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Article

The Complete Chloroplast Genome of Purdom’s Rhododendron (Rhododendron purdomii Rehder & E. H. Wilson): Genome Structure and Phylogenetic Analysis

by
Lu Yuan
1,
Ningning Zhang
2,3,
Shixin Zhu
2,3 and
Yang Lu
2,3,*
1
School of Agricultural Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
2
School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
3
Henan Funiu Mountain Biological and Ecological Environment Observatory, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
*
Author to whom correspondence should be addressed.
Forests 2025, 16(7), 1120; https://doi.org/10.3390/f16071120
Submission received: 2 June 2025 / Revised: 27 June 2025 / Accepted: 3 July 2025 / Published: 7 July 2025
(This article belongs to the Section Genetics and Molecular Biology)
Browse Figures
Versions Notes

Abstract

Rhododendron purdomii Rehder & E. H. Wilson (Ericaceae) is a threatened ornamental and medicinal shrub or small tree species primarily distributed in the Qinling-Daba Mountains of Central China. To facilitate its conservation and utilization, the complete chloroplast genome of Rh. purdomii was sequenced, assembled, and characterized. The cp genome exhibited a typical quadripartite structure with a total length of 208,062 bp, comprising a large single copy (LSC) region of 110,618 bp, a small single copy (SSC) region of 2606 bp, and two inverted repeat (IR) regions of 47,419 bp each. The overall GC content was 35.81%. The genome contained 146 genes, including 96 protein-coding genes, 42 transfer RNA genes, and 8 ribosomal RNA genes. Structure analysis identified 67,354 codons, 96 long repetitive sequences, and 171 simple sequence repeats. Comparative genomic analysis across Rhododendron species revealed hypervariable coding regions (accD, rps9) and non-coding regions (trnK-UUU-ycf3, trnI-CAU-rpoB, trnT-GGU-accD, rpoA-psbL, rpl20-trnC-GCA, trnI-CAU-rrn16, and trnI-CAU-rps16), which may serve as potential molecular markers for genetic identification. Phylogenetic reconstruction confirmed the monophyly of Rhododendron species and highlighted a close relationship between Rh. purdomii and Rh. henanense subsp. lingbaoense. These results provide essential genomic resources for advancing taxonomic, evolutionary, conservation, and breeding studies of Rh. purdomii and other species within the genus Rhododendron.

1. Introduction

The chloroplast genome serves as a powerful tool for evolutionary studies, offering advantages through its maternal inheritance, structural conservation, and moderate mutation rate [1,2]. Most angiosperm chloroplast genomes display a quadripartite structure, comprising a large single copy (LSC), small single copy (SSC), and two inverted repeat (IR) regions [3,4]. However, exceptions have been reported, such as the loss of inverted repeats (IRs), which may influence genome stability and evolutionary dynamics [5]. The advent of high-throughput sequencing technologies have enabled comprehensive chloroplast genome analyses, facilitating phylogenetic reconstruction, hybrid identification, and molecular marker developments [6,7,8].
Rhododendron L. (Ericaceae), one of the largest angiosperm genera with over 1000 species globally, holds significant horticultural value. China represents its primary diversity center, comprising approximately 571 species (409 endemic) [9,10]. This genus includes economically important species prized for ornamental and medicinal applications [11,12] while also playing crucial roles in ecosystem stability and biodiversity conservation [13,14]. However, taxonomic uncertainties persist due to extensive hybridization, recent adaptive radiation, morphological plasticity, and limited genomic data [15,16,17,18]. Traditional morphology-based classifications often prove inadequate, necessitating molecular approaches for robust phylogenetic resolution [19,20].
Rhododendron purdomii Rehder & E. H. Wilson, an evergreen shrub or small tree species primarily distributed in the Qinling-Daba Mountains of Central China, is threatened by climate change and anthropogenic activities [21,22]. As a medicinal plant, the aerial parts of Rh. purdomii contain terpenoids, fatty acids, brassins, and phenolic acids, which have anti-inflammatory and antitussive effects [23]. Listed as “Vulnerable” in China’s Higher Plant Red List [24], this ecologically and horticulturally significant species remains genomically understudied, with prior research limited to morphology, microsatellite marker development, and species distribution modeling [21,22,25,26]. As a member of the taxonomically complex subgenus Hymenanthes (>300 species), Rh. purdomii exhibits unresolved subsection-level classification, variably assigned to Taliensia, Selensia, or Pontica within Rh. subg. Hymenanthes by different authorities [9,16,17,27,28]. The absence of complete chloroplast genome data impedes phylogenetic placement and evolutionary studies within this challenging group.
This study presents the sequencing and characterization of the entire chloroplast genome of Rh. purdomii to (1) analyze its structural features, gene composition, and evolutionary patterns; (2) compare it with other Rhododendron species to identify genomic variations; and (3) reconstruct phylogenetic relationships to resolve the taxonomic placement of Rh. purdomii. Our findings provide critical genomic resources for Rh. purdomii and elucidate the understanding of chloroplast genome evolution within the genus Rhododendron.

