Next Article in Journal
Molecular Landscape and Diagnostic Model of MASH: Transcriptomic, Proteomic, Metabolomic, and Lipidomic Perspectives
Previous Article in Journal
Identification and Characterization of LINE and SINE Retrotransposons in the African Hedgehog (Atelerix albiventris, Erinaceidae) and Their Association with 3D Genome Organization and Gene Expression
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Genes
Volume 16
Issue 4
10.3390/genes16040398
genes-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Plastome Sequences Uncover the Korean Endemic Species Polygonatum grandicaule (Asparagaceae) as Part of the P. odoratum Complex

by
Joonhyung Jung
1,2,*,
Hyuk-Jin Kim
1 and
Joo-Hwan Kim
2,*
1
Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea
2
Department of Life Sciences, Gachon University, Seongnam 13120, Republic of Korea
*
Authors to whom correspondence should be addressed.
Genes 2025, 16(4), 398; https://doi.org/10.3390/genes16040398
Submission received: 4 March 2025 / Revised: 25 March 2025 / Accepted: 28 March 2025 / Published: 29 March 2025
(This article belongs to the Section Plant Genetics and Genomics)
Browse Figures
Versions Notes

Abstract

:
Background/Objectives: Polygonatum grandicaule Y.S.Kim, B.U.Oh & C.G.Jang (Asparagaceae Juss.), a Korean endemic species, has been described based on its erect stem, tubular perianth shape, and pedicel length. However, its taxonomic status remains unclear due to limited molecular data. Methods: This study presents the complete plastid genomes (plastomes) of two P. grandicaule individuals and its close relative, P. odoratum (Mill.) Druce var. thunbergii (C.Morren & Decne.) H.Hara. Results: The plastomes, ranging from 154,578 to 154,579 base pairs (bp), are identical to those of P. falcatum A.Gray, P. odoratum var. odoratum, and another Korean endemic species, P. infundiflorum Y.S.Kim, B.U.Oh & C.G.Jang. All contain 78 plastid protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes, except for the pseudogene infA. Phylogenetic analyses using 78 plastid PCGs and whole intergenic spacer (IGS) regions strongly support the three sections within Polygonatum Mill. and show that P. odoratum and its variety are nested within P. falcatum, P. grandicaule, and P. infundiflorum. Conclusions: Given the limited genomic variation and phylogenetic relationships, we propose treating P. falcatum, P. grandicaule, and P. infundiflorum as part of the P. odoratum complex, despite their morphological differences. This study offers valuable putative molecular markers for species identification and supports the application of plastome-based super-barcoding in the morphologically diverse genus Polygonatum.

1. Introduction

Species delimitation is fundamental in various fields of biology [1], especially when studying endemic plants that are restricted to specific regions. These plants are essential for understanding the evolutionary history of local flora and play a vital role in maintaining regional biodiversity [2,3]. Moreover, they provide valuable opportunities for discovering and conserving plant resources with significant economic potential [4]. Earlier studies on species delimitation primarily relied on morphological variation, often leading to ambiguous identification and classification. However, recent approaches combine both morphological and molecular data, including complete plastid genome (plastome) sequences, to more clearly define species boundaries [1,5,6].
In South Korea, 373 endemic taxa from 179 genera and 64 families have been recorded [7]. Among these, two species of Polygonatum Mill. (Asparagaceae: Nolinoideae: Polygonateae), P. grandicaule Y.S.Kim, B.U.Oh & C.G.Jang and P. infundiflorum Y.S.Kim, B.U.Oh & C.G.Jang, have been identified [8,9]. The genus Polygonatum, which contains approximately 80 species and is commonly known as Solomon’s seal, is the largest in the tribe Polygonateae and is widely distributed throughout the northern hemisphere [10,11]. Its rhizomes are used in traditional medicine, and their chemical components, biological activities, and pharmacological properties have been well-documented [12,13,14,15]. It is classified into three distinct sections based on phyllotaxis, basic chromosome number, and molecular evidence: (1) section Polygonatum, which includes species with an alternate phyllotactic pattern and a basic chromosome count of x = 9–11; (2) sect. Sibirica, which comprises species with a verticillate phyllotactic pattern and a basic chromosome count of x = 12; and (3) sect. Verticillata, which features species with diverse phyllotactic patterns and a basic chromosome count of x = 13–15 [16]. In South Korea, P. grandicaule is distinguished by its thick rhizome, cylindrical erect stem, nonbracteate type, tubular perianth shape, and glabrous, cylindroid (slightly S-shaped) filament [9]. It was classified in sect. Polygonatum based on alternate phyllotaxis [17]. However, research on P. grandicaule remains limited, with only partial genetic data available, and it is still unclear whether its diagnostic morphological traits are reliable and taxonomically informative.
Due to its crucial role in plant photosynthesis, researchers frequently use the plastome for phylogenetic reconstruction, estimating divergence times, and conducting biogeographical studies [18,19]. It is also commonly employed for species delimitation, providing valuable molecular markers based on genetic differences [20,21,22]. In general, it has a conserved structure composed of four regions: the large single-copy (LSC), the small single-copy (SSC), and two inverted repeats (IRs) [23]. Recent studies have employed complete plastome sequences to identify structural variations, determine phylogenetic positions and distribution patterns, and resolve ambiguous relationships arising from extensive morphological variation within this genus [24,25,26,27,28,29,30]. Another Korean endemic species, P. infundiflorum, has also been reported [31]; however, no plastome data for P. grandicaule are available. To clarify the status of the Korean endemic Polygonatum species, which have been identified solely on the basis of morphological characteristics, we collected two individuals of P. grandicaule and one individual of P. odoratum (Mill.) Druce var. thunbergii (C.Morren & Decne.) H.Hara from their natural habitats and sequenced their complete plastomes. These plastome sequences provide evidence to determine if the species is indeed endemic, while our comparative plastome structural study and phylogenetic analyses further substantiate its classification as a Korean endemic species. This study also provides valuable information on repeats and molecular diagnostic characteristics (MDCs), which can be used as future molecular identification markers.

