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Article

Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species

by
Zhuang Zhao
1,†,
Meng-Yao Zeng
1,†,
Yu-Wei Wu
1,
Jin-Wei Li
1,
Zhuang Zhou
1,2,
Zhong-Jian Liu
1,3,* and
Ming-He Li
1,3,*
1
Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2
Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
3
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2023, 24(19), 14437; https://doi.org/10.3390/ijms241914437
Submission received: 23 August 2023 / Revised: 10 September 2023 / Accepted: 19 September 2023 / Published: 22 September 2023
(This article belongs to the Special Issue New Trends in Genomics and Metabolomics of Horticultural Plants at Fujian Agriculture and Forestry University)
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Abstract

:
Epidendrum, one of the three largest genera of Orchidaceae, exhibits significant horticultural and ornamental value and serves as an important research model in conservation, ecology, and evolutionary biology. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete plastome of this genus (including five species) were firstly sequenced and assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. The lengths of the plastomes ranged from 147,902 bp to 150,986 bp, with a GC content of 37.16% to 37.33%. Gene annotation revealed the presence of 78–82 protein-coding genes, 38 tRNAs, and 8 rRNAs. A total of 25–38 long repeats and 130–149 SSRs were detected. Analysis of relative synonymous codon usage (RSCU) indicated that leucine (Leu) was the most and cysteine (Cys) was the least. The consistent and robust phylogenetic relationships of Epidendrum and its closely related taxa were established using a total of 43 plastid genomes from the tribe Epidendreae. The genus Epidendrum was supported as a monophyletic group and as a sister to Cattleya. Meanwhile, four mutational hotspots (trnCGCA–petN, trnDGUC–trnYGUA, trnSGCU–trnGUCC, and rpl32–trnLUAG) were identified for further phylogenetic studies. Our analysis demonstrates the promising utility of plastomes in inferring the phylogenetic relationships of Epidendrum.

1. Introduction

Orchidaceae is recognized as one of the largest families of angiosperms, encompassing approximately 736 genera and 28,000 species [1,2]. Epidendrum L., a genus of the subtribe Lealiinae (tribe Epidendreae), is frequently celebrated as an outstanding example of adaptive radiation in vascular plants. It is among the largest genera of flowering plants, with approximately 1500 species that are mainly distributed in tropical and subtropical America [3]. Epidendrum species are almost epiphytic and caespitose, and their stems typically exhibit a cane-like morphology, while their petioles are characterized by tubular sheathing [3]. They possess significant horticultural and ornamental value due to the rich variations in the colors and shapes of their flowers. Epidendrum flowers are popular wedding flowers for bouquets, decorations, boutonnieres, and table centerpieces, as well as a favorite choice for prom corsages [4]. Meanwhile, the leaves of certain species within this genus have been traditionally utilized to address various health concerns, such as kidney problems, influenza, conjunctivitis, and liver pain, alleviating kidney symptoms and exhibiting a hypoglycemic effect [5]. This genus, similar to other Orchidaceae, exhibits a higher level of endangerment compared to other angiosperms [6]. Additionally, it demonstrates notable occurrences of natural hybridization and ecological interactions, rendered as a crucial subject for conservation biology, evolution, and ecology research [7,8,9,10,11,12].
The genus exhibits remarkable morphological diversification, characterized by a wide range of ancestral traits that pose challenges in an endeavor to delineate the generic circumscription [13]. Some morphological discussions have been conducted, including assessments of pseudobulb presence, column foot, and pollinia characteristics [14,15,16]. However, these investigations yielded uncompelling results. Van den Berg et al. first utilized the nuclear ribosomal ITS sequence to explore the phylogeny of Laeliinae, including 15 Epidendrum species, and the results indicated that Epidendrum was polyphyletic [17]. With the advancement of phylogenetic investigations on Epidendrum, incorporating multiple molecular fragment markers and expanding the taxonomic sampling range [1,3,11,18,19], a consensus of polyphyletic was reached regarding the delimitation of the genus. Meanwhile, the interrelationships remain incompletely resolved due to unstable topology and low support values.
Plastids play a crucial role in sustaining life on Earth by facilitating the conversion of solar energy into carbohydrates through photosynthesis and releasing oxygen. The plastid genome (plastome) has diverse applications in horticultural breeding, crop domestication, and phylogenetic studies [20]. The distinct genetic background, straightforward structure, and ability to provide substantial information regarding site characteristics make the plastome widely utilized in Orchidaceae phylogeny. Givnish et al. sampled 39 representative species of Orchidaceae to construct a phylogenetic tree based on the plastome [21]. The results revealed 5 subfamilies, 18 tribes, and 22 subtribes with strong support of Orchidaceae. Similarly, Liu et al. conducted a phylogenetic analysis using plastomes of 53 species belonging to the Cleisostoma–Gastrochilus clade. The results strongly supported the subdivision of this clade into six subclades, representing a significant improvement over previous studies that relied on several molecular fragment markers [22]. Overall, considerable progress has been made in utilizing plastomes to elucidate phylogenetic relationships within Orchidaceae at both the tribe or subtribe level and the interspecific level of genera. Studies have also investigated the impact of plastome features on the alteration of physiological traits and lifestyle in orchids, with particular emphasis on the transformation of epiphytic characteristics and mycoheterotrophic adaptations [23,24]. Among the largest genera in the Orchidaceae, substantial sections of the plastomes of Bulbophyllum and Dendrobium have been published and researched [25,26]. However, no plastome of Epidendrum has been currently reported.
In this study, we sequenced, assembled, and annotated the complete plastomes of five Epidendrum species, with the aim of (1) characterizing and contrasting the complete plastomes of Epidendrum; (2) understanding the evolutionary pattern of the Epidendrum plastome; and (3) evaluating variations in high-variability sites and simple sequence repeats (SSRs) for accurate authentication of Epidendrum species. Our study will contribute to the expansion of the genomic resources available for Orchidaceae and provide critical information to support the identification and phylogenetic analysis of different Epidendrum species.

