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. 2026 Aug 3;11(9):997–1002. doi: 10.1080/23802359.2026.2704282

The complete chloroplast genome of Camellia hamyenensis Ninh & Le (Theaceae)

Minh Phuong Nguyen 1,✉, Viet The Ho 1
PMCID: PMC13435283  PMID: 42553665

Abstract

Camellia hamyenensis Ninh & Le is a yellow tea species endemic to Vietnam. In this study, the complete chloroplast genome of this species was sequenced, assembled, and annotated. The 156,613-bp plastome has a GC content of 37.32% and comprises an 86,187-bp large single-copy region, an 18,276-bp small single-copy region, and two 26,075-bp inverted repeat regions. It contains 134 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that C. hamyenensis clustered with C. flava, C. huulungensis, and C. tamdaoensis. These results provide useful resources for future phylogenetic and evolutionary studies of the genus Camellia.

Keywords: Plastome, phylogenetic analysis, Illumina sequencing

Introduction

The genus Camellia (Theaceae) comprises more than 200 species naturally distributed mainly in East and Southeast Asia. Several Camellia species, particularly C. sinensis, have been widely cultivated and studied due to its economic and cultural importance. In recent years, the less popular species have also attracted increasing research interest. Golden flower tea, a group of over 50 species characterized by yellow flowers, is particularly focused on for their high potential medicinal values such as anti-cancer, antimicrobial, antioxidant activities, lipid-lowering, anti-inflammatory, and liver-protective effects (Truong et al. 2024). Camellia hamyenensis Ninh & Le, 2022 is a narrowly distributed species of yellow Camellia endemic to northern Vietnam, with recorded populations occurring in Tuyen Quang province (Le et al. 2022). Due to its restricted distribution and limited documentation in the literature, genomic resources for this species and its relationships among closely related Camellia species remain poorly understood.

Complete chloroplast genome sequences have been reported and used in comparative genomic and phylogenetic studies of numerous Camellia species, including several yellow-flowered Camellia species such as C. nitidissima, C. flava, C. petelotii, and C. achrysantha (Liu et al. 2018; Tang et al. 2024; Huang et al. 2014; Lai and Tang 2021). Here, we report the sequence and characteristics of the complete chloroplast genome of C. hamyenensis. Phylogenetic analysis based on complete plastome sequences was performed to elucidate the evolutionary position of the species within the genus Camellia. These data provide a valuable genetic resource for future studies on taxonomy, phylogeny, conservation and authentication of C. hamyenensis.

Materials and Methods

Sample collection

A single plant was collected from Phu Luu, Tuyen Quang province, Vietnam (22.175°N, 105.036°E) and grown in Tam Duong Bac, Vinh Phuc Province prior to sampling (Figure 1). The plant sample was identified based on morphology characteristics by Dr. Nguyen Thi Kim Thanh. A voucher specimen was deposited at Herbarium of VNU University of Science (HNU), Hanoi, Vietnam (https://sweetgum.nybg.org/science/ih/herbarium-details/?irn=126944, contact email kimthanh_bio@yahoo.com), under voucher number: HNU 024793. From this cultivated individual, fresh healthy leaves were collected for DNA extraction and sequencing.

Figure 1.

Close-up of bright yellow flowers on a green leaf with a blurred natural background. A large textured green leaf is next to a ruler marked in centimetres for scale.

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Photographs of C. hamyenensis: (A) flowering plant and (B) adaxial leaf surface. Leaves are thick and coriaceous, elliptic, 28–35 × 12.5–16 cm, with a shortly acuminate apex (0.7–1.2 cm) and 11–12 pairs of lateral veins impressed adaxially and prominent abaxially; petioles are 1.5–1.7 cm. Flowers are axillary to terminal, with 12–15 yellow petals, and numerous smooth stamens ca. 20–28 mm long. Photos were taken by the authors.

DNA extraction and sequencing

Fresh leaves (100 mg) were used for DNA extraction using a modified CTAB method (Doyle and Doyle 1987). DNA quality and quantity were assessed by gel electrophoresis and NanoDrop spectrophotometry. Approximately 500 ng of total DNA was used to construct the sequencing library. Library quality and concentration were evaluated using Qubit and Agilent 2100 prior to sequencing. The library was sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads. The quality of raw sequencing reads was assessed using FastQC (v0.12.1) in a Conda-managed environment.