2. Materials and Methods

2.1. Taxon Sampling, DNA Extraction, and Plastome Assembly

We collected two individuals of P. grandicaule from Yeongdong, Chungcheongbuk-do (36°17′42.6″ N, 27°48′07.5″ E) and Yeongwol, Gangwon-do (37°11′52.6″ N, 128°20′47.6″ E), as well as one P. odoratum var. thunbergii from Danyang, Chungcheongbuk-do (36°55′48.8″ N, 128°21′06.4″ E), in South Korea. All taxa were collected in sunny grasslands. After collection, voucher specimens were prepared for each sample and deposited in the Gachon University Herbarium (GCU), with unique accession numbers assigned to each (Table 1). Total genomic DNA (gDNA) was isolated following a modified 2 × CTAB extraction protocol [32]. The gDNA was then used for next-generation sequencing (NGS) on an Illumina Mi-seq platform (LAS, Seoul, Republic of Korea). Raw sequencing data were processed for de novo plastome assembly using the GetOrganelle toolkit [33]. A “map to reference” analysis was performed using Geneious Prime 2024.0.5 [34] to recheck and evaluate sequence coverage. Gene content and sequence order were annotated via GeSeq [35], and tRNAs were verified using the tRNAScan-SE web server (http://lowelab.ucsc.edu/tRNAscan-SE/ (accessed on 20 January 2025)) with default parameters [36]. Plastome visualizations were subsequently generated using the chloroplot web server [37].

2.2. Phylogenetic Analyses

We obtained 50 complete plastome sequences from National Center for Biotechnology Information (NCBI), including 33 from Polygonatum taxa spanning three sections, six from Heteropolygonatum M.N.Tamura & Ogisu taxa, five from Disporopsis Hance, and six from Maianthemum F.H.Wigg. (Table S1). The Maianthemum taxa were selected as the outgroup, given their basal position within the tribe Polygonateae as indicated by recent phylogenetic studies [29,38]. From these 53 taxa, 78 plastid protein-coding genes (PCGs) and intergenic spacer (IGS) regions were separately extracted, aligned with MUSCLE, and processed using Geneious Prime 2024.0.5 software [34].
To reconstruct the phylogenetic relationships within genus Polygonatum, we employed maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI) approaches. The MP analysis was carried out using PAUP* v4.0 [39], where all characters were treated as equally weighted and unordered, with gaps considered as missing data. We performed searches with 1000 replicates of random taxon additions and utilized tree-bisection-reconnection (TBR) branch swapping in PAUP*, retaining up to ten trees at each step. We conducted bootstrap analyses (parsimony bootstrap percentages, PBPs) with 1000 pseudoreplicates under the same parameters. ML analysis used the IQ-TREE web server (http://iqtree.cibiv.univie.ac.at/ (accessed on 2 March 2025)) incorporated the mean bootstrap percentage (MBP) and SH-like approximate likelihood ratio test (SH-aLRT) scores calculated over 10,000 ultrafast bootstrap replicates [40]. Before BI analysis, we determined the most suitable substitution model based on the Bayesian Information Criterion (BIC) in MEGA 11 (Table S2) [41]. BI was performed using MrBayes v3.2.7 [42] with two independent runs starting from random trees, each spanning at least 1,000,000 generations and sampled every 1000 generations. A 25% burn-in was applied, and the remaining trees were used to construct a 50% majority-rule consensus tree. Posterior probabilities (PPs) evaluated the BI tree’s robustness, ensuring effective sample size (ESS) values exceeded 200 for all parameters. Phylogenetic trees were finalized with FigTree v1.4.4 [43].

2.3. Nucleotide Diversity (Pi), Repeat Analyses, and Molecular Diagnostic Characteristics

Nucleotide diversity (Pi) of PCGs, tRNA genes, rRNA genes, and IGS regions was assessed for all Polygonatum taxa using DnaSP v6.0 [44] with a sliding window of 100 base pairs (bp) and a step size of 25 bp. Plastomes of all Polygonatum taxa were screened for simple sequence repeats (SSRs) using the MISA Perl script [45], with thresholds set at a minimum of 10 repeats for mononucleotides, 5 for dinucleotides, 4 for trinucleotides, and 3 for tetra-, penta-, and hexanucleotides. Additionally, REPuter [46] was used to detect forward, reverse, complementary, and palindromic repeats that were at least 30 bp in length and 90% similar, permitting a Hamming distance of 3. Furthermore, plastid PCGs were examined to identify MDCs unique to each genus in the tribe Polygonateae and to each of the three sections of the genus Polygonatum, using FastaChar v0.2.4 [47].

2.4. Relative Synonymous Codon Usage (RSCU) Analysis

We used DAMBE v7.3.11 [48] to analyze relative synonymous codon usage (RSCU) values in the 78 plastid PCGs of genus Polygonatum used in this study. Then, we used the pheatmap pacage in R (https://CRAN.R-project.org/package=pheatmap (accessed on 2 March 2025)) to construct the RSCU cluster diagram.

3. Results

3.1. Plastome Characteristics

A total of 24,720 to 109,056 reads were assembled, representing 0.89–4.87% of the total 8,807,104 to 11,204,918 reads generated (Table S3). The plastomes of two P. grandicaule individuals and one P. odoratum var. thunbergii individual exhibit a quadripartite structure, with a large single-copy (LSC) region (83,527–83,528 bp), a small single-copy (SSC) region (18,457 bp), and two inverted repeat (IR) regions (26,297 bp) (Figure 1 and Table 1). Across the three individuals, five point mutations were identified, with three located in non-coding regions and two within plastid PCGs (rps11 and ycf1). The plastome comprises 131 genes, including infA identified as a pseudogene, along with 19 genes duplicated in the IR regions (Figure 1). In the analyzed sequence dataset, we identified 17 repetitive sequences. Fifteen of these sequences contain a single intron: atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC. Only three sequences, namely clpP1, pafI, and rps12, contain two introns.

3.2. Phylogenetic Relationships

We performed MP, ML, and BI analyses, all of which produced phylogenetic trees with consistent topologies. These trees strongly supported the monophyly of the four genera within the tribe Polygonateae and three sections of genus Polygonatum (Figure 2). The alignment matrix of 78 plastid PCGs consisted of 68,433 characters, of which 66,539 (97.23%) were constant and 1236 (1.8%) were parsimony informative. The most parsimonious tree from this dataset was reconstructed with a tree length of 2361, a consistency index (CI) of 0.823, and a retention index (RI) of 0.941. Similarly, the IGS matrix comprised 44,488 characters, with 41,591 (93.49%) constant and 1870 (4.2%) parsimony-informative characters. The most parsimonious tree for the IGS dataset was reconstructed with a tree length of 4030, a CI of 0.753, and an RI of 0.910. Both results supported a sister relationship between Heteropolygonatum and Polygonatum (PBP = 100/MBP = 100/SH-aLRT = 100/PP = 1). Within Polygonatum, P. humile Fisch. ex Maxim. was determined to be non-monophyletic, while P. falcatum A.Gray, P. grandicaule, and P. infundiflorum clustered within the clade containing P. odoratum and its variety, forming what we refer to as the P. odoratum complex.