2. Results

2.1. Genome Features

The genome sizes of the five Epidendrum plastomes (Table 1) were determined to be 149,741 bp (E. avicula), 149,580 bp (E. ciliare), 147,902 bp (E. diffusum), 150,986 bp (E. eburneum), and 148,859 bp (E. porpax). The overall GC contents were found to be 37.16% (E. avicula), 37.33% (E. ciliare), 37.32% (E. diffusum), 37.19% (E. eburneum), and 37.27% (E. porpax). The plastomes exhibited a typical quadripartite structure (Figure 1). The length of the large single-copy (LSC) region ranged from 83,582 bp to 85,626 bp, with a GC content of 34.68% to 34.83%. The small single-copy (SSC) regions spanned from 11,059 bp to 12,659 bp, with a GC content of approximately 27.83% to 29.18%. The inverted repeat (IR) regions had a GC content of 41.23% to 41.41% and lengths ranging from 25,813 bp to 26,544 bp (Table 1).
The plastomes of Epidendrum encoded 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. The plastome of E. avicula contained 129 genes, including 83 protein-coding genes; E. ciliare and E. eburneum contained 128 genes, including 82 protein-coding genes; E. diffusum contained 124 genes, including 78 protein-coding genes; and E. porpax contained 127 genes, including 81 protein-coding genes (Supplementary Table S1). The differences in gene numbers were due to the loss or pseudogenization of ndh genes (Supplementary Table S1). The plastomes of E. ciliare and E. eburneum encoded eight ndh genes (including two ndh B and one each of ndh C/D/E/H/J/K), E. diffusum encoded four ndh genes (including two ndh B and one each of ndh E/H), E. porpax encoded seven ndh genes (including two ndh B and one each of ndh C/D/E/F/J), and E. avicula encoded nine ndh genes (including two ndh B and one each of ndh C/D/E/F/H/J/K). The mauve visualization graphs indicated that the gene arrangement was conserved, and no significant gene rearrangement was detected among these plastomes (Supplementary Figure S1).
The IR boundary map was generated by comparing the plastomes of five Epidendrum species (Figure 2). The results showed that the rps19 gene spanned the LSC/IRb boundary and primarily occurred in the LSC region, covering a length of 314 bp, with the remaining 52 bp located in the IRb region (E. ciliare, E. diffusum, E. eburneum and E. porpax), whereas in E. avicula, it comprised 311 bp situated in the LSC and 55 bp in the IRb region. For the IRb/SSC (JSB) region, the boundary was located on the right side of the trnNGUU region, and the distance from the trnNGUU to the JSB line ranged from 269 bp (E. diffusum) to 834 bp (E. eburneum). For the SSC/IRa (JSA) region, the ycf1 gene spanned the SSC/IRa boundary and primarily occurred in the SSC region ranging from 5012 bp (E. eburneum) to 5583 bp (E. ciliare), whereas in E. diffusum, it was located on the right side of the JSA line and the distance was 54 bp. For the IRa/LSC (JLA) region, the psbA gene was located on the right side of the JLA line and the distance from the psbA to the JLA line ranged from 105 bp (E. ciliare) to 132 bp (E. eburneum).