2. Materials and Methods

2.1. Plant Material, DNA Extraction, and Sequencing

Fresh leaves of Rh. purdomii were sampled from Xi’an Zhuque National Forest Park, Shaanxi Province, China (33°49′18.11″ N, 108°36′34.08″ E, 2425 m; Figure 1). Voucher specimens were deposited at the Zhengzhou University Herbarium (ZZU, established in 2006, Zhengzhou, China; accession number: LY2021052815). Genomic DNA was isolated via a cetyltrimethylammonium bromide (CTAB) method [29]. The extracted genomic DNA was subjected to the following quality control tests: 1. Visual inspection of extracted DNA samples to check for the presence of particulate matter or impurities; 2. Agarose gel electrophoresis to assess DNA degradation; 3. Nanodrop spectrophotometry to evaluate DNA purity (A260/A280: 1.8–2.0, A260/A230: >2.0); 4. Qubit fluorometric quantification to ensure a total DNA quantity ≥ 1 μg. High-quality DNA was utilized for library preparation and sequencing. Paired-end sequencing (150 bp) was performed on the Illumina NovaSeq platform (Illumina, San Diego, CA, USA), while long-read sequencing was conducted on the Oxford Nanopore PromethION sequencer (Oxford Nanopore Technologies, Oxford, UK). All sequencing workflows were executed by Wuhan Benagen Technology Co., Ltd. (Wuhan, China).

2.2. Assembly and Annotation of Chloroplast Genome

After quality control of sequencing data, the chloroplast genome was assembled using Flye v2.8.3 [30] with default parameters. Gaps in the assembly were resolved using GapCloser v1.12 [31]. Genome annotation was performed using CPGAVAS2 (http://47.96.249.172:16019/analyzer/home, accessed on 11 September 2022) [32] and manually refined in Geneious Prime v2023.2 [33] to ensure accuracy. The identification of transfer RNA (tRNA) genes was confirmed using tRNAscan-SE v2.0 [34]. The annotated chloroplast genome sequence has been deposited in GenBank (accession number: NC_086505.1). The chloroplast genome of Rh. purdomii was visualized as a circular map using CHLOROPLOT (https://irscope.shinyapps.io/Chloroplot/, accessed on 15 September 2022) [35]. Codon usage bias was quantified by computing relative synonymous codon usage (RSCU) values for all protein-coding genes through CodonW v1.4.4 [36].

2.3. Data Analysis

2.3.1. Repeat Sequence Analysis

Genomic repeats were identified using REPuter (https://bibiserv.cebitec.uni-bielefeld.de/reputer, accessed on 4 October 2022) [37] with a minimal repeat length of 30 bp and a Hamming distance of three. Simple sequence repeats (SSRs) were identified with MISA v1.0 (https://webblast.ipk-gatersleben.de/misa/, accessed on 6 October 2022) [38], and parameters of 10, 5, 4, 3, 3, and 3 were set for mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats, respectively.