3.3. Comparative Plastome Sequences Analyses

We examined nucleotide divergences in plastid PCGs, tRNA genes, rRNA genes, and non-coding regions to characterize variants among the 36 Polygonatum taxa (Figure 3 and Table S4). The nucleotide diversity (Pi) of plastid PCGs ranged from 0 (petL, petN, psaI, psaJ, psbI, psbK, psbZ, rpl32, rps12, rps14, rps16, and rps7) to 0.00974 (rpl16), with an average value of 0.00175. In tRNA and rRNA regions, variations were detected in only five genes, with Pi values ranging from 0.0004 (rrn16) to 0.0242 (trnS-GCU). Among the non-coding regions, three IGS regions (trnM-CAU–atpE, rpl22–rps19, and ccsA–ndhD) exhibited notably high values (Pi > 0.02).
A total of 68–81 SSRs were detected in Polygonatum taxa, with a combined length of 770–938 (Figure 4). Within the P. odoratum complex, 71 SSRs were detected in P. falcatum, P. grandicaule, P. infundiflorum, four P. orodatum var. odoratum, and P. odoratum var. thunbergii, whereas 73 SSRs were found in two individuals of P. odoratum var. odoratum. Across these species, mononucleotide repeats predominated (42 and 44, respectively), accompanied by 15 dinucleotide repeats, 4 trinucleotide repeats, 8 tetranucleotide repeats, and 2 pentanucleotide repeats; no hexanucleotide repeats were observed. The total lengths ranged from 466 to 490 bp for mononucleotide repeats, 158 to 160 bp for dinucleotide repeats, 51 to 54 bp for trinucleotide repeats, 100 bp for tetranucleotide repeats, and 30 bp for pentanucleotide repeats. Most of the SSRs consisted of the A/T motif, while G/C motifs were comparatively less frequent (Table S5). Analysis of longer repeats revealed that, in Polygonatum taxa, forward and palindromic repeats occurred more frequently than reverse and complementary repeats, except in P. oppositifolium, which has 24 reverse and 13 complementary repeats and twice the total repeat length. Within the P. odoratum complex, 35 to 36 long repeats were identified, with only a single reverse repeat detected. Detailed information on the locations and frequencies of these longer repeats is provided in Table S6.
An alignment of 78 plastid PCGs from all members of the tribe Polygonateae identified 17 MDCs unique to the genus Polygonatum, 103 in Heteropolygonatum (including 42 deletions), 92 in Disporopsis, and 206 in Maianthemum (including 27 insertions and 9 deletions) (Figure 5 and Table S7). Within the genus Polygonatum, 21 MDCs were specific to the sect. Polygonatum, 49 to the sect. Sibirica (including 3 insertions), and 24 to the sect. Verticillata (including 9 insertions). It is important to note that this MDC analysis was conducted using an alignment that included all species within the tribe Polygonateae.
Using 78 plastid PCGs, we assessed the RSCU across all Polygonatum taxa (Figure 6 and Figure 7). P. hookeri exhibited the highest codon count with 22,662 codons, while P. govanianum had the lowest at 22,545 codons (Table S8). Leucine (L) was the most abundant amino acid, accounting for 10.26–10.30% of the codons, whereas cysteine (C) was the least frequent at 1.14–1.15%. Notably, about half of the codons had RSCU values above 1, indicating a preferential usage pattern that was consistent among species (Figure 7).

4. Discussion

4.1. The Characteristics of Plastomes in Polygonatum

In this study, we report the first complete plastomes for the Korean endemic species P. grandicaule and the closely related P. odoratum var. thunbergii. As noted in earlier research, the IR regions exhibit a higher GC content than both the LSC and SSC regions [24,25,26,27,28,29,30]. The infA gene, which encodes the translation initiation factor 1 involved in assembling the initiation complex, was identified as a pseudogene across all Polygonatum taxa. To confirm its pseudogene status, the presence of an intact open reading frame (ORF) and a conserved domain was examined using the NCBI Conserved Domains Database (CDD), following Wang et al. [49]. The loss and pseudogenization of infA have likewise been reported in other members of Asparagaceae [50,51,52]. In certain angiosperms, infA has been shown to transfer from the plastome to the nuclear genome, where it is expressed and the resulting protein is imported back into the chloroplast [53,54]. This transfer preserves the essential function of infA after the plastome copy becomes nonfunctional and demonstrates an evolutionary strategy in which organelle genes can migrate to the nucleus to ensure stable maintenance and regulation. During the verification process of plastome sequences, we confirmed that the nucleotide sequences of P. falcatum, P. infundiflorum, and one individual of P. odoratum var. odoratum already registered in NCBI are identical to those of P. grandicaule and P. odoratum var. thunbergii that we analyzed.