Chloroplast genome assembly and annotation

Raw paired-end sequencing reads were used directly for de novo assembly of the chloroplast genome using the GetOrganelle v1.7.7.1 implemented on the Galaxy Europe platform (https://usegalaxy.eu). The assembly was conducted using the embplant_pt mode and default seed sequences provided by GetOrganelle, with the parameter ‘-R 15 -k 21,45,65,85,105’. Assembly completeness and correctness were further evaluated by read mapping and coverage depth analysis. The circularized genome underwent annotation and mapping using Geseq program (https://chlorobox.mpimp-golm.mpg.de/geseq.html), utilizing NCBI Refseq of C. amplexicaulis as reference. The resulting annotations were manually curated by comparison with published chloroplast genomes of related Camellia species, including C. achrysantha (NC_057956.1) (Lai and Tang 2021) and C. huulungensis (NC_088067.1) (Zhou et al. 2024). The genome map was then visualized using the Chloroplot online platform (https://irscope.shinyapps.io/Chloroplot/).

Phylogenetic analysis

To determine the phylogenetic position of C. hamyenensis among Camellia species, a total of 66 complete chloroplast genome sequences of Camellia species were downloaded from the NCBI GenBank database. Two plastome sequences from Theaceae species outside Camellia (Pyrenaria pingpienensis and Polyspora hainanensis) were used as outgroups. To ensure comparability among circular plastomes, all sequences were oriented in the same direction, and each genome was subsequently circularly shifted to a common starting position. Whole-plastome alignment was performed using MAFFT v7.526 (Katoh and Standley 2013). Phylogenetic analysis was conducted using the maximum likelihood method implemented in IQ-TREE v2.0.7 (Nguyen et al. 2015; Minh et al. 2020), with the best-fit substitution model (GTR+F + R7) selected by ModelFinder (Kalyaanamoorthy et al. 2017) under the MFP+MERGE strategy. Branch support was evaluated using 1,000 ultrafast bootstrap (UFBoot) (Hoang et al. 2018) replicates and 1,000 SH-like approximate likelihood ratio test (SH-aLRT) (Guindon et al. 2010) replicates. The resulting phylogenetic tree was visualized using Interactive Tree Of Life (https://itol.embl.de/).

Results

The complete chloroplast genome of C. hamyenensis was a circular molecule of 156,613 bp in length, with an overall GC content of 37.32% (Figure 2). Its structure was typically quadripartite, consisting of a large single-copy (LSC) region of 86,187 bp, a small single-copy (SSC) region of 18,276 bp, and two inverted repeat regions (IRa and IRb), each 26,075 bp long. The whole genome contained 134 genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 2 truncated pseudogenes (including partial copies of ycf1 at the SSC/IRa boundary and rps19 at the LSC/IRb boundary). Among these, 18 genes are duplicated in the inverted repeat (IR) regions, including 7 protein-coding genes (rpl2, rpl23, rps7, rps12, ndhB, ycf2, and ycf15), 7 tRNA genes (trnA-UGC, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, trnV-GAC, and trnM-CAU), and 4 rRNA genes (rrn4.5, rrn5, rrn16, and rrn23). The chloroplast genome exhibits relatively uniform coverage with an average sequencing depth of approximately 100× (Supplementary Figure S1), and contains 11 unique cis-splicing genes, one trans-splicing gene (Supplementary Figure S2), and 64 SSR loci (Supplementary Table S1).

Figure 2.

Circular diagram of the plastid genome of Camellia hamyenensis showing gene annotations, GC content, and structural regions. The figure displays a circular diagram of the plastid genome of Camellia hamygenesins. The center includes key statistics: "Camellia hamyenensis," total of 89 genes, 8 rRNAs, 37 tRNAs, genome length 156,613 bp, and GC content at 37%. Surrounding this, colored rings depict gene categories with labels including rpoB, atpF, and others, indicating clockwise and counter-clockwise transcription. The outer ring features a GC content histogram, with variation in height reflecting GC percentage. Structural regions labeled are Large Single Copy (LSC), Inverted Repeats (IRA, IRB), and Small Single Copy (SSC), each annotated with respective nucleotide lengths.

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Chloroplast genome map of C. hamyenensis. Genes are colored based on their type of function as shown in the bottom left corner. Genes within the circle are transcribed clockwise, while those outside the circle are transcribed counter-clockwise. The dark gray bar graphs within the inner circle indicate GC content. LSC: large single-copy region, SSC: small single-copy region, IR: inverted repeat region.

