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. 2026 Jun 26;11(7):888–892. doi: 10.1080/23802359.2026.2694146

The complete chloroplast genome and phylogenetic analysis of Viburnum furcatum (adoxaceae)

Yun-Gyeong Choi 1, Sang-Hun Oh 1,✉
PMCID: PMC13312840  PMID: 42375482

Abstract

Viburnum furcatum is a deciduous shrub distributed in Korea, Japan, and Sakhalin. We sequenced, assembled, and annotated the complete chloroplast genome of a specimen from Ulleungdo Island, Korea. The genome is a typical quadripartite circular molecule of 158,284 bp, comprising a large single-copy region of 86,878 bp, a small single-copy region of 18,400 bp, and two inverted repeats of 26,503 bp each, with an average sequencing depth of 654.43×. The genome contains 128 genes, with 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis places V. furcatum as a sister to V. sympodiale. These data provide a valuable information for future studies of Viburnum.

Keywords: East Asia, genome assembly, phylogeography, the Pseudotinus clade, Ulleungdo Island

Introduction

Viburnum Linnaeus (1753), with approximately 163 species, is a well-known genus of flowering plants in the family Adoxaceae, distributed in temperate and subtropical regions throughout the Northern Hemisphere and in the cloud forests of South America (Donoghue et al. 2004). The phylogeny of Viburnum has been continuously refined through molecular phylogenetic studies using multiple nuclear and chloroplast DNA regions, greatly improving our understanding of the relationships among major lineages, the biogeography, as well as character evolution and classification of this genus (Donoghue et al. 2004; Winkworth and Donoghue 2004, 2005; Clement and Donoghue 2011, 2012; Clement et al. 2014; Choi et al. 2018; Landis et al. 2021).

Viburnum furcatum Blume ex Maxim. (1880) is a deciduous shrub distributed across northeastern Asia, occurring in South Korea (Jejudo and Ulleungdo islands), the Japanese archipelago, and Sakhalin, as well as the Kuril Islands (Choi et al. 2018). This broad and fragmented distribution across northeastern Asia provides an excellent model for studying complex infraspecific genetic structures shaped by historical range dynamics and dispersal events. For example, isolated volcanic oceanic islands, such as Ulleungdo Island, provide an important biogeographic context for evaluating population isolation and the accumulation of genetic divergence, as the restricted gene flow with the mainland and the cumulative effects of founder events and genetic drift can promote genetic differentiation (Takayama et al. 2012; Garot et al. 2019).

Informative and efficient chloroplast DNA markers are essential for understanding infraspecific variations. Complete chloroplast genome sequences can serve as a reference for developing highly variable, species-specific markers. Although complete chloroplast genomes of many Viburnum species have been reported (Clement et al. 2014; Choi et al. 2019; Ran et al. 2020; Wang et al. 2020; Zhao et al. 2020; Zhao and Pan 2020; Gu et al. 2021; Zhu et al. 2023), the chloroplast genome of V. furcatum remains undetermined.

In this study, we sequenced and annotated the complete chloroplast genome of V. furcatum collected on Ulleungdo Island in Korea and report its genomic features. In addition, we reassess its phylogenetic position within the Viburnum genus by means of a phylogenetic analysis based on the chloroplast genome, thereby providing a foundational genomic resource for future comparative genomics, phylogenetic, and biogeographic studies.

Material and methods

Plant material

Fresh leaf tissue of V. furcatum was collected from Seongin-bong, Ulleungdo Island, Gyeongsangbuk-do, Republic of Korea (37°29’39.2ʺN, 130°52’40.7ʺE) (Figure 1). The voucher specimen (DJU_ULVF01) was deposited in the Daejeon University Herbarium (TUT: https://www.dju.ac.kr/biosci/depart/profileView.do?mi=2253, contact: Sang-Hun Oh, e-mail: soh42@dju.kr).

Figure 1.

A dense cluster of white flowers of Viburnum furcatum is characterized by showy sterile marginal flowers, in which only the petals are well developed. These flowers likely attract pollinators, whereas the smaller bisexual flowers are located in the center of the inflorescence. The leaves are opposite and green, and the fruits change color from green to red and eventually to black as they mature.

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Photographs of V. furcatum. It is characterized by its naked buds (winter buds lacking scales), opposite leaves, showy sterile marginal flowers surrounding centrally positioned bisexual flowers, and fruits that mature sequentially, changing in color from red to black. (A) Inflorescence. (B) Leaves and fruits. The photographs were taken by the authors, Y.-G. Choi and S.-H. Oh.

DNA extraction and genome sequencing

Genomic DNA was extracted using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The total DNA quality was assessed by electrophoresis on a 1% agarose gel, and the concentration was measured using an Invitrogen Qubit fluorometer. A sequencing library was prepared from 1 µg of DNA using a TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA). The library was sequenced as paired-end reads (2 × 150 bp) on the Illumina NovaSeq 6000 platform at Macrogen Inc. (Seoul, Republic of Korea).