2.2. Long Repeat and Simple Sequence Repeat (SSR) Analysis

In the analysis of the five Epidendrum plastomes, a total of 152 long repeat sequences were identified, encompassing four distinct categories: forward (F), reverse (R), complement (C), and palindromic (P) repeats (Figure 3A, Supplementary Table S2). Among them, all four categories were observed within two species (E. diffusum and E. eburneum), the other three species (E. avicula, E. ciliare and E. porpax) contained three categories of repeats (F, R, and P). The number of long repeat sequences varied in E. avicula, E. ciliare, E. diffusum, E. eburneum, and E. porpax with them containing 25, 26, 34, 38, and 29 repeats, respectively. Across these five genomes, palindromic repeats (P) were the most prevalent and ranged from 20 (E. eburneum) to 14 occurrences (E. avicula). R and C repeats of E. eburneum were less abundant and exhibited the highest counts of these types (4 and 3, respectively). The long repeat (30–39 bp) sequences were the most frequently observed and ranged from 21 (E. avicula) to 30 occurrences (E. eburneum). E. eburneum also displayed the highest count of 40–49 bp repeats (Figure 3B, Supplementary Table S3). The longest of the long repeat sequences was 57 bp (Supplementary Table S3).
Simple sequence repeats (SSRs) composed of 1- to 6-nucleotide motifs were further examined. A total of 134, 144, 130, 144, and 149 SSRs were identified in the plastomes of E. avicula, E. ciliare, E. diffusum, E. eburneum, and E. porpax, respectively (Figure 4A, Supplementary Table S4). Mononucleotide SSRs were the most abundant type and accounted for 69.87%, while dinucleotide SSRs ranged from 6 (E. ciliare) to 13 occurrences (E. porpax). Tetranucleotide SSRs were more common than trinucleotide SSRs except for E. porpax, which exhibited the opposite trend. Pentanucleotide SSRs appeared only once in E. porpax and E. avicula, whereas hexanucleotide SSRs were absent from all genomes. Among the repeat motifs, the A/T mononucleotide motif was the most frequently observed, with it ranging from 108 (E. porpax) to 124 occurrences (E. avicula) (Figure 4B, Supplementary Table S4). The AT/AT dinucleotide motif was the second most prevalent and ranged from 4 (E. ciliare) to 11 occurrences (E. porpax). The C/G motifs appeared from 3 (E. porpax) to 6 occurrences (E. avicula) (Figure 4B, Supplementary Table S4).

2.3. Relative Synonymous Codon Usage Analysis

A total of 68 protein-coding genes were analyzed among the five Epidendrum plastomes, with the exception of the ndh genes due to incomplete gene loss and pseudogenization. These genes were encoded by a range of 19,305 (E. diffusum) to 19,405 (E. eburneum) codons (Table 2). The codon usage patterns are summarized in Table 2 and showed a highly conserved codon usage bias (CUB). Among them, one of the most frequent amino acids was leucine (Leu), appearing a total of 9751 times across all five plastomes. Reversely, cysteine (Cys) was the least frequent, occurring only 1062 times. Analysis of the relative synonymous codon usage (RSCU) indicated that GCU and CUU had the highest CUB, with average values of 1.866 and 1.725, respectively, whereas GCG and UAC had the lowest CUB, with average values of 0.364 and 0.374, respectively. Among the three stop codons, the frequency of UAA was the highest, accounting for 45.30%. The results also showed that 32 codons exhibited RSCU values greater than 1 and 30 codons exhibited less than 1. The RSCU values of AUG encoding for methionine (Met) and UGG encoding for threonine (Thr) were determined to be 1.

2.4. Sequence Variation and Barcoding Investigation

The divergence of the complete plastome sequences among the five Epidendrum species was analyzed using the mVISTA online platform, with Stelis montserratii as the reference. The results (Supplementary Figure S2) demonstrated that the full-length plastomes were highly conserved. The majority of the variable sites were observed in intergenic spacer regions. The coding regions exhibited greater conservation compared to the non-coding regions, and the IR regions were found to be more conserved than the LSC and SSC regions.
To explore the highly mutable hotspots of Epidendrum plastomes, DnaSP6 was utilized to calculate nucleotide diversity (Pi). The results showed that the Pi values ranged from 0 to 0.14 (trnCGCA–petN) (Figure 5A, Supplementary Table S5). The IR regions exhibited the highest conservation with a value of 0.00342. The SSC region displayed the greatest nucleotide diversity (Pi = 0.02404), followed by the LSC region (Pi = 0.01294). According to the ranking of the Pi values, four hypervariable regions, including trnCGCA–petN (Pi = 0.14), trnDGUC–trnYGUA (Pi = 0.112), trnSGCU–trnGUCC (Pi = 0.088), and rpl32–trnLUAG (Pi = 0.08), were identified. Additionally, the nucleotide diversity of protein-coding genes was also analyzed. The results showed that the protein-coding genes have higher conservation (Figure 4B, Supplementary Table S6). Among these genes, ycf1 (Pi = 0.02363), rpl22 (Pi = 0.01639), ccsA (Pi = 0.01542), and rpl32 (Pi = 0.01437) displayed the highest Pi values.

