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. 2025 Aug 19;10(9):842–846. doi: 10.1080/23802359.2025.2548850

The complete chloroplast genome of Dombeya wallichii (Malvaceae)

Yuanzhuo Wu 1,✉
PMCID: PMC12372520  PMID: 40861886

Abstract

Dombeya wallichii, which was recently introduced to China, possesses unique ornamental value. The aim of this study was to obtain the complete chloroplast genome sequence of D. wallichii using the high-throughput sequencing (NGS) on the Illumina HiSeq 6000 platform, thereby supporting its taxonomic and evolutionary research. The chloroplast genome in D. wallichii exhibited a total length of 161,278 bp, with the structural organization comprising four distinct components: a large single-copy (LSC) region spanning 89,968 bp, a small single-copy (SSC) segment measuring 20,448 bp, and two inverted repeat (IR) regions each extending 25,431 bp. Regarding base composition analysis, the LSC region displayed a GC content of 34.3%, while the SSC and IR regions showed respective values of 30.8% and 43.1%.The phylogenetic analysis showed that D. wallichii was closely related to the Corchoropsis species and shared a common ancestor.

Keywords: Dombeya wallichii, chloroplast genome, malvaceae

Introduction

Dombeya wallichii (Lindl.) Benth. ex Baill. 1885, a member of the Malvaceae family, is celebrated for its magnificent pink flower clusters (Rocha et al. 2011). As a species with high ornamental value (Yi 2023) and potential as a breeding resource for native Malvaceae species in China, D. wallichii has been introduced by the Chengdu Botanical Garden.

The classification of Malvaceae is very complex. The chloroplast genomes of 134 species in Malvaceae have been sequenced according to the data from NCBI. Previous studies have only rarely discussed the taxonomic status of Dombeyoideae within Malvaceae (Le Péchon et al. 2010), and D. wallichii was not included. Research on its classification and phylogenetic relationships within Malvaceae remains scarce (Xie et al. 2003). Addressing this research deficiency, the complete chloroplast genome of D. wallichii is reported here through systematic sequencing, marking the first genomic documentation for this species. This genomic resource helps to establish the taxonomic status of D. wallichii and the Dombeya genus it represents within the Malvaceae family. It also fills the gaps in previous studies on Dombeyoideae and provides more references for future discussions on the broad historical classification issues of the Malvaceae family.

Material and methods

Plant materials

In March 2024, leaves were collected from the D. wallichii plants located in the Chengdu Botanical Garden (30°40′N, 104°10′E). The collection of materials adhered to the guidelines established by the Chengdu Botanical Garden, and no special permission statement was necessary for the process (Figure 1). The sample was identified and collected by the author, and the voucher specimen was deposited in Sichuan University Museum (https://scudm.scu.edu.cn, Jinbo Tan, jinbotan@scu.edu.cn) under the voucher number WYZ20250304.

Figure 1.

Figure 1.

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The species image of Dombeya wallichii. Mature leaves and flower in spring (left). Whole plant morphology in spring (right). The flowers are pink to red with five petals. When fully open, they cluster and hang downward like rosy-pink floral pompoms. All photos were taken by Yuanzhuo Wu in the Chengdu Botanical Garden, Chengdu, Sichuan, China.

DNA sequencing, genome assembly, and annotation

Chloroplast genomic DNA was isolated using standardized CTAB protocols from silica-dried plant tissues. (Rishi et al. 2021). Subsequently, the sample of D. wallichii underwent re-sequencing using paired-end sequencing with 150 bp on the Illumina Hiseq 6000 platform at Novogene (Beijing, China), employing the Genome Skimming technique. Following quality control, clean data were generated by removing adapters and low-quality reads. The raw data consist of 3.9 GB. The Q30 of the sequencing data used for assembly is greater than 93%. Plastome assembly was conducted through the implementation of GetOrganelle version 1.7.7.1 (Jin et al. 2020) within a standardized bioinformatics pipeline. Plastid Genome Annotator (PGA) (Qu et al. 2019) was used to annotate the plastomes and used a previously published plastome of Corchoropsis crenata (PP840629) as a reference. The annotation results were then checked in Geneious Prime v2025.0.2 (Kearse et al. 2012) and manually adjusted and corrected any errors. The circular chloroplast genome visualization of D. wallichii was constructed employing the Chloroplast Genome Viewers (CPGView)(Liu et al. 2023), following established genome mapping protocols.

