| Home | E-Submission | Sitemap | Editorial Office |  
Korean J. Pl. Taxon > Volume 53(1); 2023 > Article
CHOI, KIM, PARK, KANG, and YANG: The complete plastid genome and nuclear ribosomal transcription unit sequences of Spiraea prunifolia f. simpliciflora (Rosaceae)


Spiraea prunifolia f. simpliciflora Nakai is a perennial shrub widely used for horticultural and medicinal purposes. We simultaneously obtained the complete plastid genome (plastome) and nuclear ribosomal gene transcription units, 45S nuclear ribosomal DNA (nrDNA) and 5S nrDNA of S. prunifolia f. simpliciflora, using Illumina short-read data. The plastome is 155,984 bp in length with a canonical quadripartite structure consisting of 84,417 bp of a large single-copy region, 18,887 bp of a short single-copy region, and 26,340 bp of two inverted repeat regions. Overall, a total of 113 genes (79 protein-coding genes, 30 tRNAs, and four rRNAs) were annotated in the plastome. The 45S nrDNA transcription unit is 5,848 bp in length: 1,809 bp, 161 bp, and 3,397 bp for 18S, 5.8S, and 26S, respectively, and 261 bp and 220 bp for internal transcribed spacer (ITS) 1 and ITS 2 regions, respectively. The 5S nrDNA unit is 512 bp, including 121 bp of 5S rRNA and 391 bp of intergenic spacer regions. Phylogenetic analyses showed that the genus Spiraea was monophyletic and sister to the clade of Sibiraea angustata, Petrophytum caespitosum and Kelseya uniflora. Within the genus Spiraea, the sections Calospira and Spiraea were monophyletic, but the sect. Glomerati was nested within the sect. Chamaedryon. In the sect. Glomerati, S. prunifolia f. simpliciflora formed a subclade with S. media, and the subclade was sister to S. thunbergii and S. mongolica. The close relationship between S. prunifolia f. simpliciflora and S. media was also supported by the nrDNA phylogeny, indicating that the plastome and nrDNA sequences assembled in this study belong to the genus Spiraea. The newly reported complete plastome and nrDNA transcription unit sequences of S. prunifolia f. simpliciflora provide useful information for further phylogenetic and evolutionary studies of the genus Spiraea, as well as the family Rosaceae.


Rosaceae, commonly known as the rose family, contains more than 95 genera and 3,000 species (Potter et al., 2007; Hummer and Janick, 2009). In the family Rosaceae, the genus Spiraea contains more than 50 species and is mainly distributed in temperate and subtropical regions of the northern hemisphere (Hummer and Janick, 2009; Oh et al., 2010; Yu et al., 2018; Kostikova and Petrova, 2021). Spiraea prunifolia f. simpliciflora is a perennial shrub with ovate to oblonglanceolate leaves and an umbel inflorescence (Jang et al., 2020). This taxon is widely distributed in East Asia and is also cultivated in South Korea from the northern to southern parts of the country. It is primarily used for ornamental purposes, along with S. prunifolia Siebold & Zucc, which has double flowers (Jang et al., 2020). The Spiraea species are known to be useful horticultural and edible plants due to their beautiful flowers and high nectar content. The Spiraea species have traditionally been used as diuretics, antidotes, and painkillers in East Asia (Woo et al., 1996; Bae et al., 2012). Recently, it has also been reported that hydrothermal and ethanol extracts from the roots of S. prunifolia f. simpliciflora have antioxidant, anti-inflammatory, anti-cancer effects and that they protect nerve cells (Sim et al., 2017; Oh et al., 2018; Kim et al., 2019).
Plastid is an endosymbiotic organelle for photosynthesis that contains its own maternally inherited genome. In most plants, the plastid genome (plastome) is a circular molecule of 150–170 kb, generally consisting of a large single copy (LSC), a short single copy (SSC), and two inverted repeats (IR). The development of next-generation sequencing (NGS) has led to extensive studies of plastomes in land plants by reducing the time and cost required to assemble the plastome, with the conserved features and sufficient polymorphisms of the plastome enabling the plastome to be used for phylogenomic studies of various plants, such as Daphne and Viburnum (Leebens-Mack et al., 2005; Xu et al., 2015; Park et al., 2020; Yoo et al., 2021).
Along with the plastome data, the 45S and 5S nuclear ribosomal DNAs (nrDNAs) in the nuclear genome, which constitute the catalytic core of ribosomes, are also widely used for phylogenetic studies in land plants (Rodnina et al., 2007). The 45S nrDNA units are composed of three subunits (18S, 5.8S, and 26S rDNAs) and two internal transcribed spacer (ITS-1 and ITS-2) regions, and thousands of 45S units are tandemly repeated in the nuclear genome (Long and Dawid, 1980). Due to their structural advantage, the 45S and 5S rDNA sequences are highly conserved, making them a useful resource for phylogenetic studies of land plants (Lagesen et al., 2007). Previously, phylogenetic studies of the genus Spiraea using the nuclear ribosomal internal transcribed spacer region and a few plastid markers have revealed problems, such as discordance between different gene trees and polytomies due to insufficient informative sites for constructing phylogenies (Oh et al., 2010; Yu et al., 2018). In this study, we document the complete plastome and two nrDNA sequences of S. prunifolia f. simpliciflora. The results of our study can serve as a fundamental resource for further studies to understand these phylogenetic relationships and establish a classification of the genus Spiraea by considering phylogenetic evidence.