2.3.2. Comparative Analysis of the Chloroplast Genome

For comparative genomics analyses, we used ten complete chloroplast genomes from the Rhododendron subgenus Hymenanthes: Rh. purdomii (NC_086505.1), Rh. henanense subsp. Lingbaoense Fang (MT239363), Rh. williamsianum Rehder & E. H. Wilson (PP690644), Rh. griersonianum Balf. f. & Forrest (MT533181), Rh. calophytum Franch (OM373082), Rh. platypodum Diels (MT985162), Rh. oreodoxa var. fargesii (Franch.) D. F. Chamb (OL639014), Rh. przewalskii Maxim (OL871190), Rh. delavayi Franch (MN413198), and Rh. shanii Fang (MW374796) (Supplementary Table S1). Multiple sequence alignment was generated using MAFFT within the PhyloSuite v1.2.2 platform [39]. Nucleotide diversity (Pi) was estimated via sliding-window analysis (window length: 600 bp; step size: 200 bp) in DnaSP v6.12 [40]. Genomic sequence divergence was visualized using mVISTA (https://genome.lbl.gov/vista/mvista/submit.shtml, accessed on 20 May 2025) [41] in Shuffle-LAGAN mode. Boundaries separating the IR, SSC, and LSC regions were analyzed using IRscope (https://irscope.shinyapps.io/irapp/, accessed on 22 May 2025) [42], enabling precise mapping of junction sites across the ten Rhododendron species.

2.3.3. Phylogenetic Analysis

To resolve the phylogenetic position of Rh. purdomii within Ericaceae, we constructed a phylogenetic tree using the chloroplast genomes of newly annotated Rh. purdomii and the other 26 Rhododendron species retrieved from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/, accessed on 24 May 2025). A total of 27 species representing six subgenera (Hymenanthes, Azaleastrum, Tsutsusi, Choniastrum, Pentanthera, and Rhododendron) of Rhododendron were included (Supplementary Table S1) [9,11,28]. Two Gaultheria species (G. fragrantissima Wall and G. nummularioides D. Don) were selected as outgroups. Multiple sequence alignment was generated using MAFFT within the PhyloSuite v1.2.2 platform [39]. A maximum likelihood (ML) phylogenetic tree was constructed using IQ-TREE v2.0.6 [43] with 1000 bootstrap replicates. The optimal substitution model (TVM+F+R2) was determined under the Bayesian information criterion (BIC). The final tree topology was visualized and annotated in iTOL (https://itol.embl.de/, accessed on 26 May 2025) [44].

3. Results

3.1. Chloroplast Genome Structure

We obtained 221,648 reads with an average length of 9385.48 bp for long-read sequencing and 34,235,862 reads for paired-end sequencing (150 bp). The complete chloroplast genome of Rh. purdomii (208,062 bp) exhibited a canonical quadripartite structure, featuring a LSC region of 110,618 bp, an SSC region of 2606 bp, and two IR regions of 47,419 bp each (Figure 2 and Table 1). The average coverage depth of the final assembly was 178.62×.
The overall GC content was 35.81%, with regional values of 35.27% (LSC), 30.05% (SSC), and 36.59% (IR) (Table 1). The genome contained 146 functional genes, consisting of 96 protein-coding, 42 tRNA, and 8 rRNA genes (Table 1). Of these, 113 genes were unique. Thirteen genes contained single introns, while two genes (rps12 and ycf3) contained two introns (Table 2). Notably, rps12 exhibited trans-splicing with three exons. Additionally, two putative pseudogenes (petA and ndhH) were identified.
The Rh. purdomii chloroplast genome contained 67,354 codons, with UUU being the most frequent codon and CGC the least frequent (Figure 3). The most abundant amino acid was leucine (Leu), while tryptophan (Trp) was the least abundant one. Among 30 codons with an RSCU value ≥ 1, AGA exhibited the highest RSCU, whereas CGC showed the lowest preference (Figure 3).