2.5. Phylogenetic Analysis

The phylogenetic analysis was conducted using complete plastome sequences and 68 protein-coding genes from 43 Epidendreae species (Figure 6, Supplementary Figure S3, Supplementary Table S7). The alignment matrix of complete plastome sequences was 207,121 bp, with 42,905 variable sites and 23,167 parsimony informative sites. The matrix of 68 protein-coding genes was 62,292 bp, with 10,746 variable sites and 57,000 parsimony informative sites. The results revealed a consistent topological structure, and the main clades were strongly supported (Figure 6, Supplementary Figure S3). Specifically, Epidendrum was robustly supported as a monophyletic group (BS = 100, PP = 1.00) and as a sister to Cattleya. Within the genus, the analyses collectively supported the following relationships: ((E. ciliare, E. diffusum) (E. porpax (E. eburneum, E. avicula))). Furthermore, the tribe phylogenetic tree unveiled that Epidendreae were recovered as a monophyletic group and the following relationships of five subtribes were unveiled: (Agrostophyllinae (Calypsinae (Bletiinae (Pleurothallidinae, Laeliinae)))).

3. Discussion

3.1. Plastome Characteristics and Structure

In this study, the complete plastomes (including five species) of Epidendrum were first reported and a total of five species were sequenced and assembled. This provides a valuable opportunity to gain further insights into the evolution of plastomes in this complex genus. Similar to most angiosperms, the Epidendrum plastome exhibited a typical quadripartite structure, consisting of one LSC, one SSC, and two IR regions. The genome size (ranging from 147,902 to 150,986 bp) and GC content (ranging from 37.16% to 37.33%) fall within the range of other orchids, such as the epiphytic orchids Dendrobium, Holcoglossum, and Paraphalaenopsis [26,27,28]. The five Epidendrum plastomes identified a total of 124 to 129 genes, consisting of 78 to 83 protein-coding genes, 38 tRNAs, and 8 rRNAs (Figure 1, Supplementary Table S1). The variations in gene content were revealed due to the incomplete loss of ndh genes, which was also found in other orchid species, such as Dendrobium and Polystachya [26,29]. These phenomena may potentially indicate a correlation with the epiphytic lifestyle [30]. Analyses of Mauve collinearity and plastome boundaries were conducted in this study (Supplementary Figure S1), which revealed a highly conserved structure among these plastomes. It is well-known that the contraction and expansion of the IR boundary are common during the evolution of plastids, significantly contributing to the variation in plastome length and gene content in angiosperms [31]. In terms of gene arrangement at the boundaries within the five Epidendrum plastomes (Figure 2), we observed a high degree of conservation at JLA and JLB. However, the variations of JSB (Figure 2) could be attributed to the loss of ndhF in E. ciliare and E. diffusum.
The identification of long repeat sequences and SSRs within chloroplast genomes plays a crucial role in recognizing plant germplasm resources and molecular markers, making it an essential aspect of scientific research in this field [32]. For long repeat sequences (Figure 3), complement repeats were only observed in E. diffusum and E. eburneum. The other three repeat units were shared among all five plastomes, with slight differentiation in terms of the number of repeat units and their proportions. Simple-sequence repeats (SSRs) are short tandem repeat DNA sequences that consist of repeating 1–6 nucleotide motifs (Figure 4). These motifs are widely distributed throughout the plastomes and serve as crucial molecular markers for analyzing genetic diversity and species relationships [33]. In this study, a total of 134 to 149 SSRs were identified in the plastomes of Epidendrum (Figure 4). A/T SSRs were found to be more abundant compared to G/C SSRs, which is consistent with other orchids [29,34]. Additionally, the numbers of Dinucleotide SSRs varied across the five Epidendrum plastomes, which can be employed for further population genetic and phylogenetic research [32]. The relative synonymous codon usage (RSCU) is highly valuable in understanding the preference for synonymous codon usage [35]. The codon frequency and RSCU values displayed similar patterns in Epidendrum plastomes (Table 2). Among all codons, leucine (Leu) exhibited the highest occurrence, while cysteine (Cys) had the lowest frequency. These findings are consistent with previous studies on codon preference in Orchidaceae [27,33,36] and further demonstrate the high level of plastome conservation in Epidendrum.