Fresh leaves of S. prunifolia f. simpliciflora were collected from one plant identified at Mt. Gwanaksan in Seoul, South Korea. A voucher specimen was deposited in the National Institute of Biological Resources Herbarium (KB) under voucher number ZFTDVP0000000009. Total DNA was extracted from 100 mg of fresh leaves using the GeneAll Plant SV midi kit (GeneAll Biotechnology, Seoul, Korea) according to the manufacturer’s protocol. The DNA quality and quantity were examined using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Whole-genome sequencing was conducted with the Illumina NovaSeq 6000 platform with paired-end reads of 2 × 151 bp at LabGenomics Co. Ltd. (Seongnam, Korea). Phred scores of 20 or lower were removed from the total NGS paired-end reads with the CLC-quality trim tool included in the CLC Assembly Cell package (ver. 4.06 beta). The plastome was de novo assembled using two methods, GetOrganelle v1.7.6.1 and the modified dnaLCW method (Kim et al., 2015; Jin et al., 2020). Assembly errors and gaps in the assembled plastome were manually corrected by mapping raw reads with Minimap2 (Li, 2018). Gene annotation of the assembled plastome was performed using BLAST and Chloe v. 0.1.0 in GeSeq and manually curated using the Artemis annotation tool (Altschul et al., 1990; Carver et al., 2012; Tillich et al., 2017). A circular map of the S. prunifolia f. simpliciflora plastome was drawn using OGDRAW v 1.3.1 (Greiner et al., 2019).
The 45S nrDNA unit sequences of S. prunifolia f. simpliciflora were assembled using the modified dnaLCW method. The start and end positions for each 45S nrDNA subunit (18S, ITS1, 5.8S, ITS2, and 26S) were determined using BLAST. The 45S nrDNA sequence of Musa acuminate cv. Formosana (LC610757.1) was used as a reference. The 5S nrDNA sequence was assembled by mapping raw reads to the sequence of Arabidopsis thaliana (AF330993.1). After determining the 5S nrDNA sequence, the intergenic spacer (IGS) region was assembled by elongation, with this step repeated until the elongated sequence reached the next 5S nrDNA unit. The total 5S nrDNA unit with the corresponding IGS region was confirmed using BLAST (Altschul et al., 1990). In addition, a total of seven sequence-read-archive (SRA) data consisting of one Aruncus dioicus and six Spiraea (S. media, S. chamaedryfolia, S. × rosalba, S. alba var. latifolia, and two S. × billardii) were downloaded from NCBI GenBank with accession numbers ERR5555288, ERR5554804, ERR5554733, ERR5554594, ERR555281, ERR5554552, and ERR5554770, respectively, and used for assembly and annotation of the plastome and nrDNA transcription units via the assembly strategies described above.
Twenty-four plastome sequences in the tribe Spiraeeae and two plastome sequences of the genus Gillenia in the tribe Gillenieae (outgroup) were included in the phylogenetic analysis. A total of 76 protein-coding genes shared by 26 plastomes were used for the phylogenetic analysis. Each gene was aligned using MAFFT v. 7.427 with the --maxiterate 1000 option (Katoh and Standley, 2013), and then concatenated into a matrix. Phylogenetic analysis was performed using the RAxML v. 8.2.12 with 1,000 replicates and the GTRGAMMA model (Stamatakis, 2014). To compare the phylogenetic relationships of the genus Spiraea between plastome and nrDNA phylogenies, eight plastome and nrDNA sequences (seven Spiraea and one Aruncus) assembled in this study were used. The plastome sequences with only one copy of the IR region and entire 45S nrDNA sequences were aligned using MAFFT, after which RAxML was used for phylogenetic reconstruction. The options used for alignment and phylogenetic reconstruction steps were identical to those described above.