4.2. Taxonomic Ambiguity of Korean Endemic Polygonatum: A Phylogenetic Reassessment

Due to its complex morphological diversity, the phylogenetic relationships and intrageneric classification of Polygonatum have long been controversial. Earlier studies have reported non-monophyletic relationships among various Polygonatum species [16,24,25,26,27,28]. In our study, we reconstructed the phylogenetic relationships of Polygonatum alongside its closely related genera (Heteropolygonatum, Disporum, and Maianthemum) and found well-supported monophyletic relationships among these genera, which is consistent with previous findings [26,27,28,29,38]. However, several ambiguous relationships emerged among species within the sect. Polygonatum. Notably, P. humile exhibited a paraphyletic pattern, while P. odoratum and its variety, P. odoratum var. thunbergii were nested within a clade comprising P. falcatum, P. grandicaule, and P. infundiflorum, suggesting complex interrelationships among these taxa. Despite examining 78 plastid PCGs and the entire set of IGS regions, we detected minimal genetic variation among P. falcatum, P. grandicaule, P. infundiflorum, P. odoratum var. odoratum, and P. odoratum var. thunbergii, making it difficult to resolve their relationships with high confidence.
Research on P. odoratum has revealed extensive morphological and karyological diversity. For instance, an analysis of four Chinese cultivars revealed morphological differentiation and potential hybridization, as indicated by conflicting plastid and nuclear phylogenies [25]. Moreover, variation in ploidy levels and stem shape was observed, with some populations having quadrangular stems while others had cylindrical stems [55,56]. Given its broad distribution across Eurasia and significant trait variability among populations [10], a comprehensive worldwide study is needed to address both the morphological and molecular differences within this species.
The Korean endemic Polygonatum species were reported [8,9], and morphological differences between two endemic species and P. thunbergii C.Morren & Decne. were described [8]. Among the three species, a distinct feature of P. grandicaule is its erect stem and tubular perianth shape. Subsequently, Jang [17] classified the Korean Polygonatum species and highlighted key characteristics for their identification. P. thunbergii was identified by its thick rhizome, cylindrical stem, nonbracteate type, distinctive perianth shape, and glabrous, cylindroid (slightly S-shaped) filament. In contrast, Tamura [57] positioned P. thunbergii as P. odoratum var. thunbergii, noting that their stems are angled except at the base. Additionally, Jang [17] suggested that the key distinguishing characteristic separating P. odoratum (including its variety P. odoratum var. pluriflorum (Miq.) Ohwi) from P. robustum (Korsh.) Nakai, P. grandicaule, P. infundiflorum, and P. odoratum var. thunbergii is stem shape, which can be either quadrangular or cylindrical. Cytological studies of Korean Polygonatum species have shown that P. grandicaule, P. infundiflorum, and P. odoratum var. thunbergii share the same chromosome number (2n = 2x = 18), whereas P. odoratum differs (2n = 2x = 18 or 20) [58]. Since chromosome numbers can vary even within the same species [59], including P. odoratum, there is no issue in treating it as part of the P. odoratum complex. In previous palynological research, variables such as grain size, surface sculpturing, and pollen fertility were found to be highly variable, making them unsuitable as diagnostic characteristics for species recognition within the genus [60]. Recently, however, pollen shape has been found to be well-conserved, while pollen size and exine ornamentation are recognized as better identification characteristics in Polygonatum [61,62]. Further studies on palynological characteristics will aid in the revised classification of Korean Polygonatum species. Phylogenetic analyses of Korean Polygonatum using four plastidial loci also failed to resolve the positions of these taxa due to limited informative sites and identical sequences shared with P. involucratum (Franch. & Sav.) Maxim., P. lasianthum Maxim., P. odoratum var. pluriflorum, and P. robustum [63].
As mentioned earlier, the morphological characteristics used to classify each species, such as the presence or absence of an angular stem, stem curvature, filament length, and attachment position, should be re-evaluated when describing species delimitation in Polygonatum. Consequently, we propose that P. falcatum, P. grandicaule, P. infundiflorum, and P. odoratum var. thunbergii could be treated as part of a P. odoratum complex, despite their diverse morphological characteristics. Notably, individuals of Chinese P. odoratum were nested within P. falcatum, P. grandicaule, and P. infundiflorum in our phylogenetic analysis, raising further questions about the taxonomic status of two Korean endemic Polygonatum species. Hybrid capture with high-throughput sequencing (Hyb-Seq) analyses of 40 Korean Polygonatum taxa also revealed morphological ambiguity and classified both P. grandicaule and P. odoratum var. thunbergii as P. odoratum var. odoratum, which partially supports this treatment [64]. To establish a more comprehensive basis for the taxonomic revision of Korean Polygonatum, future research should incorporate a broader sampling of species and individuals, including those from different regions such as China.
Furthermore, phylogenomic studies based on nuclear genes have shown considerable discordance with plastid genome data in Polygonatum [38]. To build a more robust phylogenetic framework, expanded sampling across diverse habitats and the use of integrated genomic approaches, such as transcriptome and whole-genome sequencing, are essential.

4.3. Comparative Analyses and Putative Markers for Polygonatum

We identified trnM-CAU–atpE, rpl22–rps19, and ccsA–ndhD as notably divergent regions, each with a Pi value exceeding 0.02. Notably, the ccsA–ndhD locus aligns with previous findings [28]. Additionally, further research is needed to evaluate whether regions with a high Pi value may serve as effective markers for phylogenetic analysis and species identification.
SSRs are widely regarded for their high polymorphism and utility in genetic diversity assessments, molecular identification, and population genetics. In the present study, mononucleotide repeats composed mainly of A/T bases predominated and were primarily located in non-coding regions, mirroring patterns reported in other members of Asparagaceae [65,66]. Additionally, we detected extended repeats in Polygonatum, which showed minor variations among different repeat types. We also analyzed the MDCs in four genera of the tribe Polygonateae as well as in the genus Polygonatum. In the P. orodatum complex, a total of sixteen MDCs were identified across the tribe, including one each in accD, ndhI, psaA, psbT, rpoA, rpoB, rpoC2, and rps15, and two each in atpB, psaB, rpl20, and ycf1. We observed that substitutions in atpB, rpl20, rps15, and ycf1 led to alterations in translation, resulting in changes in protein structure depending on whether the substitutions were conservative or non-conservative. Notably, all these genetic variations will enhance species identification in the morphologically diverse genus Polygonatum.
An analysis of codon usage in plastid PCGs underscores the influence of mutation trends and selective pressures at the species level. Overrepresented codons predominantly ended in A or U, while those with a lower frequency typically terminated in G or C. The codon AUU (Ile) was the most prevalent, consistent with patterns observed in other Asparagaceae species [67,68]. Overall, these results highlight the value of codon usage studies in elucidating evolutionary processes.

5. Conclusions

In this study, we examined the complete plastome sequences of the Korean endemic P. grandicaule and its close relatives. Our results support the monophyly of the genus Polygonatum, which can be divided into three sections based on the current sampling. Phylogenetic analyses also highlight the taxonomic complexity among the Korean endemic Polygonatum species. We propose that P. falcatum, P. grandicaule, and P. infundiflorum could be considered part of a P. odoratum complex, as P. odoratum individuals are nested within three species. Due to the limited genetic divergence among members of this complex, analyses of SSRs, dispersed repeats, and RSCU further support their close relationship. Additionally, we identified MDCs of members of the tribe Polygonateae, including those within the genus Polygonatum. These findings offer valuable resources for developing robust molecular markers and provide important insights for future super-barcoding research in this morphologically diverse genus. Although the current infrageneric classification of Polygonatum is generally accepted, intrageneric classification remains ambiguous, as it relies heavily on morphological traits in several species. To resolve these relationships more accurately, future studies should incorporate broader sampling across species and populations, using Hyb-Seq, transcriptome sequencing, and whole-genome sequencing.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes16040398/s1, Table S1. List of species used for phylogenetic analyses. Table S2. Maximum Likelihood fits of 24 different nucleotide substitution models. Table S3. List of sampling taxa and plastome assembly information. Table S4. Nucleotide diversity (Pi) and standard deviation of Pi for 33 Polygonatum taxa. Table S5. The feature of SSRs in the complete plastomes of Polygonatum. Table S6. The feature of long repeats in the complete plastomes of Polygonatum. Table S7. The molecular diagnostic characteristics (MDCs) in the 78 plastid protein-coding genes. Table S8. Relative synonymous codon usage values of Polygonatum.

Author Contributions

J.J. collected the plant materials, performed the experiments, analyzed the data, prepared figures and tables, and wrote the initial draft. H.-J.K. and J.-H.K. designed the experiments and revised the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by grants [KNA1-1-13, 14-1] received from the scientific research fund of the Korea National Arboretum.

Institutional Review Board Statement

This study including plant samples complies with relevant institutional, national, and international guidelines and legislation. No specific permits were required for plant collection. This study did not require ethical approval or consent, as no endangered or protected plant species were involved.