3.2. Plastid Genomic Evolutionary Hotspots

Earlier studies have shown that the IR regions are highly conserved, and coding regions exhibit greater conservation compared to the non-coding regions in the plastomes of Orchidaceae [27,28,29,34,36]. The results of complete plastome divergence among Epidendrum (Figure 5) are consistent with previous findings. DNA barcoding can be employed as a method to identify species [37]. With advancements in molecular phylogenetics, DNA barcoding of Orchidaceae has successfully utilized rbcL, matK, atpB, psaB, Xdh, trnL-F, and ITS [38,39,40]. While these phylogenetics have established an initial framework for understanding the phylogeny of orchids, most taxonomic complexities, especially the intrageneric phylogenetic relationships, still pose various challenges. Currently, plastomes are commonly used in phylogenetic studies and species identification [41]. In this study, four hypervariable regions, including trnCGCA–petN, trnDGUC–trnYGUA, trnSGCU–trnGUCC, and rpl32–trnLUAG, were identified. Although four protein-coding genes, including ycf1, rpl22, ccsA, and rpl32, also displayed high Pi values, they still remain highly conserved. These results demonstrate that the aforementioned intergenic spacer regions are more suitable as candidate barcodes compared to protein-coding genes.

3.3. Phylogeny of Epidendrum and Its Related Taxon

The tribe Epidendreae was initially defined as a group of tropical epiphytic orchids, and the circumscription has constantly changed with the discovery of a large number of tropical orchids [42]. Based on molecular phylogenetics, the Epidendreae were supported and divided into five subtribes: Bletiinae, Chysiinae, Laeliinae, Ponerinae, and Pleurothallidinae [42]. Szlachetko proposed that Epidendreae consisted of Coellinae, Chysiinae, Meiracyllinae, Laellinae (including Cattleya), Epidendrinae (including Epidendrum), Ponerinae, and Pleurothallidinae based on morphological characteristics [43]. Among these subtribes, Epidendrinae and Laellinae were closest and had the same seed morphology but differed in gynostemium and anther. This classification was widely accepted by subsequent studies until Chase et al. [1]. In this study, the phylogenetic analysis based on 68 protein-coding genes and complete plastome sequences robustly supported the sister relationship between Cattleya and Epidendrum. Five monophyletic groups, Agrostophyllinae, Calypsoinae, Bletiinae, Pleurothallidinae, and Laeliinae, were also unveiled with high support (Figure 6, Supplementary Figure S3). These findings are consistent with previous studies and demonstrate the effectiveness of using plastomes to subtribe the phylogenetics of Epidendreae.
Van den Berg et al. proposed a hypothesis for the circumscription of the Epidendrum alliance based on ITS sequences. Subsequently, more samples and the matK fragment were added to further explore this alliance [2,17]. The findings revealed that the range of Epidendrum has been significantly underestimated. The phylogenetic analysis, conducted using several molecular fragments, indicated that the Epidendrum alliance consists of Epidendrum, Caularthron, Orleanesia, Barkeria, and Myrmecophila, with a close relationship with the Laelia alliance [18]. Considering the unstable topologies and low support rates [2,17,18], it is crucial to conduct further investigations into the phylogenetic relationships of Epidendrum and its related taxa. In certain groups within the Orchidaceae, which have undergone rapid radiation and consist of numerous species, plastomes have shown excellent performance in phylogenetic studies [23]. In this study, the phylogenetic analysis based on 68 protein-coding genes and complete plastomes demonstrated a stable topology and provided high support for five Epidendrum species (Figure 5, Supplementary Figure S3). The results demonstrate the power of plastid phylogenomics to improve the phylogenetic relationships of Epidendrum.

4. Materials and Methods

4.1. Sample Sampling, DNA Extraction and Sequencing, Plastome Assembly and Annotation

In this study, we sequenced five Epidendrum species, and their voucher specimens were stored at the herbarium of the College of Forestry, Fujian Agriculture and Forestry University (FJFC). A total of 49 plastomes from 24 genera were selected, including 4 genera with 6 species designated as outgroups based on the classification of Chase et al. [1]. Supplementary Table S7 provides details on the taxa, including voucher information and GenBank accession numbers. To perform DNA extraction, sequencing, plastome assembly, and annotation, we followed the protocols outlined in our previous study [23].

4.2. Analysis of Plastome Structure, Repeat Sequences, and Codon Usage

To identify rearrangements among different Epidendrum plastomes, we utilized the software Mauve (http://gel.ahabs.wisc.edu/mauve, accessed on 22 August 2023) [44]. The online R Shiny application CPJSdraw 0.0.1 [45] was employed to visually analyze and evaluate the differences in the boundaries of the LSC/IR/SSC regions across all five Epidendrum plastomes. Using REPuter (https://bibiserv.cebitec.uni-bielefeld.de/reputer, accessed on 22 August 2023) [46] with default parameters, we detected four types of long repeats (F—forward, P—palindrome, R—reverse, and C—complement) in the five plastomes. Simple sequence repeats (SSRs) were detected using the Perl script MISA [47], with the minimum thresholds for mono-, di-, tri-, tetra-, penta-, and hexa-motif microsatellites set at 10, 5, 4, 3, 3, and 3 nucleotide repeats, respectively. The R package ggplot2 [48] was used to visualize the results.
To extract the 68 protein-coding genes from the five Epidendrum plastomes, we employed PhyloSuite v1.2.2 [49]. These genes were then concatenated using Phylosuite v1.2.2, and their relative synonymous codon usage (RSCU) for each Epidendrum species was analyzed using DAMBE7 [50].