A total of 22,962,984 reads were generated by means of whole-genome shotgun sequencing. Approximately 13.02% of the obtained reads were determined as the plastome reads with 2,643.92× coverage. The assembled plastome sequence of S. prunifolia f. simpliciflora was 155,984 bp in length with a GC content of 36.7% and with a quadripartite structure, consisting of 84,417 bp of a LSC region (GC content: 34.5%), 18,887 bp of a SSC region (GC content: 30.3%), and 26,340 bp of two IR regions (GC content: 42.5%). The plastome contained 113 genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes (Fig. 1A). The assembled plastome sequence, BioProject, BioSample, and SRA data can be accessed via accession numbers OP874593, PRJNA904405, SAMN31842511, and SRR22385993, respectively. The assembled 45S nrDNA sequence was 5,848 bp in length with a GC content of 55.9%, consisting of 1,809 bp of 18S, 161 bp of 5.8S, and 3,397 bp of 26S which were separated by two ITS regions, 261 bp of ITS-1 and 220 bp of ITS-2 (Fig. 1B). The total length of the assembled 5S nrDNA unit was 512 bp, made up of 121 bp of a 5S transcription unit and 391 bp of an IGS region (Fig. 1C). The assembled 45S nrDNA and 5S nrDNA sequences can be accessed via accession numbers OP966298 and OP957414, respectively.
The phylogenetic result based on 26 plastome sequences indicated that the genus Spiraea was monophyletic (Fig. 2). In the tribe Spiraeeae, Sibiraea angustata, Petrophytum caespitosum, and Kelseya uniflora formed a single clade that was a sister to the genus Spiraea, and this result was consistent with previous studies (Suh et al., 2021; Park et al., 2022). Most clades in the genus Spiraea were well supported by nearly 100% bootstrap values, except for the sect. Spiraea. Sect. Glomerati, including S. pruniflora f. simpliciflora, S. thunbergii, and S. media, was nested within sect. Chamaedryon (Fig. 2); this phylogenetic relationship has previously been reported as well (Yu et al., 2018).
A comparison between the plastome and nrDNA phylogenies showed that S. prunifolia f. simpliciflora has a consistent position as a sister to S. media in both phylogenies (Fig. 3). However, the sect. Spiraea, composed of S. alba var. latifolia and its hybrid species, S. × rosalba and two S. × billardii, showed discordance between the two phylogenies owing to the different inheritance systems between the plastid and nuclear genomes (Zhang et al., 2012; Khan et al., 2014). In the phylogeny based on biparentally inherited nrDNA sequences, two S. × billardii formed their own subclade; S. alba var. latifolia formed a subclade with S. × rosalba (Fig. 3A), but they were not in the plastome-based phylogeny with relatively low branch support values (Fig. 3B). The plastome-based phylogeny showed a short branch length in the clade of S. alba var. latifolia and its hybrid species (Fig. 3B). The low resolution of plastome-based phylogeny may be caused by the maternal inheritance of the plastome in the genus Spiraea, providing some genetic evidence of the artificial hybridization of S. × rosalba and S. × billardii with S. alba as their maternal parent (Plants of the World Online, 2023). A comparison between plastome and nrDNA phylogenies may reveal the other inherited patterns of the two species originating from hybridization, S. × rosalba and S. × billardii. It is known that S. × rosalba was generated by hybridization between S. alba and S. salicifolia, and S. × billardii was generated from that between S. alba and S. douglasii (Plants of the World Online, 2023). The nrDNA phylogeny showed that two individuals of S. × billardii, whose paternal parent was S. douglasii, formed their own subclade, and S. × rosalba, whose paternal parent was S. salicifolia, formed a subclade with S. alba var. latifolia, suggesting that the nrDNA phylogeny provides the evolutionary patterns of the biparental inheritance, including the paternal inheritance.
Consequently, the infrageneric relationships of the genus Spiraea remain unclear (Oh et al., 2010; Lee and Hong, 2011), and conflicts between morphological and molecular evidence still exist (Yu et al., 2018). Further studies using both biparental nuclear and uniparental plastome data with extensive sampling will be needed to reveal the infrageneric relationships of the genus Spiraea. We believe that the complete plastome and nrDNA sequences of S. prunifolia f. simpliciflora will be useful in further studies to understand the phylogenetic relationships and the evolutionary history of the genus Spiraea, as well as the family Rosaceae.