Phylogenetic tree construction

Phylogenetic analyses based on 49 complete chloroplast genomes clarified D. wallichii’s molecular position relative to other related species. The Grewia chungii (NC-054166) was used as the out group. Chloroplast genome sequence alignment was executed via MAFFT v7.490 (Katoh and Standley 2013) embedded within Geneious Prime’s computational environment, maintaining default algorithmic parameters. Subsequently, maximum likelihood phylogenetic reconstruction was conducted through PhyloSuite (http://phylosuite.jushengwu.com/) (Zhang et al. 2020) with model specifications configured as GTR substitution matrix and 1000 bootstrap replicates. Phylogenetic tree graphical annotation was implemented through iTOL v6 (Letunic and Bork 2024) with enhanced topological features, following standard phylogenetic visualization protocols.

Results

The completed annotation of the D. wallichii chloroplast genome has been deposited in GenBank under accession number PV275532. The chloroplast genome of D. wallichii is 161,278 base pairs (bp) long, with an average coverage depth of 1,486× (minimum 615×, maximum 2,697×) (Figure S1), a typical quadripartite structure, and the highest proportion of thymine (T) at 32.2%. It included two IRs regions (25,431 bp each), an SSC region (20,448 bp), and an LSC region (89,968 bp). The GC contents of LSC, SSC, and two IRs were 34.3%, 30.8%, and 43.1%, respectively (Figure 2). Computational annotation of the D. wallichii chloroplast genome identified 129 functional genetic elements, comprising a functional triad of 84 protein-encoding loci, 37 transfer RNA genes, and eight ribosomal RNA genes. Dombeya wallichii has unique genetic characteristics: the infA gene and a single copy of ycf1 are missing. Among cis-splicing genes, nine genes (rpl2, rpl16, rps16, atpF, rpoC1, ndhA, ndhB, petB, petD) contain one intron, and two genes (ycf3 and clpP) contain two introns (Figure S2). In the trans-splicing gene map, the trans-splicing gene (rps12) has three unique exons, with two in the inverted repeat and thus duplicate (Figure S3). Additionally, the results of the gene collinearity analysis indicate that D. wallichii shows slight rearrangements compared to its close relatives (Figure S4). Compared with its related genera, the IRa of D. wallichii has a slight expansion toward the ycf1 and trnH genes, and the IRb has a slight expansion toward the rps19 gene (Figure S5).

Figure 2.

Figure 2.

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Chloroplast genome map of Dombeya wallichii. The circular map of the chloroplast genome was created using the CPGview tool, available at http://47.96.249.172:16085/cpgview/home.Genes are categorized by function and assigned corresponding colors. The transcription orientations of the genes on the inner and outer circles are clockwise and counterclockwise, respectively. A legend for the functional classification of the genes is provided in the lower left corner.

The study thoroughly examined the phylogenetic relationships among 49 species based on their complete chloroplast genome sequences (Figure 3). Dombeya wallichii occupies a relatively independent position within the Malvaceae family, and its closest relatives are the C. crenata, which also belongs to Subfamily Dombeyoideae. The next most closely related species are Pterospermum kingtungense, Pterospermum truncatolobatum, and Excentrodendron hsienmu, which are grouped within the same clade. The results are in good agreement with the phylogenetic tree of Malvaceae based on nuclear genes in a previous article (Le Péchon et al. 2010). SSR analysis (Figure S6) reveals that compared with P. kingtungense, P. truncatolobatum, and E. hsienmu, D. wallichii is more similar to C. crenata. This similarity indirectly supports the closer phylogenetic relationship between D. wallichii and C. crenata, validating the phylogenetic results.