4.3. Analysis of Sequence Variation, Barcoding Investigation, and Phylogeny

To analyze the diversity of Epidendrum plastome sequences, the online program mVISTA (https://genome.lbl.gov/vista/mvista, accessed on 22 August 2023) was utilized, employing the Shuffle-LAGAN alignment program [51]. The plastome of Stelis montserratii (MW375125) was used as the reference. Nucleotide variability (Pi) for the five Epidendrum plastomes and 68 protein-coding genes of the plastome was calculated using DnaSP 6 [52] with a window length of 100 bp and a step size of 25 bp.
For phylogenetic tree construction, a concatenated matrix of the 68 protein-coding genes and a matrix of complete plastomes were used. The 68 protein-coding genes were extracted and concatenated using PhyloSuite v1.2.2 [50]. The complete plastomes and the concatenated 68 protein-coding genes were aligned using MAFFT v7.471 [53]. Phylogenetic relationships were then analyzed using maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI), following the protocols described in our previous study [23].

5. Conclusions

In this study, we firstly report the complete plastomes (including five species) of Epidendrum, and a total of five species were sequenced and assembled. Our findings reveal a high degree of conservation in terms of sequence lengths, boundaries of inverted repeats (IR), repeat sequences, and codon usage among Epidendrum plastomes. Moreover, we have identified certain regions (trnCGCA–petN, trnDGUC–trnYGUA, trnSGCU–trnGUCC, and rpl32–trnLUAG) as mutational hotspots, which hold potential for further phylogenetic investigations. By employing phylogenomic analysis, we have demonstrated that plastomes offer valuable insights into the phylogenetic relationships within Epidendrum. These findings underscore the significance of plastomes as a robust tool for studying the evolutionary history of Epidendrum. Overall, our study contributes to the expanding library of sequenced plastomes in Epidendrum. Future research can capitalize on these findings to deepen our understanding of the plastome evolutionary relationships within Epidendrum and related taxa.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms241914437/s1.

Author Contributions

Conceptualization, M.-H.L. and Z.-J.L.; methodology, Z.Z. (Zhuang Zhao) and M.-Y.Z.; software, Z.Z. (Zhuang Zhao); validation, Z.Z. (Zhuang Zhao), M.-H.L. and Z.-J.L.; formal analysis, Z.Z. (Zhuang Zhao), M.-Y.Z., Y.-W.W., J.-W.L., and Z.Z. (Zhuang Zhou); investigation, Z.Z. (Zhuang Zhao), M.-Y.Z. and Y.-W.W.; resources, J.-W.L. and Z.Z. (Zhuang Zhou); data curation, Z.Z. (Zhuang Zhao), M.-Y.Z., and J.-W.L.; writing—original draft, Z.Z. (Zhuang Zhao) and M.-Y.Z.; writing—review and editing, M.-H.L. and Z.-J.L.; supervision, M.-H.L. and Z.-J.L.; project administration, M.-H.L.; funding acquisition, M.-H.L. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Outstanding Youth Scientific Fund of Fujian Agriculture and Forestry University (XJQ202005), the Nature Science Foundation of Fujian Province, China (2021J01134), and the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University (72202200205).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The five newly obtained complete plastid genome sequences that support the findings of the study have been deposited in the NCBI with accession numbers as followes: OR460022-OR460026.

Acknowledgments

We would like to express our sincere gratitude to Zhuo-Xiao Kang for his invaluable assistance in proofreading and critically reviewing this paper.

Conflicts of Interest

The authors declare that no competing interests exist.