3.2. Repeat Sequences

A total of 96 long repeats were identified in the Rh. purdomii cp genome, comprising 46 tandem repeats (48%), 32 forward repeats (33%), and 18 palindromic repeats (19%) (Supplementary Figure S1). Tandem repeats were generally shorter than 60 bp, whereas forward and palindromic repeats typically exceeded 89 bp in length. A total of 171 SSRs were detected, comprising 69 mononucleotides, 18 dinucleotides, 66 trinucleotides, 16 tetranucleotides, one pentanucleotide, and one hexanucleotide (Supplementary Figure S2a). Among these, A (mononucleotide) and TA (dinucleotide) repeats were the dominant repeat types. In addition, ten (A) repeats and four (GAA) repeats were the most abundant in mononucleotides and trinucleotides (Supplementary Figure S2a). SSR distribution analysis revealed that 144 SSRs (84%) were located in intergenic regions, 16 (9%) in protein-coding regions, and 11 (7%) in intronic regions (Supplementary Figure S2b,c).

3.3. Genome Comparison and Nucleotide Diversity

Among the ten Rhododendron species analyzed, chloroplast genomes were largely conserved, with sequence divergence highest in the LSC region and then the IR regions (Figure 4). Comparative analyses identified hypervariable coding regions (accD, rps9) and non-coding regions (trnK-UUU-ycf3, trnI-CAU-rpoB, trnT-GGU-accD, rpoA-psbL, rpl20-trnC-GCA, trnI-CAU-rrn16, and trnI-CAU-rps16), which constitute candidate molecular markers for species identification within Rhododendron.
Comparative analysis of IR boundaries revealed species-specific junction patterns (Figure 5). The LSC/IRb boundary in Rh. shanii, Rh. Griersonianum, and Rh. purdomii was positioned between ycf15 and trnR. The SSC/IRb boundary consistently retained the complete ndhF gene within the SSC region, occupying identical positions in Rh. williamsianum, Rh. shanii, Rh. przewalskii, Rh. griersonianum, Rh. henanense subsp. lingbaoense, Rh. delavayi, and Rh. purdomii. The SSC/IRa junction exhibited expansion into the IRa region by 37−316 bp beyond ndhF. Most species displayed the LSC/IRa junction 128 bp downstream of trnH, with exceptions observed in Rh. przewalskii, Rh. henanense subsp. lingbaoense, and Rh. delavayi.
Nucleotide diversity (Pi) across the chloroplast genomes exhibited substantial regional variation (range: 0 to 0.23452), with a mean value of 0.00690 (Figure 6). Three regions with high nucleotide diversity (Pi value higher than 0.045) were identified in the LSC region of trnI-CAU-rpoB, the IR region of trnM-CAU-trnI-CAU, and the SSC region of ndhF. Notably, ndhF exhibited the highest nucleotide diversity, highlighting its potential as a molecular marker for population genetic studies in Rhododendron.

3.4. Phylogenetic Relationship

Phylogenetic reconstruction confirmed the monophyly of Rhododendron, with all 27 examined species forming a highly supported clade (Figure 7). However, the topological structure within Rhododendron did not fully align with traditional taxonomic classifications at the subgenus level [9]. While subgenera Hymenanthes and Azaleastrum were supported as monophyletic, subgenera Tsutsusi and Rhododendron were not. The ten species within subgenus Hymenanthes formed a well-supported monophyletic group and were resolved as sister clades to other subgenera (Azaleastrum, Tsutsusi, Choniastrum, and Pentanthera). Within Hymenanthes, the three species of subsection Fortunea (Rh. calophytum, Rh. platypodum, and Rh. oreodoxa var. fargesii) were clustered into a single clade (Supplementary Table S1). In contrast, subsection Taliensia (Hymenanthes) was not monophyletic. Notably, Rh. purdomii formed a sister clade with Rh. henanense subsp. lingbaoense. Among subgenus Rhododendron, the three species in subsection Lapponica (Rh. capitatum, Rh. nivale, and Rh. thymifolium) were clustered into one clade, while the two species of subsection Triflora (Rh. ambiguum and Rh. concinnum) formed a distinct clade (Supplementary Table S1 and Figure 7).