Figure 3.

Figure 3.

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The maximum likelihood (ML) phylogenetic tree was constructed using the complete chloroplast genome of 49 species. Grewia chugii (NC-054166) was used as the out group. The following sequences were used:[Dombeya wallichii] PV275532, [Corchoropsis crenata] PP840627 (Jung et al. 2024), [Corchoropsis crenata] PP840628(Jung et al. 2024), [Corchoropsis crenata] PP840629(Jung et al. 2024), [Pterospermum kingtungense] MK962315(Tran et al. 2024), [Pterospermum truncatolobatum] NC_054168 (Tran et al. 2024), [excentrodendron hsiemmu] ON086805, [Tilia platyphyllus] NC_062378 (Carvalho Leonardo et al. 2023), [Tilia nobilis] NC_085570, [Tilia miqueliana] NC_060401, [Tilia taihsanensis] NC_051557, [Tilia mongolica] NC_057237 (Tran et al. 2024), [Theobroma cacao] NC_014676 (Cheon et al. 2017), [Theobroma cacao] MZ725364 (Tineo et al. 2025), [Theobroma cacao] JQ228387 (Gutiérrez-López et al. 2016), [Theobroma grandiflorum] JQ228388 (Gao et al. 2018), [Reevesia botingensis] OP586555, [Brachychiton acerifolius] NC_071829 (Tran et al. 2024), [Adansonia gregorii] MT053000, [Adansonia suarezensis] MT053005, [Abutilon megapotamicum] NC_077649 (Tran et al. 2024), [Abutilon megapotamicum] OK274070, [Gossypium stocksii] NC_023217 (Niu et al. 2019), [Gossypium sturtianum] NC_023218 (Gao et al. 2018), [Abelmoschus sagittifolius] NC_053354 (Tran et al. 2024), [Abelmoschus moschatu] NC_053355 (Tran et al. 2024), [Abelmoschus manihot] NC_053353, [Hibiscus taiwanensis] MK937807 (Xu et al. 2019), [Talipariti tiliacium] PQ383398 (Yuan et al. 2025), [Talipariti tiliacium] NC_053627 (Tran et al. 2024), [Hibiscus trionum] NC_060636, [Hibiscus richardsonii] OZ174217, [Hibiscus sabdariffa] MZ522720 (Hou et al. 2023), [Gossypium incanum] NC_018109 (Zhou et al. 2022), [Gossypium areysianum] NC_018112 (Niu et al. 2019), [Gossypium hirsutum] MK792862, [Gossypium aridum] NC_033396, [Gossypium schwendimanianum] NC_039570, [Gossypium trilobum] NC_033397, [Gossypium robinsonii] NC_018113, [Gossypium nandewarense] NC_039568, [Thespesia populnea] MF314194, [Thespesia howii] NC_070216 (Zhou et al. 2022), [thespesia lampas] NC_070217 (Tran et al. 2024), [Tilia mandschurica] NC_028589 (Cheon et al. 2017), [Tilia oliveri] NC_028590 (Nguyen et al. 2024), [Tilia endochrysea] OK624380 (Wang et al. 2022), [Tilia amurensis] NC_028588 (Cheon et al. 2017), [Grewia chungi] NC_054166 (Tran et al. 2024). All sequences are downloaded from NCBI GenBank.

Discussion and conclusion

Dombeya wallichii is a highly ornamental urban greening tree widely planted in the tropics but newly introduced to China. This study first completed the sequencing and assembly of the D. wallichii chloroplast genome, with a length of 161,278 bp and encoding 129 genes. The chloroplast genome manifests a canonical four-segment architectural organization and its size is comparable to that of its close relatives. Phylogenetic analyses based on complete chloroplast genome sequences can offer improved resolution that aligns with morphological observations (Lee et al. 2021).