This study was supported by the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR202206101).


The authors declare that there are no conflicts of interest.

Fig. 1.
Circular map of the plastid genome and structures of the nuclear ribosomal DNA (nrDNA) of Spiraea prunifolia f. simpliciflora. A. This figure was drawn by OGDRAW v. 1.3.1 and annotated by BLAST and Chloe v. 0.1.0 in GeSeq. Large single copy, small single copy, and inverted repeats are indicated as LSC, SSC, and IR (IRA and IRB), respectively. B. 45S nrDNA structure with corresponding subunits and length. C. 5S nrDNA structure with the corresponding IGS region and length. IGS, intergenic spacer; ITS, internal transcribed spacer.
Fig. 2.
Maximum likelihood (ML) phylogenetic tree inferred from 26 plastid genome sequences of the tribe Spiraeeae in Rosaceae. The infrageneric classification proposed by Yu and Kuan (1963) is shown in the clade of the genus Spiraea. The taxon in bold is the plastome sequence newly assembled in this study. Bootstrap values are indicated near the branches (indicated only if the bootstrap value is greater than 50).
Fig. 3.
Comparison of phylogenetic relationships between plastome and nuclear ribosomal DNA (nrDNA) phylogenies. A. Phylogenetic tree based on 45S nrDNA sequences. B. Phylogenetic tree based on plastid genome sequences. Colored lines indicate the same individual in each phylogeny. Bootstrap values are indicated near the branches. Red line: genus Aruncus, Pink line: sect. Spiraea, Blue line: sect. Glomerati, Green line: sect. Chamaedryon.


Altschul, S. F. Gish, W. Miller, W. Myers, E. W and Lipman, D. J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
crossref pmid
Bae, J. Y. Ahn, M. J and Park, J. H. 2012. Pharmacognostical studies on the folk medicine. Korean Journal of Pharmacognosy 43: 1-5.

Carver, T. Harris, S. R. Berriman, M. Parkhill, J and McQuillan, J. A. 2012. Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28: 464-469.
crossref pmid pmc pdf
Greiner, S. Lehwark, P and Bock, R. 2019. OrganellarGenome-DRAW (OGDRAW) version 1.3.1: Expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 47: W59-W64.
crossref pmid pmc
Hummer, K. E and Janick, J. 2009. Rosaceae: Taxonomy, economic importance, genomics. Folta, K. M. Gardiner, S. E (eds.), Genetics and Genomics of Rosaceae. Springer, New York. 1-17.
crossref pmid
Jang, C. G. Na, N and Park, M. S. 2020. Spiraea prunifolia var. simpliciflora (Nakai) Nakai. Silvics of Korea. 5: Korea National Arboretum (ed.), Korea National Arboretum, Pocheon. 191-200.