4. Discussion

In the present study, the chloroplast genome of Rh. purdomii was determined to be 208,062 bp in size, similar to other Rhododendron species, including Rh. henanense subsp. lingbaoense (208,015 bp) [45], Rh. griersonianum (206,467  bp) [46], Rh. delavayi (202,169 bp) [47], and Rh. oreodoxa var. fargesii (200,787 bp) [48]. Furthermore, most Rhododendron chloroplast genomes exhibit conserved quadripartite structures, demonstrating conservation in genome size, gene number, and GC content. Introns, which play an important role in gene expression and regulation [49], were identified in the Rh. purdomii chloroplast genome. Specifically, ycf3 and rps12 genes each contain two introns. This intron configuration aligns with observations in the chloroplast genome of Rh. oreodoxa var. fargesii [48], indicating evolutionary structural conservation in intron organization among these species.
Codon usage bias, a critical evolutionary feature of chloroplast genomes, arises from the interplay of natural selection and mutation [50]. In the Rh. purdomii chloroplast genome, codons encoding leucine were the most frequent, while tryptophan codons were the least frequent. Notably, 27 of the 30 codons with an RSCU index ≥ 1 terminated with A or U, mirroring patterns observed in other Rhododendron species [51,52]. This underscores a pronounced preference for A/U-ending codons, likely shaped by evolutionary pressures such as selection, mutation, and gene regulation. Such codon usage patterns provide insights into gene expression mechanisms and molecular evolution [53].
The chloroplast genome of Rh. purdomii displayed the highest abundance of tandem repeats, with most repeats measuring less than 60 bp in length. These repetitive sequences are known to facilitate genome recombination and structural rearrangements in chloroplast genomes [54]. SSRs represent valuable molecular markers for both basic and applied botanical research [55]. Our analysis identified 171 SSRs in the Rh. purdomii chloroplast genome, predominantly distributed in intergenic regions. This count is comparatively lower than those reported for congeneric Rhododendron species Rh. farrerae (270 SSRs) [56] and Rh. × pulchrum (221 SSRs) [51], highlighting the genetic complexity within this plant family. Chloroplast-derived SSRs (cpSSRs) have proven effective as polymorphic markers for interspecific and intraspecific differentiation at population scales [57]. The SSRs and repetitive sequences identified in this study establish a foundation for future studies on population genetics and evolutionary patterns within Rhododendron species.
The evolutionary dynamics of IR regions, particularly their expansion and contraction, are fundamental to chloroplast genome evolution, directly influencing genome size and gene organization [58,59]. These boundary regions (LSC/IRa/SSC/IRb) generally exhibit high conservation of gene content within genera, with only minor shifts in IR borders reported across closely related species [60,61]. Boundary comparisons across Rhododendron chloroplast genomes revealed distinct positional variations, including differential base positions and copy numbers for key genes (ycf15, trnR, ndhF, and trnH) at the IR-LSC and IR-SSC junctions.
Sequence comparisons using the mVISTA method demonstrated high similarity in coding regions among the nine examined chloroplast genomes, with most structural divergence localized to non-coding sequences in the LSC region. This pattern aligns with broader trends observed in angiosperm chloroplast genomes [62,63]. Nucleotide diversity (Pi) analysis across ten Rhododendron species identified three highly variable regions, including the ndhF region in the SSC compartment, which displayed the highest polymorphism. Similar variability hotspots have been documented in Chenopodium album [64] and Utricularia amethystine [65], suggesting their potential utility as molecular markers for phylogeographic research and population genetic analyses.
As a species-rich genus with persistent taxonomic challenges, Rhododendron exhibits complex and contentious classification schemes and phylogenetic relationships [17]. Previous phylogenetic investigations have employed molecular markers including nuclear internal transcribed spacers (ITSs), chloroplast DNA (cpDNA) fragments, and SSRs [66,67], yet these approaches yielded insufficient resolution for robust phylogenetic reconstruction. Recent advances in chloroplast genome sequencing have demonstrated superior utility in resolving taxonomic uncertainties among closely related taxa [6,7]. Our chloroplast genome-based phylogeny aligns closely with traditional taxonomic frameworks for Rhododendron [11,28] (Supplementary Table S1). Despite limited taxon sampling, two of the six recognized subgenera of Rhododendron were supported as monophyletic. The ten species within subgenus Hymenanthes formed a strongly supported clade, consistent with prior phylogenetic analyses [16,17]. Our findings validate the taxonomic elevation of former sections Azaleatrum and Choniastrtum (previously classified under subgenus Azaleastrum) to the subgeneric rank [20,28,68]. Rh. × pulchrum is considered as a horticultural cultivar of “Omurasaki” and Hirado azalea cultivars with its putative parents being Rh. scabrum, Rh. ripense, Rh. × mucronatum, and other related cultivars [69,70]. This species’ hybrid origin may account for the non-monophyly of subg. Rhododendron in this study. At the subsection level, monophyly was confirmed for subsection Fortunea (subgenus Hymenanthes) and subsections Lapponica and Triflora (subgenus Rhododendron). These results underscore the efficacy of the chloroplast genome for elucidating phylogenetic relationships within this large genus. Notably, subgenus Tsutsusi was not supported as monophyletic, and subsection Taliensia (subgenus Hymenanthes) was also not monophyletic. These inconsistencies align with prior reports [20,71], emphasizing the need for expanded sampling and multilocus approaches to refine lower-level taxonomy. Interestingly, Rh. purdomii formed a sister relationship with Rh. henanense subsp. lingbaoense, warranting denser taxon sampling to clarify its phylogenetic position within subgenus Hymenanthes. Given the very limited number of species we used, our study only provides a preliminary exploration of the phylogenetic relationships within the genus Rhododendron. Meanwhile, it should be noted that molecular techniques alone are not sufficient, and further studies should be conducted in combination with the use of morphological, phenological, and phytochemical markers.