The chloroplast genomic architecture in this study provides new phylogenetic perspectives, aiding in understanding evolutionary trajectories and taxonomic delineation in the Dombeya. A phylogenetic tree was constructed based on chloroplast genomic data of 49 Malvaceae species, clarifying D. wallichii’s taxonomic position in Malvaceae and its phylogenetic relationships with other congeners. The placement of D. wallichii in a more distant branch of the phylogenetic tree indicates that its divergence occurred relatively recently. Dombeya wallichii and C. crenata form a sister relationship, and this clade is sister to the clade formed by Pterospermum and Excentrodendron. This result is consistent with the findings of previous studies (Jung et al. 2024). The four genera form a common clade (Subfamily Dombeyoideae), which is consistent with the classification of the APG IV system (The Angiosperm Phylogeny Group 2016).

The phylogenetic tree showed distant relationships between closely related species in the same genus (Tilia and Hibiscus), suggesting that the taxonomic status of some Malvaceae genera may need reevaluation. Further analysis requires combining nuclear genomic data of D. wallichii with congeneric species data to explore Dombeya’s phylogenetic relationships. More evidence on morphological comparisons between D. wallichii and its congeners is needed in future studies to support the results of its taxonomic status from molecular studies.

Supplementary Material

SSR analysis.jpg
TMDN_A_2548850_SM1478.jpg (276.9KB, jpg)
depth coverage.jpg
TMDN_A_2548850_SM1477.jpg (1MB, jpg)
Cis splicing gene map.jpg
TMDN_A_2548850_SM1476.jpg (1.6MB, jpg)
Trans splicing gene map.jpg
TMDN_A_2548850_SM1475.jpg (808.5KB, jpg)
Schematic diagram of the inverted repeat region boundaries.jpg
TMDN_A_2548850_SM1474.jpg (1.8MB, jpg)
gene collinearity analysis.jpg
TMDN_A_2548850_SM1473.jpg (1.5MB, jpg)

Acknowledgments

The project concept, sample collection, experimental design and operation, and article writing were all completed by Yuanzhuo Wu.

Funding Statement

This work was supported by Tissue Culture and MolecularBreeding of Hibiscus mutabilis at the Chengdu Institute of Landscape Architecture [18H0567].

Ethics statement

The collection of specimens adhered to international ethical standards, causing no harm to the environment or the species. The objectives and procedures of this experimental research complied with the policies of our institution, and no ethical concerns or specific permissions were required.

Disclosure statement

No potential conflict of interest was reported by the author.

Data availability statement

The genome sequence data that support the findings of this study are available in GenBank at https://www.ncbi.nlm.nih.gov/ under accession no. PV275532. The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive (Genomics, Proteomics and Bioinformatics 2021) in National Genomics Data Center (Nucleic Acids Res 2022), China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (GSA: CRA024181; Bioproject: PRJCA037857; Bio-Sample: SAMC4916127) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa.

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Associated Data

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

Supplementary Materials

SSR analysis.jpg
TMDN_A_2548850_SM1478.jpg (276.9KB, jpg)
depth coverage.jpg
TMDN_A_2548850_SM1477.jpg (1MB, jpg)
Cis splicing gene map.jpg
TMDN_A_2548850_SM1476.jpg (1.6MB, jpg)
Trans splicing gene map.jpg
TMDN_A_2548850_SM1475.jpg (808.5KB, jpg)
Schematic diagram of the inverted repeat region boundaries.jpg
TMDN_A_2548850_SM1474.jpg (1.8MB, jpg)
gene collinearity analysis.jpg
TMDN_A_2548850_SM1473.jpg (1.5MB, jpg)

Data Availability Statement

The genome sequence data that support the findings of this study are available in GenBank at https://www.ncbi.nlm.nih.gov/ under accession no. PV275532. The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive (Genomics, Proteomics and Bioinformatics 2021) in National Genomics Data Center (Nucleic Acids Res 2022), China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (GSA: CRA024181; Bioproject: PRJCA037857; Bio-Sample: SAMC4916127) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa.

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