Jin, J.-J. Yu, W.-B. Yang, J.-B. Song, Y. dePamphilis, C. W. Yi, T.-S and Li, D.-Z. 2020. GetOrganelle: A fast and versatile tool-kit for accurate de novo assembly of organelle genomes. Genome Biology 21: 241.
crossref pmid pmc pdf
Katoh, K and Standley, D. M. 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 30: 772-780.
crossref pmid pmc
Khan, G. Zhang, F. Gao, Q. Fu, P.-C. Xing, R. Wang, J. Liu, H and Chen, S. 2014. Molecular phylogeography and intraspecific divergence of Spiraea alpina (Rosaceae) distributed in the Qinghai-Tibetan Plateau and adjacent regions inferred from nrDNA. Biochemical Systematics and Ecology 57: 278-286.
Kim, K. Lee, S.-C. Lee, J. Yu, Y. Yang, K. Choi, B.-S. Koh, H.-J. Waminal, N. E. Choi, H.-I. Kim, N.-H. Jang, W. Park, H.-S. Lee, J. Lee, H. O. Joh, H. J. Lee, H. J. Park, J. Y. Perumal, S. Jayakodi, M. Lee, Y. S. Kim, B. Copetti, D. Kim, S. Kim, S. Lim, K.-B. Kim, Y.-D. Lee, J. Cho, K.-S. Park, B.-S. Wing, R. A and Yang, T.-J. 2015. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Scientific Reports 5: 15655.
crossref pmid pmc pdf
Kim, S. Suhr, J. Lee, S. Ly, S and Park, C. 2019. Anti-oxidative activity of water-ethanol fractions from Spiraea prunifolia var. simpliciflora ethanol extract. Korean Journal of Human Ecology 28: 727-737.
Kostikova, V. A and Petrova, NV. 2021. Phytoconstituents and bioactivity of plants of the genus Spiraea L. (Rosaceae): A review. International Journal of Molecular Sciences 22: 11163.
Lagesen, K. Hallin, P. Rødland, E. A. Stærfeldt, H.-H. Rognes, T and Ussery, D. W. 2007. RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research 35: 3100-3108.
crossref pmid pmc
Lee, C and Hong, S.-P. 2011. Phylogenetic relationships of the rare Korean monotypic endemic genus Pentactina Nakai in the tribe Spiraeeae (Rosaceae) based on molecular data. Plant Systematics and Evolution 294: 159-166.
crossref pdf
Leebens-Mack, J. Raubeson, L. A. Cui, L. Kuehl, J. V. Fourcade, M. H. Chumley, T. W. Boore, J. L. Jansen, R. K and dePamphilis, C. W. 2005. Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one’s way out of the Felsenstein zone. Molecular Biology and Evolution 22: 1948-1963.
crossref pmid
Li, H. 2018. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34: 3094-3100.
crossref pmid pmc pdf
Long, E. O and Dawid, I. B. 1980. Repeated genes in eukaryotes. Annual Review of Biochemistry 49: 727-764.
crossref pmid
Oh, S.-H. Chen, L. Kim, S.-H. Kim, Y.-D and Shin, H. 2010. Phylogenetic relationship of Physocarpus insularis (Rosaceae) endemic on Ulleung Island: Implications for conservation biology. Journal of Plant Biology 53: 94-105.
crossref pdf
Oh, S. M. Choi, D. J. Kim, H.-G. Lee, J. W. Lee, Y.-S. Lee, J.-H. Lee, S.-E. Kim, G.-S. Baek, N.-I and Lee, D. Y. 2018. Neuro-protective effects of phenolic compounds isolated from Spiraea prunifolia varsimpliciflora . Journal of Applied Biological Chemistry 61: 397-403.
Park, J. Suh, H.-J and Oh, S.-H. 2022. The complete chloroplast genome of Aruncus aethusifolius (Rosaceae), a species endemic to Korea. Korean Journal of Plant Taxonomy 52: 118-122.
crossref pdf
Park, J. Xi, H and Oh, S.-H. 2020. Comparative chloroplast genomics and phylogenetic analysis of the Viburnum dilatatum complex (Adoxaceae) in Korea. Korean Journal of Plant Taxonomy 50: 8-16.