Phylogenetic relationships were reconstructed using chloroplast genome sequences of C. hamyenensis, together with 66 other Camellia species and two outgroup taxa (Polyspora hainanensis and Pyrenaria pingpienensis) obtained from GenBank. The resulting maximum likelihood tree resolved the Camellia species into several major clades with generally high support values (Figure 3). C. hamyenensis clustered within a clade comprising several yellow-flowered Camellia species distributed in northern Vietnam and southern China with strong support. In particular, C. hamyenensis formed a subgroup with C. flava, C. huulungensis, C. aurea, C. zhaiana, C. amplexifolia and C. tamdaoensis, most, but not all, of which belong to Sect. Chrysantha (Ming and Bartholomew 2007). This clade was nested within a larger lineage that also included related species such as C. petelotii, C. chrysanthoides, and C. impressinervis, and clearly separated from other major groups of the genus, including the C. japonica, C. sinensis, and C. oleifera complexes. Overall, the topology of the tree was consistent with previous plastome-based phylogenetic studies of the genus (Tang et al. 2024).

Figure 3.

Phylogenetic tree showing evolutionary relationships among species, with an orange-highlighted clade and C. hamyenensis emphasized in red. The image depicts a complex phylogenetic tree based on a scale of 0.001, illustrating relationships among about 69 species labeled with accession numbers. Key features include an orange-highlighted clade that includes C. hamyenensis, marked in red, along with other species like C. flava and C. zhaiana. Bootstrap support values ranging 90 to 100 are indicated at branch points, reflecting branch stability. The tree structure shows varying branch lengths that represent genetic distances, indicating evolutionary relationships among clusters of species.

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Maximum likelihood phylogenetic tree based on complete chloroplast genome sequences of Camellia. The analysis included 66 plastomes of representative Camellia species retrieved from GenBank and the newly assembled plastome of C. hamyenensis. The clade containing Camellia hamyenensis is highlighted in yellow. Numbers at the nodes represent ultrafast bootstrap support values (UFBoot ≥ 90%). The following sequences were used: C. achrysantha NC057956 (Lai and Tang 2021), C. albosericea NC085496 (Hu et al. 2026), C. amplexicaulis NC051559 (Wu et al. 2020), C. anlungensis NC050354 (Zhu et al. 2020), C. atuberculata NC082980 (Ran et al. 2024), C. aurea NC062050 (Jiang et al. 2025), C. brevistyla NC052752 (Wang et al. 2020), C. chekiangoleosa NC037472 (Yin et al. 2021), C. chrysanthoides NC057957 (Lai and Tang 2021), C. chuongtsoensis MT663341 (Yu et al. 2021), C. confusa NC058854 (Wu et al. 2022), C. crapnelliana NC024541 (Yang et al. 2014), C. cuspidata NC022459 (Yang et al. 2013), C. danzaiensis NC022460 (Yang et al. 2013), C. debaoensis NC057958 (Zheng and Wei 2021), C. delicata PQ539948 (Xiao et al. 2025), C. elongata NC035652 (Yu et al. 2017), C. flava NC084240 (Tang et al. 2024), C. fluviatilis NC058853 (Yang et al. 2021), C. formosensis NC065198 (LiangJong et al. 2024), C. gauchowensis NC053541 (Zhang and Wang 2020), C. grandibracteata NC024659 (Huang et al. 2014), C. granthamiana NC038181 (Li et al., 2018), C. gymnogyna NC039626 (Zeng et al. 2018), C. huulungensis NC088067 (Zhou et al. 2024), C. ilicifolia NC082976 (Ran et al. 2024), C. impressinervis NC022461 (Yang et al. 2013), C. japonica MK353210 (Park et al. 2019), C. kweichowensis PQ539949 (Xiao et al. 2025), C. leptophylla NC024660 (Huang et al. 2014), C. leyensis OK046127 (Ran et al. 2024), C. lipingensis NC067613 (Ran et al. 2024), C. longistyla PQ539950 (Xiao et al. 2025), C. mairei NC035688 (Yu et al. 2017), C. mingii NC046699 (Zhang et al. 2019), C. neriifolia NC082979 (Ran et al. 2024), C. nitidissima NC039645 (Liu et al. 2018), C. obtusifolia OM937020 (Chen et al. 2026), C. oleifera NC023084 (Shi et al. 2013), C. paucipetala PQ539951 (Xiao et al. 2025), C. perpetua NC054364 (Pei et al. 2020), C. petelotii NC024661 (Huang et al. 2014), C. pitardii NC022462 (Yang et al. 2013), C. polyodonta NC060777 (Chen et al. 2022), C. ptilophylla NC038198 (Li et al., 2018), C. pubicosta NC024662 (Huang et al. 2014), C. pubipetala NC054365 (Zheng and Wei 2021), C. pyxidiacea NC070214 (Ran et al. 2024), C. renshanxiangiae NC041672 (Lin et al., 2019), C. reticulata NC024663 (Huang et al. 2014), C. rhytidocarpa NC082981 (Ran et al. 2024), C. rostrata NC058254 (Zhang et al. 2021), C. rubimuricata NC082975 (Ran et al. 2024), C. sasanqua NC041473 (Lin et al., 2019), C. sinensis KJ806281 (Huang et al. 2014), C. szechuanensis NC035651 (Shi et al. 2013), C. tachangensis NC056149 (Hao et al. 2019), C. taliensis NC022264 (Yang et al. 2013), C. tamdaoensis NC069227, C. tetracocca OK405020 (Yi et al. 2024), C. tianeensis NC086748 (Chen et al. 2025), C. vietnamensis NC060778 (Huang et al. 2014), C. yunnanensis NC022463 (Yang et al. 2013), C. zengii NC082977 (Ran et al. 2024), C. zhaiana NC058253 (Wu et al. 2021), C. zijinica OR567094 (Lin et al. 2024). Polyspora hainanensis NC035693 (Yu et al. 2017) and Pyrenaria pingpienensis NC035642 [31] were used as outgroups.