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Ijms 24 14437 g001
Figure 1. Annotation maps of five Epidendrum plastomes. The darker gray in the inner circle corresponds to the GC content. The IRa and IRb (two inverted repeating regions); LSC (large single-copy region); and SSC (small single-copy region) are indicated outside of the GC content.
Figure 1. Annotation maps of five Epidendrum plastomes. The darker gray in the inner circle corresponds to the GC content. The IRa and IRb (two inverted repeating regions); LSC (large single-copy region); and SSC (small single-copy region) are indicated outside of the GC content.
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Figure 2. Comparison of the borders of LSC, SSC, and IR regions in the five Epidendrum species.
Figure 2. Comparison of the borders of LSC, SSC, and IR regions in the five Epidendrum species.
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Figure 3. Comparison of long repeat sequences among five Epidendrum plastomes. (A) The number of each of four long repeat types (P, palindromic; F, forward; R, reverse; C, complement). (B) The number of long repeat sequences of different lengths.
Figure 3. Comparison of long repeat sequences among five Epidendrum plastomes. (A) The number of each of four long repeat types (P, palindromic; F, forward; R, reverse; C, complement). (B) The number of long repeat sequences of different lengths.
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Figure 4. Comparison of simple sequence repeats (SSRs) among the five Epidendrum plastomes. (A) The number of SSRs containing one- to five-nucleotide motifs. (B) The number of different SSR motifs.
Figure 4. Comparison of simple sequence repeats (SSRs) among the five Epidendrum plastomes. (A) The number of SSRs containing one- to five-nucleotide motifs. (B) The number of different SSR motifs.
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Figure 5. The nucleotide diversity (Pi) of Epidendrum plastomes and 68 protein-coding sequences. (A) For the nucleotide diversity of the complete plastome using a sliding window test, four mutation hotspot regions were annotated. The window size was set to 100 bp and the sliding windows size was 25 bp. X-axis, the position of the midpoint of a window; Y-axis, Pi values of each window. (B) The nucleotide diversity of 68 protein-coding sequences. X-axis, gene; Y-axis, Pi values of each gene.
Figure 5. The nucleotide diversity (Pi) of Epidendrum plastomes and 68 protein-coding sequences. (A) For the nucleotide diversity of the complete plastome using a sliding window test, four mutation hotspot regions were annotated. The window size was set to 100 bp and the sliding windows size was 25 bp. X-axis, the position of the midpoint of a window; Y-axis, Pi values of each window. (B) The nucleotide diversity of 68 protein-coding sequences. X-axis, gene; Y-axis, Pi values of each gene.
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Figure 6. The phylogenetic tree of 43 Epidendreae species obtained by maximum-likelihood analysis based on complete plastome sequences. The numbers near the nodes are bootstrap percentages and Bayesian posterior probabilities (BPML, BPMP, PP); * the node is the 100 bootstrap percentage or 1.00 posterior probability.
Figure 6. The phylogenetic tree of 43 Epidendreae species obtained by maximum-likelihood analysis based on complete plastome sequences. The numbers near the nodes are bootstrap percentages and Bayesian posterior probabilities (BPML, BPMP, PP); * the node is the 100 bootstrap percentage or 1.00 posterior probability.
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Table 1. Complete plastome features of Epidendrum.
Table 1. Complete plastome features of Epidendrum.
FeathersE. aviculaE. ciliareE. diffusumE. eburneumE. porpax
Total length (bp)149,741149,580147,902150,986148,859
GC content (%)37.1637.3337.3237.1937.27
LSC length (bp)85,45685,62683,58285,47685,344
GC content (%)34.7234.8334.8034.6834.72
SSC length (bp)12,65912,22612,51812,42211,059
GC content (%)28.3229.1828.9328.6527.83
IR length (bp)25,81325,86425,90126,54426,228
GC content (%)43.3743.4143.4143.2343.40
Number of genes129128124128127
Protein-coding genes8382788281
tRNA genes3838383838
rRNA genes88888
ndh genes98487
Specimen voucherMHLi or147MHLi or123MHLi or137MHLi or140MHLi or131
Accession numberOR460026OR460022OR460023OR460025OR460024
