheongsuri, Hangyeong-myeon, Jeju-si, Jeju-do, Korea (33°18′08.7″N, 126°16′36.2″E; 158.5 m). The collected plant material was stored at the Korea National Arboretum Herbarium under the voucher number Cheongsuri-220427-001.

DNA was isolated from silica-dried leaves using a DNeasy Plant kit (Qiagen, USA). Subsequently, the extracted DNA was verified using 2% agarose gel electrophoresis, and a DNA library was prepared using a TruSeq Nano DNA Kit according to the protocol specified in the Sample Preparation Guide provided by the manufacturer (Macrogen Inc., Seoul, Korea). Genome paired-end sequencing was performed at Macrogen Inc. on an Illumina platform, MiSeq sequencer (Illumina Inc., San Diego, CA, USA), based on a 301-bp read size. A total of 7,439,526 paired-end reads were obtained, of which 115,105 reads (1.5%) were identified as cp genome sequences.

The complete cp genome was assembled using Geneious v9.0.5 (Biomatters, Auckland, New Zealand) and annotated using the GeSeq tool (Tillich et al., 2017) and Geneious v9.0.5 (Biomatters). A circular map of the M. japonica cp genome was constructed using CPGview available at http://www.1 kmpg.cn/cpgview (Liu et al., 2023).

To infer the phylogenetic relationships of M. japonica with other species within Myrsinaceae, the complete cp genome sequences of 11 species were downloaded from the NCBI GenBank (https://www.ncbi.nlm.nih.gov/genbank/). Primula farinosa var. koreana T. Yamaz. was used as an outgroup. Phylogenetic analysis was performed for 88 coding sequences of Maesa and related species. Alignments were performed using MAFFT v7.450 in Geneious v9.0.5 (Biomatters) (Katoh et al., 2002; Katoh and Standley, 2013). A maximum likelihood (ML) bootstrap analysis with 1,000 replicates was performed with the best-fit model (TVM+F+I+G4) determined using the IQ-tree web server (Trifinopoulos et al., 2016). Bayesian inference (BI) analysis was conducted using MrBayes v3.2.6 (Ronquist et al., 2012) implemented in PhyloSuite (Zhang et al., 2020). The best molecular evolution model for the BI analysis with the cp genome-dataset (GTR+F+I+G4) was obtained using ModelFinder v2.0 (Kalyaanamoorthy et al., 2017).

The complete cp genome sequence of M. japonica is 157,189 bp in length, with the cp reads showing an average coverage depth of 228.62. The sequence was deposited in GenBank under the accession number OQ759651. The LSC, SSC, and IRs of the cp genome sequence were 87,780 bp, 18,143 bp, and 35,633 bp, respectively. The overall GC content of the cp genome was 37.3%, while those of the LSC, SSC, and each IR were 35.2%, 30.9%, and 43.1%, respectively. The cp genome contained 130 unique genes, including 85 coding genes, eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes (Fig. 1). Seventeen genes (six coding genes, four tRNA, and seven rRNA) were duplicated in the IRs (Table 1). Nine protein-coding genes contained one intron, whereas two protein-coding genes contained two introns. Additionally, rps12 was identified as a trans-spliced gene.

Sequences from 12 species including Primula farinosa var. koreana as an outgroup were used to infer ML- and BI-based phylogenies, both of which showed the same topology and high support for each branch (Fig. 2). Phylogenetic analysis revealed that the Maesa is monophyletic and is a sister group to other taxa within Myrsinaceae. Additionally, M. japonica was found to be closely related to M. salicifolia E. Walker (MW801082.1).

To the best of our knowledge, this is the first study to assemble and annotate the complete cp genome sequence of Maesa japonica. Originally, the generic limits and alignments in Myrsinaceae s.str. clade are rather unclear (Yan et al., 2019). In our study, the phylogenetic tree is shown to contain two main subclades, and the topology of tree is almost identical with previous phylogenetic study based on 78 protein-coding genes (Yan et al., 2019). Additionally, phylogenetic tree analysis revealed that the Maesa is a monophyletic group and that M. japonica is closely related to M. salicifolia, showing a high percentage (99.9%) of pairwise identity with identical gene order and contents. M. salicifolia is morphologically distinct from M. japonica by its leaf blade, which is linear to lanceolate or bullate, with revolute or entire margins; fruits are reddish, punctate-lineate, and wrinkled (Chen and Pipoly, 1996). However, only a few cp genome sequences of Maesa were reported, further studies are needed to understand fully resolved evolutionary and phylogenetic relationships within the genus. The cp genome sequence of M. japonica provides useful information for future studies aimed at understanding the phylogenetic and evolutionary relationships among related species.