5. Conclusions

This study presents the first complete chloroplast genome assembly of the threatened horticultural and medicinal species Rh. purdomii. The circular genome spans 208,062 bp, exhibiting a typical quadripartite structure and encoding 146 functional genes: 96 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. Structural characterization identified 96 long repetitive sequences and 171 SSRs. Comparative analysis revealed two highly variable coding regions (accD, rps9) and seven polymorphic intergenic spacers (trnK-UUU-ycf3, trnI-CAU-rpoB, trnT-GGU-accD, rpoA-psbL, rpl20-trnC-GCA, trnI-CAU-rrn16, and trnI-CAU-rps16), which represent promising molecular markers for species authentication and population studies. Phylogenetic reconstruction using whole chloroplast genomes strongly supports the utility of these data for resolving complex relationships within Rhododendron. Notably, Rh. purdomii forms a sister clade with Rh. henanense subsp. lingbaoense, underscoring their close evolutionary affinity. In conclusion, this study provides critical genomic resources that advance systematic studies and clarify some taxonomic uncertainties in the genus Rhododendron. The identified molecular markers and phylogenetic insights will inform conservation strategies and sustainable utilization of Rh. purdomii and its congeners.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/f16071120/s1, Supplementary Figure S1: Analysis of repeat sequences of Rh. purdomii Rehder & E. H. Wilson chloroplast genomes; Supplementary Figure S2: The number of different SSR units in the chloroplast genome of Rh. purdomii Rehder & E. H. Wilson; Supplementary Table S1: The species names, taxonomic information, GenBank accession numbers, sampling locations, and voucher numbers of Rhododendron species examined in this study.