Plants of the World Online. 2023. Facilitated by the Royal Botanic Gardens, Kew. Retrieved Mar. 6, 2023, available from http://www.plantsoftheworldonline.org/..

Potter, D. Eriksson, T. Evans, R. C. Oh, S. Smedmark, J. E. E. Morgan, D. R. Kerr, M. Robertson, K. R. Arsenault, M. Dickinson, T. A and Campbell, C. S. 2007. Phylogeny and classification of Rosaceae. Plant Systematics and Evolution 266: 5-43.
crossref pdf
Rodnina, M.V. Beringer, M and Wintermeyer, W. 2007. How ribosomes make peptide bonds. Trends in Biochemical Sciences 32: 20-26.
crossref pmid
Sim, M.-O. Lee, H. J. Jang, J. H. Lee, H. E. Jung, H.-K. Kim, T.-M. No, J. H. Jung, J. Jung, D. E and Cho, H.-W. 2017. Anti-inflammatory and antioxidant effects of Spiraea prunifolia Sieb. et Zucc. var. simpliciflora Nakai in RAW 264.7 cells. Korean Journal of Plant Resources 30: 335-342.

Stamatakis, A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
crossref pmid pmc pdf
Suh, H.-J. Min, J. Park, J and Oh, S.-H. 2021. The complete chloroplast genome of Aruncus dioicus var. kamtschaticus (Rosaceae). Mitochondrial DNA Part B Resources 6: 1256-1258.
crossref pmid pmc
Tillich, M. Lehwark, P. Pellizzer, T. Ulbricht-Jones, E. S. Fischer, A. Bock, R and Greiner, S. 2017. GeSeq: Versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45: W6-W11.
crossref pmid pmc
Woo, M. H. Lee, E. H. Chung, S. O and Kim, C. W. 1996. Constituents of Spiraea prunifolia varsimpliciflora . Korean Journal of Pharmacognosy 27: 389-396.

Xu, J.-H. Liu, Q. Hu, W. Wang, T. Xue, Q and Messing, J. 2015. Dynamics of chloroplast genomes in green plants. Genomics 106: 221-231.
crossref pmid
Yoo, S.-C. Oh, S.-H and Park, J. 2021. Phylogenetic position of Daphne genkwa (Thymelaeaceae) inferred from complete chloroplast data. Korean Journal of Plant Taxonomy 51: 171-175.
crossref pdf
Yu, S.-X. Gadagkar, S. R. Potter, D. Xu, D.-X. Zhang, M and Li, Z.- Y. 2018. Phylogeny of Spiraea (Rosaceae) based on plastid and nuclear molecular data: Implications for morphological character evolution and systematics. Perspectives in Plant Ecology, Evolution and Systematics 34: 109-119.
Yü, T.T and Kuan, K.C. 1963. Taxa Nova Rosacearum sinicarum (1). Acta Phytotaxnomica Sinica 8: 202-234.

Zhang, F.-Q. Gao, Q.-B. Zhang, D.-J. Duan, Y.-Z. Li, Y.-H. Fu, P.-C. Xing, R. Gulzar, K and Chen, S.-L. 2012. Phylogeography of Spiraea alpina (Rosaceae) in the Qinghai–Tibetan Plateau inferred from chloroplast DNA sequence variations. Journal of Systematics and Evolution 50: 276-283.
Editorial Office
Korean Journal of Plant Taxonomy
Department of Biology, Daejeon University, Daejeon 34520, Korea
TEL: +82-42-280-2434   E-mail: kjpt1968@gmail.com
About |  Browse Articles |  Current Issue |  For Authors and Reviewers
Copyright © Korean Society of Plant Taxonomists.                 Developed in M2PI