Informed Consent Statement

Not applicable.

Data Availability Statement

The three plastome sequences we obtained from this study were archived in NCBI. The accession numbers are presented in Table 1 (PV199344–PV199346).

Acknowledgments

The authors would like to thank Kashish Kamra for collecting the plant material for this study.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Duminil, J.; Di Michele, M. Plant species delimitation: A comparison of morphological and molecular markers. Plant Biosyst. 2009, 143, 528–542. [Google Scholar]
  2. Li, Q.; Guo, X.; Niu, J.; Duojie, D.; Li, X.; Opgenoorth, L.; Zou, J. Molecular phylogeography and evolutionary history of the endemic species Corydalis hendersonii (Papaveraceae) on the Tibetan Plateau inferred from chloroplast DNA and ITS sequence variation. Front. Plant Sci. 2020, 11, 436. [Google Scholar]
  3. Soto, M.; Jaén-Molina, R.; Marrero, Á.; Mesa, R.; Díaz-Pérez, A.; Caujapé-Castells, J. New molecular evidence for Canarian endemic Ruta (Rutaceae: Ruteae) reveals a complex evolutionary history and overlooked diversification processes. Bot. J. Linn. Soc. 2023, 201, 80–99. [Google Scholar]
  4. Myers, N.; Mittermeier, R.A.; Mittermeier, C.G.; Da Fonseca, G.A.; Kent, J. Biodiversity hotspots for conservation priorities. Nature 2000, 403, 853–858. [Google Scholar]
  5. Wang, J.; Fu, C.-N.; Mo, Z.-Q.; Möller, M.; Yang, J.-B.; Zhang, Z.-R.; Li, D.-Z.; Gao, L.-M. Testing the complete plastome for species discrimination, cryptic species discovery and phylogenetic resolution in Cephalotaxus (Cephalotaxaceae). Front. Plant Sci. 2022, 13, 768810. [Google Scholar]
  6. Zheng, X.; Qin, K.; Li, T.; Qu, T.; Luo, J.; Zhang, G.; Li, B.; Li, P.; Fu, Z. A new species, Aster yaoshanensis (Asteracae, Astereae), from Guangxi (China), based on morphology and molecular phylogenetic data. Front. Plant Sci. 2024, 15, 1367917. [Google Scholar] [CrossRef] [PubMed]
  7. Chung, G.Y.; Hyun-Do, J.; Chang, K.S.; Choi, H.J.; Son, D.C. A checklist of endemic plants on the Korean Peninsula II. Korean J. Plant Taxon. 2023, 53, 79–101. [Google Scholar]
  8. Jang, C.G.; Oh, B.U.; Kim, Y.S. A new species of Polygonatum (Liliaceae) from Korea: P. infundiflorum. Korean J. Plant Taxon. 1998, 28, 209–215. [Google Scholar]
  9. Jang, C.G.; Oh, B.U.; Kim, Y.S. A new species of Polygonatum from Korea; P. grandicaule. Korean J. Plant Taxon. 1998, 28, 41–47. [Google Scholar]
  10. Chen, X.; Tamura, M.; Wu, Z.; Raven, P. Polygonatum mill. Flora China 2000, 24, 225–235. [Google Scholar]
  11. Judd, W.S. The genera of Ruscaceae in the southeastern United States. Harv. Pap. Bot. 2003, 7, 93–149. [Google Scholar]
  12. Motohashi, N.; Zhang, G.-W.; Shirataki, Y. Functional bioactivity of Polygonatum species. Orient. Pharm. Exp. Med. 2003, 3, 163–179. [Google Scholar]
  13. Zhao, P.; Zhao, C.; Li, X.; Gao, Q.; Huang, L.; Xiao, P.; Gao, W. The genus Polygonatum: A review of ethnopharmacology, phytochemistry and pharmacology. J. Ethnopharmacol. 2018, 214, 274–291. [Google Scholar] [CrossRef]
  14. Khan, H.; Rauf, A. Phytochemistry of genus Polygonatum: A review. Am. J. Biomed. Sci. 2015, 3, 5–20. [Google Scholar] [CrossRef]
  15. Zhao, X.; Li, J. Chemical constituents of the genus Polygonatum and their role in medicinal treatment. Nat. Prod. Commun. 2015, 10, 1934578X1501000439. [Google Scholar] [CrossRef]
  16. Meng, Y.; Nie, Z.-L.; Deng, T.; Wen, J.; Yang, Y.-P. Phylogenetics and evolution of phyllotaxy in the Solomon’s seal genus Polygonatum (Asparagaceae: Polygonateae). Bot. J. Linn. Soc. 2014, 176, 435–451. [Google Scholar] [CrossRef]
  17. Jang, C.-G. A taxonomic review of Korean Polygonatum (Ruscaceae). Korean J. Plant Taxon. 2002, 32, 417–447. [Google Scholar] [CrossRef]
  18. Lubna; Asaf, S.; Khan, I.; Jan, R.; Asif, S.; Bilal, S.; Kim, K.-M.; AL-Harrasi, A. Genetic characterization and phylogenetic analysis of the Nigella sativa (black seed) plastome. Sci. Rep. 2024, 14, 14509. [Google Scholar] [CrossRef] [PubMed]
  19. Liu, X.Y.; Zhang, D.Q.; Zhang, J.Q. Plastomic data shed new light on the phylogeny, biogeography, and character evolution of the family Crassulaceae. J. Syst. Evol. 2023, 61, 990–1003. [Google Scholar] [CrossRef]
  20. Xu, Y.; Fang, B.; Li, J.; Wang, Y.; Liu, J.; Liu, C.; Yu, J. Phylogenomic analysis and development of molecular markers for the determination of twelve plum cultivars (Prunus, Rosaceae). BMC Genom. 2022, 23, 745. [Google Scholar] [CrossRef]
  21. Fu, Q.-L.; Mo, Z.-Q.; Xiang, X.-G.; Milne, R.I.; Jacquemyn, H.; Burgess, K.S.; Sun, Y.-N.; Yan, H.; Qiu, L.; Yang, B.-Y. Plastome phylogenomics and morphological traits analyses provide new insights into the phylogenetic position, species delimitation and speciation of Triplostegia (Caprifoliaceae). BMC Plant Biol. 2023, 23, 645. [Google Scholar] [CrossRef] [PubMed]
  22. Hu, H.; Wang, Q.; Hao, G.; Zhou, R.; Luo, D.; Cao, K.; Yan, Z.; Wang, X. Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome. PeerJ 2023, 11, e16642. [Google Scholar] [PubMed]
  23. Ruhlman, T.A.; Jansen, R.K. The plastid genomes of flowering plants. In Chloroplast Biotechnology: Methods and Protocols; Springer: Berlin/Heidelberg, Germany, 2014; pp. 3–38. [Google Scholar]
  24. Floden, A.; Schilling, E. Using phylogenomics to reconstruct phylogenetic relationships within tribe Polygonateae (Asparagaceae), with a special focus on Polygonatum. Mol. Phylogenetics Evol. 2018, 129, 202–213. [Google Scholar]