Discussion and conclusion

The chloroplast genome of C. hamyenensis exhibits the conserved quadripartite structure, gene content, gene order, genome size, and GC content characteristic of other Camellia species, consistent with the strong plastome conservation reported within the genus (Zhou et al. 2024; Yang et al. 2013). Phylogenetic analysis grouped C. hamyenensis with C. huulungensis, C. flava, C. tamdaoensis, and C. aurea, a small clade that has been consistently recovered in previous plastome-based studies of Camellia (Tang et al. 2024; Jiang et al. 2025). However, C. hamyenensis did not cluster directly with other well-known yellow-flowered species such as C. petelotii and C. nitidissima. This pattern suggests that the traditional concept of ‘golden camellias’, which is primarily based on floral morphology, does not necessarily represent a natural monophyletic group and that floral color alone may not accurately reflect evolutionary relationships within the genus. Moreover, the recovered clades did not correspond to the traditional sectional classification of Camellia adopted in Flora of China (Ming and Bartholomew 2007). Similar incongruences have also been observed in other plastome phylogenies of Camellia (Lin et al. 2022; Ran et al. 2024; Wei et al. 2023) and may reflect the maternal inheritance of chloroplast genomes, coupled with historical hybridization, chloroplast capture, or incomplete lineage sorting. Overall, this study provides valuable genomic resources for future phylogenetic, taxonomic, and conservation studies of Camellia.

Supplementary Material

Supplementary materials revisedv3.docx
TMDN_A_2704282_SM6586.docx (1.6MB, docx)

Acknowledgments

The authors acknowledge the use of ChatGPT (OpenAI, USA) to improve the grammatical structure and clarity of the manuscript. The tool was used solely for language editing of author-generated text. All outputs were carefully reviewed, verified, and edited by the authors to ensure accuracy and scientific integrity.

Funding Statement

This work was financially supported by Ho Chi Minh City University of Industry and Trade under Contract No. 18/HĐ-DCT dated 17/01/2025.

Disclosure statement

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

Ethical approval

The collection of plant material complied with institutional, national, and international guidelines. No specific permits were required for the collection of plant material used in this study.

Data availability statement

The complete chloroplast genome sequence of Camellia hamyenensis is available in GenBank under accession number PZ054906. The associated raw sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) under accession number SRR37535838, within BioProject PRJNA1432484 and BioSample SAMN56343773.

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Associated Data

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

Supplementary Materials

Supplementary materials revisedv3.docx
TMDN_A_2704282_SM6586.docx (1.6MB, docx)

Data Availability Statement

The complete chloroplast genome sequence of Camellia hamyenensis is available in GenBank under accession number PZ054906. The associated raw sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) under accession number SRR37535838, within BioProject PRJNA1432484 and BioSample SAMN56343773.

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