Table 2. The relative synonymous codon usage (RSCU) values of all 64 codons for the five Epidendrum plastomes. * indicates stop codon.
Table 2. The relative synonymous codon usage (RSCU) values of all 64 codons for the five Epidendrum plastomes. * indicates stop codon.
CodonAAE. aviculaE. ciliareE. diffusumE. eburneumE. porpax
FrequencyRSCUFrequencyRSCUFrequencyRSCUFrequencyRSCUFrequencyRSCU
UAA*321.412 301.324 291.279 311.368 321.412
UAG*170.750 190.838 190.838 190.838 190.838
UGA*190.838 190.838 200.882 180.794 170.750
GCAAla3211.224 3201.220 3221.221 3231.234 3221.233
GCCAla1450.553 1440.549 1400.531 1410.539 1430.547
GCGAla930.355 970.370 990.375 940.359 940.360
GCUAla4901.868 4881.861 4941.873 4891.868 4861.860
UGCCys550.524 510.474 530.495 520.491 540.512
UGUCys1551.476 1641.526 1611.505 1601.509 1571.488
GACAsp1480.376 1490.376 1520.386 1490.375 1470.373
GAUAsp6391.624 6431.624 6351.614 6451.625 6411.627
GAAGlu8211.519 8321.524 8221.522 8391.532 8281.523
GAGGlu2600.481 2600.476 2580.478 2560.468 2590.477
UUCPhe3760.701 3790.704 3820.712 3790.703 3760.697
UUUPhe6961.299 6971.296 6911.288 6991.297 7031.303
GGAGly5071.543 5061.536 5071.542 5101.547 5151.561
GGCGly1300.396 1330.404 1300.395 1330.403 1280.388
GGGGly2360.718 2390.725 2360.718 2330.707 2320.703
GGUGly4411.342 4401.335 4421.344 4431.343 4451.348
CACHis1100.448 1100.451 1110.452 1100.453 1100.451
CAUHis3811.552 3781.549 3801.548 3761.547 3781.549
AUAIso4730.880 4920.909 4830.898 4850.902 4840.900
AUCIso3320.618 3350.619 3270.608 3320.617 3330.619
AUUIso8071.502 7971.472 8031.493 7961.480 7971.481
AAALys8261.495 8231.484 8141.485 8271.486 8191.470
AAGLys2790.505 2860.516 2820.515 2860.514 2950.530
CUALeu2551.123 2641.140 2631.142 2611.129 2711.172
CUCLeu1250.551 1270.549 1240.539 1260.545 1220.528
CUGLeu1360.599 1370.592 1340.582 1370.592 1370.592
CUULeu3921.727 3981.719 4001.737 4011.734 3951.708
UUALeu6171.198 6121.192 6091.183 6161.194 6151.198
UUGLeu4130.802 4150.808 4210.817 4160.806 4120.802
AUGMet4391.000 4381.000 4361.000 4461.000 4391.000
AACAsp1920.413 1880.409 1900.410 1910.411 1930.420
AAUAsp7371.587 7311.591 7361.590 7381.589 7251.580
CCAPro2111.098 2131.095 2111.090 2121.091 2081.081
CCCPro1740.905 1740.895 1750.904 1760.906 1730.899
CCGPro850.442 840.432 850.439 840.432 860.447
CCUPro2991.555 3071.578 3031.566 3051.570 3031.574
CAAGlu5681.548 5651.546 5641.547 5691.546 5711.550
CAGGlu1660.452 1660.454 1650.453 1670.454 1660.450
AGAArg3761.510 3881.525 3851.513 3841.509 3831.520
AGGArg1220.490 1210.475 1240.487 1250.491 1210.480
CGAArg2751.558 2691.528 2721.541 2711.535 2711.542
CGCArg640.363 670.381 670.380 670.380 650.370
CGGArg820.465 810.460 810.459 810.459 820.467
CGUArg2851.615 2871.631 2861.620 2871.626 2851.622
AGCSer800.409 780.394 790.406 780.397 790.403
AGUSer3111.591 3181.606 3101.594 3151.603 3131.597
UCASer2871.073 2881.076 2831.062 2841.059 2901.074
UCCSer2300.860 2270.848 2240.841 2310.861 2320.859
UCGSer1090.407 1120.418 1130.424 1150.429 1110.411
UCUSer4441.660 4441.658 4461.674 4431.651 4471.656
ACAThr2961.221 2981.214 2941.212 3061.250 3011.229
ACCThr1770.730 1730.705 1750.722 1720.703 1790.731
ACGThr1050.433 1040.424 1040.429 1000.409 1010.412
ACUThr3921.616 4071.658 3971.637 4011.638 3991.629
GUAVal3851.454 3861.464 3851.462 3841.449 3861.458
GUCVal1350.510 1320.500 1330.505 1350.509 1310.495
GUGVal1590.601 1600.607 1580.600 1600.604 1640.619
GUUVal3801.435 3771.429 3771.432 3811.438 3781.428
UGGTry3401.000 3401.000 3361.000 3371.000 3361.000
UACTyr1260.370 1240.368 1280.383 1280.378 1250.370
UAUTyr5561.630 5501.632 5401.617 5501.622 5511.630
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Zhao, Z.; Zeng, M.-Y.; Wu, Y.-W.; Li, J.-W.; Zhou, Z.; Liu, Z.-J.; Li, M.-H. Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species. Int. J. Mol. Sci. 2023, 24, 14437. https://doi.org/10.3390/ijms241914437

AMA Style

Zhao Z, Zeng M-Y, Wu Y-W, Li J-W, Zhou Z, Liu Z-J, Li M-H. Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species. International Journal of Molecular Sciences. 2023; 24(19):14437. https://doi.org/10.3390/ijms241914437

Chicago/Turabian Style

Zhao, Zhuang, Meng-Yao Zeng, Yu-Wei Wu, Jin-Wei Li, Zhuang Zhou, Zhong-Jian Liu, and Ming-He Li. 2023. "Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species" International Journal of Molecular Sciences 24, no. 19: 14437. https://doi.org/10.3390/ijms241914437

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