  25. Lee, S.Y.; Chen, Z.; Chen, Z.; Chen, J.; Zhang, X.; Pan, J.; Fan, Q.; Liao, W. Plastid genome sequencing, identification of nuclear SNP markers, and quality assessment of medicinal rhizomatous herb Polygonatum odoratum (Asparagaceae) cultivars. Ecol. Evol. 2021, 11, 7660–7676. [Google Scholar]
  26. Wang, J.; Qian, J.; Jiang, Y.; Chen, X.; Zheng, B.; Chen, S.; Yang, F.; Xu, Z.; Duan, B. Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Polygonatum and tribe Polygonateae. Front. Plant Sci. 2022, 13, 882189. [Google Scholar] [CrossRef]
  27. Xia, M.; Liu, Y.; Liu, J.; Chen, D.; Shi, Y.; Chen, Z.; Chen, D.; Jin, R.; Chen, H.; Comes, H.P. Out of the Himalaya-Hengduan Mountains: Phylogenomics, biogeography and diversification of Polygonatum Mill. (Asparagaceae) in the Northern Hemisphere. Mol. Phylogenetics Evol. 2022, 169, 107431. [Google Scholar]
  28. Zhang, D.; Ren, J.; Jiang, H.; Wanga, V.O.; Dong, X.; Hu, G. Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae). Sci. Rep. 2023, 13, 7237. [Google Scholar] [CrossRef]
  29. Ji, Y.; Landis, J.B.; Yang, J.; Wang, S.; Zhou, N.; Luo, Y.; Liu, H. Phylogeny and evolution of Asparagaceae subfamily Nolinoideae: New insights from plastid phylogenomics. Ann. Bot. 2023, 131, 301–312. [Google Scholar]
  30. Yan, M.; Dong, S.; Gong, Q.; Xu, Q.; Ge, Y. Comparative chloroplast genome analysis of four polygonatum species insights into DNA barcoding, evolution, and phylogeny. Sci. Rep. 2023, 13, 16495. [Google Scholar] [CrossRef]
  31. Lee, S.R.; Ha, Y.-H.; Son, D.C.; Kim, S.-C. First record of the complete chloroplast genome of Polygonatum infundiflorum (Asparagaceae), a Korean endemic species. Mitochondrial DNA Part B 2023, 8, 603–606. [Google Scholar]
  32. Doyle, J. DNA protocols for plants. In Molecular Techniques in Taxonomy; Springer: Berlin/Heidelberg, Germany, 1991; pp. 283–293. [Google Scholar]
  33. Jin, J.-J.; Yu, W.-B.; Yang, J.-B.; Song, Y.; DePamphilis, C.W.; Yi, T.-S.; Li, D.-Z. GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020, 21, 241. [Google Scholar]
  34. Kearse, M.; Moir, R.; Wilson, A.; Stones-Havas, S.; Cheung, M.; Sturrock, S.; Buxton, S.; Cooper, A.; Markowitz, S.; Duran, C. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012, 28, 1647–1649. [Google Scholar] [PubMed]
  35. Tillich, M.; Lehwark, P.; Pellizzer, T.; Ulbricht-Jones, E.S.; Fischer, A.; Bock, R.; Greiner, S. GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017, 45, W6–W11. [Google Scholar]
  36. Chan, P.P.; Lowe, T.M. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences; Springer: Berlin/Heidelberg, Germany, 2019. [Google Scholar]
  37. Zheng, S.; Poczai, P.; Hyvönen, J.; Tang, J.; Amiryousefi, A. Chloroplot: An online program for the versatile plotting of organelle genomes. Front. Genet. 2020, 11, 576124. [Google Scholar]
  38. Qin, Y.-Q.; Zhang, M.-H.; Yang, C.-Y.; Nie, Z.-L.; Wen, J.; Meng, Y. Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region. Mol. Phylogenetics Evol. 2024, 190, 107962. [Google Scholar]
  39. Swofford, D. PAUP* 4.0 b. 4a. In Phylogenetic Analysis Using Parsimony* (and Other Methods); Sinauer Associates: Sunderland, MA, USA, 2000. [Google Scholar]
  40. Trifinopoulos, J.; Nguyen, L.-T.; von Haeseler, A.; Minh, B.Q. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016, 44, W232–W235. [Google Scholar] [PubMed]
  41. Tamura, K.; Stecher, G.; Kumar, S. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 2021, 38, 3022–3027. [Google Scholar]
  42. Ronquist, F.; Teslenko, M.; Van Der Mark, P.; Ayres, D.L.; Darling, A.; Höhna, S.; Larget, B.; Liu, L.; Suchard, M.A.; Huelsenbeck, J.P. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012, 61, 539–542. [Google Scholar]
  43. Rambaut, A.; FigTree. Tree Figure Drawing Tool. 2009. Available online: http://tree.bio.ed.ac.uk/software/figtree/ (accessed on 3 March 2025).
  44. Rozas, J.; Ferrer-Mata, A.; Sánchez-DelBarrio, J.C.; Guirao-Rico, S.; Librado, P.; Ramos-Onsins, S.E.; Sánchez-Gracia, A. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 2017, 34, 3299–3302. [Google Scholar]
  45. Beier, S.; Thiel, T.; Münch, T.; Scholz, U.; Mascher, M. MISA-web: A web server for microsatellite prediction. Bioinformatics 2017, 33, 2583–2585. [Google Scholar]
  46. Kurtz, S.; Choudhuri, J.V.; Ohlebusch, E.; Schleiermacher, C.; Stoye, J.; Giegerich, R. REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001, 29, 4633–4642. [Google Scholar] [CrossRef] [PubMed]
  47. Merckelbach, L.M.; Borges, L.M. Make every species count: Fastachar software for rapid determination of molecular diagnostic characters to describe species. Mol. Ecol. Resour. 2020, 20, 1761–1768. [Google Scholar] [CrossRef]
  48. Xia, X. DAMBE7: New and improved tools for data analysis in molecular biology and evolution. Mol. Biol. Evol. 2018, 35, 1550–1552. [Google Scholar] [CrossRef]
  49. Wang, J.; Chitsaz, F.; Derbyshire, M.K.; Gonzales, N.R.; Gwadz, M.; Lu, S.; Marchler, G.H.; Song, J.S.; Thanki, N.; Yamashita, R.A. The conserved domain database in 2023. Nucleic Acids Res. 2023, 51, D384–D388. [Google Scholar] [CrossRef]
  50. Lu, Q.-X.; Chang, X.; Gao, J.; Wu, X.; Wu, J.; Qi, Z.-C.; Wang, R.-H.; Yan, X.-L.; Li, P. Evolutionary comparison of the complete chloroplast genomes in Convallaria species and phylogenetic study of asparagaceae. Genes 2022, 13, 1724. [Google Scholar] [CrossRef] [PubMed]