Genome assembly and annotation

Raw sequencing data (6.23 Gb) were quality-checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The chloroplast genome was de novo assembled using GetOrganelle v1.7.7.1 with default parameters (Jin et al. 2020). The assembled chloroplast genome was annotated in Geneious Prime 2025.2 (Kearse et al. 2012) based on the chloroplast genome of Viburnum erosum (GenBank accession no. MN641480) (Choi et al. 2019). A circular gene map of the chloroplast genome was visualized using CPGView (http://www.1kmpg.cn/cpgview/). The complete annotated chloroplast DNA sequence was submitted to GenBank.

Phylogenetic tree construction

To determine the phylogenetic position of V. furcatum, complete chloroplast genomes of 26 Viburnum species and three Sambucus species (outgroups) were downloaded from the NCBI GenBank database and included in the analysis. A total of 30 chloroplast genomes were aligned with MAFFT v7 (Katoh et al. 2002). The maximum-likelihood (ML) phylogenetic tree was constructed in IQ-TREE v3.0.1 (Wong et al. 2025) under the TVM+I + G model, selected as the best-fit substitution model based on the Akaike information criterion (AIC) in jModelTest v2.1.10 (Darriba et al. 2012). ML bootstrap support (BS) was assessed with 1,000 ultrafast bootstrap replicates. Bayesian inference (BI) was performed using MrBayes v3.2.6 (Ronquist et al. 2012) with 1,000,000 MCMC generations, discarding the first 25% as burn-in, and posterior probabilities (PP) were calculated as a measure of node support. The resulting phylogenetic tree was visualized and edited using iTOL v7 (Letunic and Bork 2024).

Results

Characteristics of the chloroplast genome

The complete chloroplast genome of V. furcatum (GenBank accession no. PX673849) had an average depth of 654.43 x (Figure S1). It comprised four regions: a large single-copy (LSC) region of 86,878 bp, a small single-copy (SSC) region of 18,400 bp, and a pair of inverted repeats (IRA and IRB) of 26,503 bp each (Figure 2). The chloroplast genome contained 128 genes, consisting of 83 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Among these genes, 14 (atpF, ndhA, ndhB, petB, petD, rpl2, rpoC1, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) contained one intron, whereas two (clpP and ycf3) contained two introns. In addition, ten cis-splicing genes (atpF, clpP, ndhA, ndhB, petB, petD, rpl2, rpoC1, rps16, and ycf3) and one trans-splicing gene (rps12) were identified (Figures S2 and S3).

Figure 2.

Circular diagram of Viburnum furcatum plastid genome showing gene structures, categories, GC content, and connections. The figure illustrates a detailed circular diagram of the Viburnum furcatum plastid genome, with the outer ring displaying color-coded gene annotations categorized by functions like photosystems and ATP synthesis. Gene names and values indicate expression levels. A histogram represents GC content variation across the genome. The diagram includes structural regions (LSC, SSC, IRA, IRB) and interconnecting lines highlight genetic relationships, emphasizing the organization and connectivity of genomic components.

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Complete chloroplast genome map of V. furcatum generated using CPGView. The map consists of six concentric circles. From the center outward; the first circle shows forward and reverse repeats connected by red and green arcs, respectively; the second circle shows tandem repeats as short blue bars; the third circle shows microsatellite sequences as short green and yellow bars; the fourth circle indicates the positions of the large single-copy (LSC), small single-copy (SSC), and inverted repeat regions (IRA and IRB); the fifth circle shows the GC content along the genome; and the sixth circle displays genes, which are color-coded according to the corresponding functional categories (legend in the lower-left corner). Genes on the inner and outer circles are transcribed in the clockwise and counterclockwise directions, respectively.

Phylogenetic relationships

The phylogenetic analysis showed that the 27 Viburnum species analyzed in this study formed a strongly supported monophyletic group (Figure 3). Viburnum furcatum was determined to be a sister to V. sympodiale with high support (BS = 100, PP = 1.0). These two species, classified in the Pseudotinus clade, were resolved as a sister to the Euviburnum-Lentago clade. The phylogenetic relationships among major Viburnum lineages in our analysis are consistent with previous phylogenetic and systematic conclusions.

Figure 3.

Phylogenetic tree illustrating relationships among *Viburnum* and *Sambucus* species with branch lengths and support values. This phylogenetic tree depicts the evolutionary relationships among 27 *Viburnum* species and 3 *Sambucus* species as an outgroup. Branch lengths indicate genetic divergence, with support values noted at each node, such as 1/100 or 0.9262/66. Species names are accompanied by accession numbers, and the tree is color-coded by eleven subgenera, including Succinus (light blue) and Pseudotinus (yellow). The scale bar at the bottom represents 0.003 substitutions per site. The species 'Viburnum furcatum [PX673849]' is highlighted in red.