Author Contributions

Conceptualization, N.Z. and Y.L.; methodology, L.Y.; validation, N.Z., Y.L. and S.Z.; formal analysis, L.Y.; investigation, Y.L.; resources, Y.L.; writing—original draft preparation, L.Y.; writing—review and editing, Y.L. and N.Z.; supervision, S.Z.; funding acquisition, Y.L. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China, grant number: 31800551.

Data Availability Statement

Data are contained within the article and Supplementary Materials.

Acknowledgments

We wish to thank Peiliang Liu, Shuai Li, and Hao Dong for their help during the field survey. This work was partly supported by the Supercomputing Center in Zhengzhou University (Zhengzhou).

Conflicts of Interest

The authors declare no conflicts of interest.

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Forests 16 01120 g001
Figure 1. The morphology of Rhododendron purdomii Rehder & E. H. Wilson. (a,b) Plant and habitat, (c) inflorescence, (d) branch, (e) leaf, (f) capsular fruit, (g) seedling, (h,i) flower bud.
Figure 1. The morphology of Rhododendron purdomii Rehder & E. H. Wilson. (a,b) Plant and habitat, (c) inflorescence, (d) branch, (e) leaf, (f) capsular fruit, (g) seedling, (h,i) flower bud.
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Forests 16 01120 g002
Figure 2. Circular visualization of Rh. purdomii Rehder & E. H. Wilson chloroplast genome. Genes are color-coded by functional category, with arrows indicating transcriptional direction. GC content is represented by darker gray, while lighter gray reflects AT content.
Figure 2. Circular visualization of Rh. purdomii Rehder & E. H. Wilson chloroplast genome. Genes are color-coded by functional category, with arrows indicating transcriptional direction. GC content is represented by darker gray, while lighter gray reflects AT content.
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Forests 16 01120 g003
Figure 3. Codon content and codon usage of 20 amino acids and stop codons of all protein-coding genes of Rh. purdomii Rehder & E. H. Wilson.
Figure 3. Codon content and codon usage of 20 amino acids and stop codons of all protein-coding genes of Rh. purdomii Rehder & E. H. Wilson.
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Forests 16 01120 g004
Figure 4. Comparative complete chloroplast genome architectures of ten Rhododendron species. The VISTA-based identity plots were visualized through mVISTA in Shuffle-LAGAN.
Figure 4. Comparative complete chloroplast genome architectures of ten Rhododendron species. The VISTA-based identity plots were visualized through mVISTA in Shuffle-LAGAN.
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Forests 16 01120 g005
Figure 5. Analysis of expansion and contraction of inverted repeats in the ten Rhododendron chloroplast genomes.
Figure 5. Analysis of expansion and contraction of inverted repeats in the ten Rhododendron chloroplast genomes.
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Forests 16 01120 g006
Figure 6. Nucleotide diversity analysis across ten Rhododendron chloroplast genomes. Sliding window analysis with genomic position on the X-axis and Pi values on the Y-axis.
Figure 6. Nucleotide diversity analysis across ten Rhododendron chloroplast genomes. Sliding window analysis with genomic position on the X-axis and Pi values on the Y-axis.
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Forests 16 01120 g007