  51. Yang, J.; Choi, M.-J.; Kim, S.-H.; Choi, H.-J.; Kim, S.-C. Plastome characterization and phylogenomic analysis yield new insights into the evolutionary relationships among the species of the subgenus Bryocles (Hosta; Asparagaceae) in East Asia. Plants 2021, 10, 1980. [Google Scholar] [CrossRef] [PubMed]
  52. Garnett, G.J.; Könyves, K.; Bilsborrow, J.; David, J.; Culham, A. The complete plastome of Hyacinthoides non-scripta (L.) Chouard ex Rothm.(Asparagaceae). Mitochondrial DNA Part B 2020, 5, 1003–1004. [Google Scholar] [CrossRef]
  53. Millen, R.S.; Olmstead, R.G.; Adams, K.L.; Palmer, J.D.; Lao, N.T.; Heggie, L.; Kavanagh, T.A.; Hibberd, J.M.; Gray, J.C.; Morden, C.W. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 2001, 13, 645–658. [Google Scholar] [CrossRef]
  54. Filip, E.; Skuza, L. Horizontal gene transfer involving chloroplasts. Int. J. Mol. Sci. 2021, 22, 4484. [Google Scholar] [CrossRef]
  55. Zhao, L.H.; Zhou, S.D.; He, X.J. A phylogenetic study of Chinese Polygonatum (Polygonateae, Asparagaceae). Nord. J. Bot. 2019, 37. [Google Scholar] [CrossRef]
  56. De-Yuan, H.; Xiang-Yun, Z. Report on karyotypes of 6 species in 4 genera of Polygonateae from China. J. Syst. Evol. 1990, 28, 185. [Google Scholar]
  57. Tamura, M.N. Biosystematic studies on the genus Polygonatum (Asparagaceae) V. Taxonomic revision of species in Japan. Acta Phytotaxon. Et Geobot. 2008, 59, 15–29. [Google Scholar]
  58. Han, M.K.; Jang, C.G.; Oh, B.U.; Kim, Y.S. A cytotaxonomic study of genus Polygonatum in Korea. Korean J. Plant Taxon. 1998, 28, 187–208. [Google Scholar]
  59. Rice, A.; Glick, L.; Abadi, S.; Einhorn, M.; Kopelman, N.M.; Salman-Minkov, A.; Mayzel, J.; Chay, O.; Mayrose, I. The Chromosome Counts Database (CCDB)—A community resource of plant chromosome numbers. New Phytol. 2015, 206, 19–26. [Google Scholar] [PubMed]
  60. Jang, C.G.; Kim, Y.S. The palynological study on the Korean Polygonatum (Liliaceae). Korean J. Plant Taxon. 1999, 29, 1–17. [Google Scholar] [CrossRef]
  61. Ali, M.; Liu, Y.J.; Xia, Q.P.; Bahadur, S.; Hussain, A.; Shao, J.W.; Shuaib, M. Pollen micromorphology of eastern Chinese Polygonatum and its role in taxonomy by using scanning electron microscopy. Microsc. Res. Tech. 2021, 84, 1451–1461. [Google Scholar]
  62. Ding, M.; Xie, Q.; Jiang, L.; Liu, L.; Luo, W.; Su, H.; Chen, Q. Pollen Morphological Characteristics of 46 Germplasm Resources of Polygonatum and Its Taxonomic Implications. Plants 2024, 13, 3509. [Google Scholar] [CrossRef]
  63. Kim, J.H.; Seo, J.W.; Byeon, J.H.; Ahn, Y.S.; Cha, S.W.; Cho, J.H. Morphological characteristics and phylogenetic analysis of Polygonatum species based on chloroplast DNA sequences. Korean J. Med. Crop Sci. 2014, 22, 489–496. [Google Scholar]
  64. Choi, T.Y.; Won, H.S.; Lee, S.R. Species delimitation in the Polygonatum odoratum complex (Asparagaceae) based on phylogenomic and morphometric data. Taxon 2025, 1–19. [Google Scholar]
  65. Xie, P.; Wang, T.; Tan, J.; Liu, C.; Yan, H. Plastid genome comparison and phylogenetic analyses of the Chinese group of medicinal species and related taxa within Asparagus genus. Front. Plant Sci. 2025, 16, 1508898. [Google Scholar]
  66. Celiński, K.; Kijak, H.; Wiland-Szymańska, J. Complete chloroplast genome sequence and phylogenetic inference of the Canary Islands Dragon Tree (Dracaena draco L.). Forests 2020, 11, 309. [Google Scholar] [CrossRef]
  67. Tian, Y.; Liu, X.; Xu, Y.; Yu, B.; Wang, L.; Qu, X. Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et SC Chen plastomes and utility of plastomes mutational hotspots. Sci. Rep. 2023, 13, 15622. [Google Scholar]
  68. Yang, J.; Kim, S.-C. Hosta clausa (Asparagaceae) in East Asia: Intraspecific chloroplast genome variation and its phylogenomic implications. PLoS ONE 2025, 20, e0317884. [Google Scholar]
Genes 16 00398 g001
Figure 1. The complete plastome map of P. grandicaule and P. odoratum var. thunbergii, along with their gene contents. Colored boxes indicate conserved plastid genes. Genes inside the circle are transcribed clockwise, whereas those outside are transcribed counterclockwise. Additionally, the gray bar graphs in the inner circle show the GC content of the plastome.
Figure 1. The complete plastome map of P. grandicaule and P. odoratum var. thunbergii, along with their gene contents. Colored boxes indicate conserved plastid genes. Genes inside the circle are transcribed clockwise, whereas those outside are transcribed counterclockwise. Additionally, the gray bar graphs in the inner circle show the GC content of the plastome.
Genes 16 00398 g001
Genes 16 00398 g002
Figure 2. The maximum likelihood (ML) tree, constructed from (A) 78 plastid protein-coding genes (PCGs) and (B) whole intergenic spacer (IGS) regions, includes 53 taxa. Numbers indicate support values, represented as parsimony bootstrap percentages (PBPs)/mean bootstrap percentages (MBPs)/SH-aLRT support/posterior probability (PP). Only support values with MBP ≤ 90%, MBP ≤ 90%, SH-aLRT ≤ 90%, and PP ≤ 0.95 are displayed. Nodes with values below 50/50/50/0.5, or nodes exhibiting a different topology, are marked with “-”. The bold names indicate genomes obtained in this study. Abbreviations; YD: Yeongdong individual, YW: Yeongwol individual.
Figure 2. The maximum likelihood (ML) tree, constructed from (A) 78 plastid protein-coding genes (PCGs) and (B) whole intergenic spacer (IGS) regions, includes 53 taxa. Numbers indicate support values, represented as parsimony bootstrap percentages (PBPs)/mean bootstrap percentages (MBPs)/SH-aLRT support/posterior probability (PP). Only support values with MBP ≤ 90%, MBP ≤ 90%, SH-aLRT ≤ 90%, and PP ≤ 0.95 are displayed. Nodes with values below 50/50/50/0.5, or nodes exhibiting a different topology, are marked with “-”. The bold names indicate genomes obtained in this study. Abbreviations; YD: Yeongdong individual, YW: Yeongwol individual.