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Maximum likelihood (ML) phylogenetic tree inferred from complete chloroplast genome sequences of V. furcatum and 26 additional viburnum species. Clade names follow Clement et al. (2014) and are indicated alongside the corresponding branches. The complete chloroplast genomes of sambucus adnata (MT457823; Ran et al. 2020), sambucus javanica (MT457822; Ran et al. 2020), and Sambucus nigra (MT457821; Ran et al. 2020) were used as outgroups. The newly assembled chloroplast genome of V. furcatum generated in this study (PX673849) is highlighted in red. Bayesian inference (BI) and ML bootstrap support (BS) values are shown above each branch in that order. The complete chloroplast genomes included in the analysis were as follows: Viburnum acerifolium (PP101997), viburnum amplificatum (PP109814), viburnum betulifolium (MG738665), viburnum brachybotryum (MN524624), viburnum burejaeticum (MW296956; Gu et al. 2021), viburnum carlesii (MN985820), viburnum carlesii x viburnum macrocephalum (NC_048464), viburnum chinshanense (OP994186), viburnum dentatum (PP101998), viburnum erosum (MN641480; Choi et al. 2019), viburnum farreri (MT133259; Zhao and Pan 2020), viburnum grandiflorum (PP109815), viburnum japonicum (OP644292; Zhu et al. 2023), viburnum lentago (PP102001), viburnum molle (PP025520), viburnum mongolicum (PX111644), viburnum odoratissimum (MN894600; Wang et al. 2020), viburnum opulus (LT996894), viburnum opulus var. sargentii (MW788538), viburnum plicatum (PP102000), viburnum rhytidophyllum (MT374829), viburnum schensianum (MT003225; Zhao et al. 2020), viburnum setigerum (PX530810), viburnum sympodiale (PP078695), viburnum tinus (PP101999), and viburnum utile (KX792264).

Discussion and conclusion

The complete chloroplast genome of V. furcatum exhibits the typical quadripartite organization of angiosperm chloroplast genomes and a conserved gene complement, including intron-containing genes and the canonical trans-splicing structure of rps12 (Daniell et al. 2016). Together with the high sequencing depth, these features support the conclusion that the V. furcatum chloroplast genome is highly conserved in terms of the genomic content and gene order compared with those reported for other Viburnum species (Clement et al. 2014; Choi et al. 2019; Ran et al. 2020; Wang et al. 2020; Zhao et al. 2020; Zhao and Pan 2020; Gu et al. 2021; Zhu et al. 2023).

Our phylogenetic analysis of chloroplast genomes strongly supports the placement of V. furcatum within the Pseudotinus clade, consistent with previous systematic frameworks (Clement et al. 2014). The reference chloroplast genome generated in this study provides a valuable resource for future phylogeographic and comparative studies of V. furcatum across its range, including investigations of genetic diversity among populations on Ulleungdo, Jejudo, various parts of Japan, and Sakhalin (Takayama et al. 2012; Garot et al. 2019). The chloroplast genome data also contribute to a better understanding of the phylogenetics and evolution of Viburnum in the Northern Hemisphere.

Supplementary Material

figure S1.tif
TMDN_A_2694146_SM1379.tif (23.7MB, tif)
figure S3.tif
TMDN_A_2694146_SM1378.tif (14.2MB, tif)
figure S2.tif
TMDN_A_2694146_SM1377.tif (45.6MB, tif)

Acknowledgments

Y.-G. Choi and S.-H. Oh contributed to the study conception and design, data analysis, interpretation, and drafting of the manuscript. Y.-G. Choi conducted the sampling and laboratory work, assembled and analyzed the chloroplast genome data, and prepared the initial draft of the manuscript. S.-H. Oh coordinated the project, secured funding, developed the initial research ideas, and revised and edited the manuscript. All authors approved the final manuscript and agreed to be accountable for all aspects of the work.

Funding Statement

This research was supported by a grant from the National Institute of Biological Resources, the Ministry of Climate, Energy, and Environment, Korea (NIBR202527202) and the Korea Research Foundation (RS-2023-00280375).

Ethical approval

The authors declare that no ethical or legal violations occurred during the collection of the study materials or the conduct of this research. The study species is not listed on the IUCN Red List. Samples were collected legally in accordance with applicable national and international regulations. The materials were collected from a site that is not designated as a protected area in Korea. Ethical approval and an Institutional Review Board (IRB) review by Daejeon University were not required for this study.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the findings of this study are openly available in GenBank (https://www.ncbi.nlm.nih.gov/) under accession number PX673849. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA1402911, SRR36840912, SAMN54606365, respectively.

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Associated Data

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

Supplementary Materials

figure S1.tif
TMDN_A_2694146_SM1379.tif (23.7MB, tif)
figure S3.tif
TMDN_A_2694146_SM1378.tif (14.2MB, tif)
figure S2.tif
TMDN_A_2694146_SM1377.tif (45.6MB, tif)

Data Availability Statement

The data that support the findings of this study are openly available in GenBank (https://www.ncbi.nlm.nih.gov/) under accession number PX673849. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA1402911, SRR36840912, SAMN54606365, respectively.

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