Figure 7. Maximum likelihood (ML) phylogenetic tree of Ericaceae based on 29 complete chloroplast genomes. Numbers at the nodes represent bootstrap support values.
Figure 7. Maximum likelihood (ML) phylogenetic tree of Ericaceae based on 29 complete chloroplast genomes. Numbers at the nodes represent bootstrap support values.
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Table 1. Features of the Rh. purdomii Rehder & E. H. Wilson complete chloroplast genome.
Table 1. Features of the Rh. purdomii Rehder & E. H. Wilson complete chloroplast genome.
Genome FeaturesRh. purdomii
Genome size (bp)/GC content (%)208,062/35.81
LSC size (bp)/GC content (%)110,618/35.27
SSC size (bp)/GC content (%)2606/30.05
IR size (bp)/GC content (%)47,419/36.59
Total gene number146
Protein-coding genes96
tRNAs42
rRNAs8
LSC, large single copy region; SSC, small single copy region; IR, inverted repeat.
Table 2. Genes present in the Rh. purdomii Rehder & E. H. Wilson chloroplast genome.
Table 2. Genes present in the Rh. purdomii Rehder & E. H. Wilson chloroplast genome.
Category of GenesGroup of GenesName of Genes
Photosynthesis-related genesphotosystem IpsaApsaBpsaCpsaIpsaJ
photosystem IIpsbApsbBpsbCpsbDpsbE
psbFpsbIpsbJpsbKpsbL
psbMpsbNpsbTpsbZpsbH
NADH dehydrogenasendhA *ndhB *ndhCndhDndhE
ndhFndhGndhIndhJndhK
ndhH
ATP synthaseatpA
atpI		atpBatpEatpF *atpH
rubiscorbcL
cytochrome b/f complexpetB *petD *petGpetLpetN
petA
cytochrome c synthesisccsA
Transcription- and translation-related genesribosome proteinsrpl2
rpl23
rps3
rps12 **
rps19		rpl14
rpl32
rps4
rps14		rpl16 *
rpl33
rps7
rps15		rpl20
rpl36
rps8
rps16 *		rpl22
rps2
rps11
rps18
transcriptionrpoArpoBrpoC1rpoC2
translational initiation factorinfA
RNA genesribosomal RNArrn4.5rrn5rrn16rrn23
transfer RNAtrnA-UGC *trnC-GCAtrnD-GUCtrnE-UUCtrnF-GAA
trnfM-CAUtrnG-GCCtrnG-UCC *trnH-GUGtrnI-CAU
trnI-GAU *trnK-UUU *trnL-CAAtrnL-UAA *trnL-UAG
trnM-CAUtrnN-GUUtrnP-UGGtrnQ-UUGtrnR-ACG
trnR-UCUtrnS-GCUtrnS-GGAtrnS-UGAtrnT-GGU
trnT-UGUtrnV-GACtrnV-UAC *trnW-CCAtrnY-GUA
Other genesfatty acid synthesisaccD
carbon metabolismcemA
RNA processingmatK
Unknownconserved reading framesycf1ycf3 **ycf4ycf15ycf68
* Gene containing a single intron, ** Gene containing two introns.
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Yuan, L.; Zhang, N.; Zhu, S.; Lu, Y. The Complete Chloroplast Genome of Purdom’s Rhododendron (Rhododendron purdomii Rehder & E. H. Wilson): Genome Structure and Phylogenetic Analysis. Forests 2025, 16, 1120. https://doi.org/10.3390/f16071120

AMA Style

Yuan L, Zhang N, Zhu S, Lu Y. The Complete Chloroplast Genome of Purdom’s Rhododendron (Rhododendron purdomii Rehder & E. H. Wilson): Genome Structure and Phylogenetic Analysis. Forests. 2025; 16(7):1120. https://doi.org/10.3390/f16071120

Chicago/Turabian Style

Yuan, Lu, Ningning Zhang, Shixin Zhu, and Yang Lu. 2025. "The Complete Chloroplast Genome of Purdom’s Rhododendron (Rhododendron purdomii Rehder & E. H. Wilson): Genome Structure and Phylogenetic Analysis" Forests 16, no. 7: 1120. https://doi.org/10.3390/f16071120

APA Style

Yuan, L., Zhang, N., Zhu, S., & Lu, Y. (2025). The Complete Chloroplast Genome of Purdom’s Rhododendron (Rhododendron purdomii Rehder & E. H. Wilson): Genome Structure and Phylogenetic Analysis. Forests, 16(7), 1120. https://doi.org/10.3390/f16071120

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