Genes 16 00398 g002
Genes 16 00398 g003
Figure 3. Nucleotide diversity (Pi) values of the plastomes of 36 Polygonatum taxa.
Figure 3. Nucleotide diversity (Pi) values of the plastomes of 36 Polygonatum taxa.
Genes 16 00398 g003
Genes 16 00398 g004
Figure 4. Statistics on different types of SSRs and repeats in Polygonatum. (A) The number of simple sequence repeats (SSRs) categorized by repeat unit length. “mono”, “di”, “tri”, “tetra”, and “penta” correspond to mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotide repeats, respectively. (B) The total length of each SSR type. (C) The count of dispersed repeats, including forward, reverse, complementary, and palindromic repeats. (D) The cumulative length of the respective dispersed repeats. Abbreviations; YD: Yeongdong individual, YW: Yeongwol individual.
Figure 4. Statistics on different types of SSRs and repeats in Polygonatum. (A) The number of simple sequence repeats (SSRs) categorized by repeat unit length. “mono”, “di”, “tri”, “tetra”, and “penta” correspond to mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotide repeats, respectively. (B) The total length of each SSR type. (C) The count of dispersed repeats, including forward, reverse, complementary, and palindromic repeats. (D) The cumulative length of the respective dispersed repeats. Abbreviations; YD: Yeongdong individual, YW: Yeongwol individual.
Genes 16 00398 g004
Genes 16 00398 g005
Figure 5. Quantitative analysis of molecular diagnostic characteristics (MDCs) in 78 plastid protein-coding genes (PCGs) across 53 Polygonateae species. The blue bars represent cases with more than 80 MDCs across genera, the green bars indicate cases with more than 30 MDCs within the genus Polygonatum, and the gray bars denote cases with fewer than 30 MDCs.
Figure 5. Quantitative analysis of molecular diagnostic characteristics (MDCs) in 78 plastid protein-coding genes (PCGs) across 53 Polygonateae species. The blue bars represent cases with more than 80 MDCs across genera, the green bars indicate cases with more than 30 MDCs within the genus Polygonatum, and the gray bars denote cases with fewer than 30 MDCs.
Genes 16 00398 g005
Genes 16 00398 g006
Figure 6. Relative synonymous codon usage (RSCU) analysis of 20 amino acids in 78 plastid protein-coding genes (PCGs) from the complete plastomes of the P. odoratum complex. The values at the top of each stacked bar indicate the usage frequency for each amino acid.
Figure 6. Relative synonymous codon usage (RSCU) analysis of 20 amino acids in 78 plastid protein-coding genes (PCGs) from the complete plastomes of the P. odoratum complex. The values at the top of each stacked bar indicate the usage frequency for each amino acid.
Genes 16 00398 g006
Genes 16 00398 g007
Figure 7. The heat map of codon usage bias in the plastomes of genus Polygonatum. The red color indicates higher relative synonymous codon usage (RSCU) values and the blue color indicates lower RSCU values. Abbreviations; YD: Yeongdong individual, YW: Yeongwol individual.
Figure 7. The heat map of codon usage bias in the plastomes of genus Polygonatum. The red color indicates higher relative synonymous codon usage (RSCU) values and the blue color indicates lower RSCU values. Abbreviations; YD: Yeongdong individual, YW: Yeongwol individual.
Genes 16 00398 g007
Table 1. Features of the LSC, SSC, and IR of plastomes obtained in this study.
Table 1. Features of the LSC, SSC, and IR of plastomes obtained in this study.
TaxaLength and G+C ContentGenBank
Accession No.		Voucher
(Accession)
LSC bp
(G+C%)		SSC bp
(G+C%)		IR bp
(G+C%)		Total bp
(G+C%)
P. grandicaule Y.S.Kim, B.U.Oh & C.G.Jang (Yeongdong, Chungcheongbuk-do)83,527
(35.8)		18,457
(31.6)		26,297
(43.0)		154,578
(37.7)		PV199344JH220610014
P. grandicaule Y.S.Kim, B.U.Oh & C.G.Jang (Yeongwol, Gangwon-do)83,528
(35.8)		18,457
(31.6)		26,297
(43.0)		154,579
(37.7)		PV199345JH220617027
Polygonatum odoratum var. thunbergii (C.Morren & Decne.) H.Hara (Danyang, Chungcheongbuk-do)83,527
(35.8)		18,457
(31.6)		26,297
(43.0)		154,578
(37.7)		PV199346JH220617013
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Jung, J.; Kim, H.-J.; Kim, J.-H. Plastome Sequences Uncover the Korean Endemic Species Polygonatum grandicaule (Asparagaceae) as Part of the P. odoratum Complex. Genes 2025, 16, 398. https://doi.org/10.3390/genes16040398

AMA Style

Jung J, Kim H-J, Kim J-H. Plastome Sequences Uncover the Korean Endemic Species Polygonatum grandicaule (Asparagaceae) as Part of the P. odoratum Complex. Genes. 2025; 16(4):398. https://doi.org/10.3390/genes16040398

Chicago/Turabian Style

Jung, Joonhyung, Hyuk-Jin Kim, and Joo-Hwan Kim. 2025. "Plastome Sequences Uncover the Korean Endemic Species Polygonatum grandicaule (Asparagaceae) as Part of the P. odoratum Complex" Genes 16, no. 4: 398. https://doi.org/10.3390/genes16040398

APA Style

Jung, J., Kim, H.-J., & Kim, J.-H. (2025). Plastome Sequences Uncover the Korean Endemic Species Polygonatum grandicaule (Asparagaceae) as Part of the P. odoratum Complex. Genes, 16(4), 398. https://doi.org/10.3390/genes16040398

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop