Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis.

BACKGROUND: Calanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae.
RESULTS: The complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius.
CONCLUSION: This study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.

Background

Calanthe is the largest genus in tribe Collabieae (Epidendroideae; Orchidaceae), with more than 220 species [1], distributed across tropical and subtropical Asia, Australia, Madagascar, Africa, Central and South America, and the Caribbean [2-4]. Calanthe species are evergreen or deciduous plants, terrestrial (rarely epipetric or epiphytic) with thick roots, small oval pseudobulbs, highly ridged leaves, and upright, occasionally arching flowering stems [5]. Their flowers arise from the basal leaf with showy, white, yellow, or pink colors with a resupinate opening, ranging from small, medium and large [6]. They often turn dark blue after damage or during senescence [7]. Calanthe is the first orchid species to be artificially used by humans for hybridization purposes [8]. Its species have numerous ornamental and medicinal values and were popular ornamental house plants during the Victorian era [9]. In traditional systems of medicine such as Chinese Traditional Medicine (TCM) and Indian Ayurveda, Calanthe has diverse uses, including detoxification and body cooling, resolving hard lumps, promoting blood circulation, treatment of arthritis, rheumatism, ulcers, common colds, and traumatic injuries. In addition, some species are used as tonics and as aphrodisiacs [10, 11].

Calanthe has undergone a series of intrageneric taxonomic revisions for many centuries since its establishment in 1821 [12]. The genus was first subdivided into two subgenera and various sections by Schlechter in 1914, and most authors have observed this subgeneric classification in the subsequent years in their studies [13]. Subgenus Preptanthe (Rchb.f.) Schltr. is characterized by swollen pseudobulbs and annual leaves, whereas subgenus Calanthe lacks prominent pseudobulbs and has evergreen leaves. The Calanthe group, a well-defined group of orchids in tribe Collabieae of subfamily Epidendroideae, was identified to include the genera Calanthe R. Br., Cephalantheropsis Guillaumin, and Phaius Lour. [14]. The three genera have been shown to have a close relationship hence leading to delimitation challenges, especially in the genera Calanthe and Phaius. Generally, species in this group are characterized by plicate leaves, simple, widely spreading sepals and petals, fused lip base and column, and eight waxy pollinia [6]. Morphologically, Cephalantheropsis is characterized by a spurless labellum, free from the column, and pollinia growing directly on the globose viscidium, while the Phaius labellum has a spur, grows at the column base but lacks adnation with column wings with pollinia attached by short caudicles. On the other hand, Calanthe is characterized by its labellum adnate to column wings forming a tube and spurred base having pollinia bound by conspicuous or inconspicuous caudicles, adherent to a sticky viscidium [15]. However, adnation of the lip to the column has been shown to have evolved several times independently, and some species, such as Phaius delavayi (Finet) P.J.Cribb & Perner, have an intermediate column type between these two states hence taxonomic incongruences [16].

In terms of molecular studies, the family Orchidaceae generally has been subjected to two classification systems (i.e., Dressler 1993 and Chase et al. (1994)) [17-21] that try to infer its phylogeny and evolution from genus to subfamily levels. Within the Subfamily Epidendroideae, three genera; Calanthe, Cephalantheropsis and Phaius, form an independent alliance known as the Calanthe alliance, which can be easily distinguished from other taxa within the subfamily [1, 4, 15]. However, the phylogenetic relationships and affinities within the Calanthe alliance remain unresolved. Previous molecular studies conducted on Epidendroideae treated two lineages of the traditional Calanthe, namely: Preptanthe Rchb. f. and Styloglossum Breda, as distinct genera [3, 5]. Additionally, other molecular studies on the Calanthe group reported that Calanthe is a polyphyletic genus that clusters with its relatives Cephalantheropsis and Phaius, forming an independent alliance within Epidendroideae (Orchidaceae) named the Calanthe alliance [3, 15, 16]. This alliance can be differentiated from other taxonomic groups within the family based on plicate leaves, similar sepals and petals, basal and lateral inflorescence, resupinate flowers with free sepals and petals, spurred lips, and eight waxy pollinia forming two groups [15]. However, determining the phylogenetic and taxonomic relationships within this alliance is difficult. This is due to the uncertainties in the precise delimitation characters and the incongruent molecular phylogeny within the Calanthe alliance, that has led to poor taxonomic classification; thus, the phylogenetic and taxonomic relationships within the Calanthe alliance remain inconclusive. To better understand their phylogenetic relationships, it is necessary for us to identify discrepancies in the genetic information of the major clade the Calanthe alliance.

Genus Phaius contains ca. 40 known species, out of which 9 occur in China [6, 21]. The species in this genus are also characterized by a labellum growing at the base of the column having a spur but lacks adnation to column wings, and a pollinium usually attached by short caudicles [15]. Based on morphological data, this genus is separated into two types: bract caducous or persistent [6]. Calanthe, on the other hand, is characterized by a labellum which is adnate to column wings forming a tube and spurred base, and pollinium having conspicuous or inconspicuous caudicles, usually adhering to a sticky viscidium [6, 14, 21]. Previously, the genera Calanthe and Phaius were distinguished by the lip being adnate to or almost free from the column, respectively, but all intermediate conditions exist [22]. However, there are limited genetic studies on these species, and the aforementioned characteristics are ambiguous, thus not sufficient to distinguish among the genera or infrageneric taxa of the Calanthe alliance. Therefore, there is a need for more in-depth studies to resolve these relationships.

Systematics and phylogeny, since its establishment, has promoted classification and interpretation of the evolutionary relationships among angiosperms via genomic analysis [23]. Chloroplasts are essential in photosynthesis and form part of the primary genetic system together with the nucleus and the mitochondria [24]. Plastome (Chloroplast genome) sizes range from 120 to 170 kb in many angiosperms [25]. The plastome is relatively conserved in terms of the size of the gene, gene content, arrangement of the genes, and genome structure [26]. Compared to the nuclear genome, the chloroplast genome undergoes very few nucleotide substitutions and gene rearrangements; hence has been a perfect model to study genetic change and phylogeny in complex terrestrial plants [27].

In the current study, we sequenced, assembled and annotated the complete chloroplast genome of 8 species from the two genera in the Calanthe alliance, namely: Calanthe and Phaius. The aim of this study was to; 1.) Understand the genetic structure and variation within the plastomes; 2.) Identify and describe the characteristics of the cp genome structure, sequence divergence, mutational hotspot regions, and repeat regions across the plastomes and, 3.) Evaluate the phylogenetic relationships between the genera Calanthe and Phaius, which may be useful for further species evolution studies.

Results

Chloroplast genome organization of the Calanthe group species

The complete chloroplast genomes of 8 species of the Calanthe group display a common quadripartite structure consisting of two Inverted Repeat (IR) regions (IRa and IRb), a Large Single Copy (LSC) region, and a Small Single Copy (SSC) region. Their sizes range as follows: IRs (25,222bp-26,430bp), LSC (83,364bp-87,450bp), and an SSC (16,297bp-18,586bp) (Fig. 1; Table 1).

Fig. 1

Gene map of the complete chloroplast genomes of 8 species of the Calanthe group. Annotated genes are colored according to functional categories whereby the genes outside the circle were transcribed clockwise, while the genes placed inside the circle were transcribed counterclockwise. The dark grey color in the inner circle represents GC content, whereas the light grey color corresponds to AT content

Table 1

Basic features of the chloroplast genome of the 8 Calanthe group species

Species	Calanthe alpina	Calanthe brevicornu	Calanthe ecarinata	Calanthe nipponica	Calanthe taibaishanensis	Calanthe tricarinata	Phaius delavayi	Phaius flavus
Accession no.	OL322023	OL348396	OL348397	OL348398	OL351366	OL351367	OL351368	OL351369
Total Length (bp)	156591	158384	158329	158714	157959	158343	150105	158556
LSC Size (bp)	85489	87155	87293	87450	87129	87285	83364	87216
LSC GC%	34.3	34.3	34.3	34.2	34.2	34.3	34.5	34.6
LSC Length (%)	54.6	55.0	55.1	55.1	55.2	55.1	55.5	55.0
SSC Size (bp)	18436	18531	18500	18404	18424	18522	16297	18586
SSC GC%	29.5	29.6	29.7	29.7	29.6	29.7	29.4	29.8
SSC Length (%)	13.1	11.7	11.7	11.6	11.7	12.0	11.0	11.7
IR Size (bp)	26333	26349	26268	26430	26203	26268	25222	26377
IR GC%	43.1	43.1	43.1	43.0	43.1	43.1	43.3	43.0
IR Length (%)	16.2	16.6	16.6	16.7	16.6	16.4	16.8	16.6
PCGs region size (bp)	78678	79083	79083	79275	79251	79083	73473	79353
tRNA size (bp)	2870	2870	2870	2870	2870	2870	2870	2812
rRNA size (bp)	9042	9042	9042	9042	9042	9042	9042	9042
GC content (%)	36.7	36.7	36.7	36.6	36.6	36.7	36.9	36.8
No. of PCGs	88	88	88	88	88	88	85	88
No. of tRNA	38	38	38	38	38	38	38	37
No. of rRNA	8(4)	8(4)	8(4)	8(4)	8(4)	8(4)	8(4)	8(4)
No. of genes	134	134	134	134	134	134	131	133

The GC content was varied within the LSC, SSC, and IR regions, ranging between 34.2-34.6%, 29.4-29.8%, and 43.0-43.1%, respectively, in the regions (Table 1).

Most of the genomes encoded 134 differential genes, containing 88 CDS and 38 tRNA. However, only 131 and 133 genes, 85 and 88 CDs, and 38 and 37 tRNA genes were recorded in P. delavayi and P. flavus, respectively. All of these species encoded eight rRNA genes. The 8 Calanthe group plastomes had identical numbers, order, and names except for the three genes lost in P. delavayi, namely, ndhC, ndhF, and ndhK. In addition, the Calanthe group plastome contained 6 tRNA genes (trnA-UGC, trnI-GAU, trnG-UCC, trnK-UUU, trnL-UAA and trnV-UAC) and nine protein-coding genes (rpl2, rpl16, rps16, rpoC1, ndhA, ndhB, atpF, petB and petD) having one intron and three genes (ycf3, clpP, and rps12) containing two introns. A total of 19 genes were duplicated in the IR regions, including three types of genes, namely, seven coding genes (rps12, rps19, rps7, rpl2, rpl23, ndhB, ycf2), eight tRNA (trnH-GUG, trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-ACG, trnN-GUU) genes and four rRNA (rrn16, rrn23, rrn4.5, rrn5) genes (Table 2). The rps12 gene was trans-spliced, overlapping two regions in the cp genome whereby the 5′-end exon was found in the LSC region and the intron, 3′-end exon located in the IR region. Moreover, three pairs of genes, trnK-UUU/matK, atpE/atpB, and psbD/psbC had overlapping sequences.

Table 2

Group of genes encoded in the complete cp genome of the 8 Calanthe group species

Category for Genes	Group of Genes	Name of Genes
Self-replication	transfer RNAs	trnK-UUUa, trnQ-UUG, trnS-GCU, trnG-GCC, trnR-UCU, trnC-GCA, trnD-GUC, trnY-GUA, trnE-UUC, trnT-GGU, trnS-UGA, trnG-UCCa, trnfM-CAU, trnS-GGA, trnT-UGU, trnL-UAAa, trnF-GAA, trnV-UACa, trnM-CAU, trnW-CCA, trnP-UGG, trnH-GUG*, trnI-CAU*, trnL-CAA*, trnV-GAC*, trnI-GAUa*, trnA-UGCa*, trnR-ACG*, trnN-GUU*, trnL-UAG
	ribosomal RNAs	rrn16*, rrn23*, rrn4.5*, rrn5*
	RNA polymerase	rpoA, rpoB, rpoC1a, rpoC2
	Small subunit of ribosomal proteins (SSU)	rps11, rps12a*, rps14, rps15, rps16a, rps18, rps19*, rps2, rps3, rps4, rps7*, rps8
	Large subunit of ribosomal proteins (LSU)	rpl14, rpl16a, rpl2a*, rpl20, rpl22, rpl23*, rpl32, rpl33, rpl36
Genes for photosynthesis	Subunits of NADH-dehydrogenase	ndhAa, ndhBa*, ndhCb, ndhD, ndhE, ndhFb, ndhH, ndhI, ndhJ, ndhKb
	Subunits of photosystem I	psaA, psaB, psaC, psaI, psaJ
	Subunits of photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ,
	Subunits of cytochrome b/f complex	petA, petBa, petDa, petG, petL, petN
	Subunits of ATP synthase	atpA, atpB, atpE, atpFa, atpH, atpI
	Large subunit of rubisco	rbcL
Other genes	Translational initiation factor	infA
	Protease	clpPa
	Maturase	matK
	Subunit of Acetyl-CoA-carboxylase	accD
	Envelope membrane protein	cemA
	C-type cytochrome synthesis gene	ccsA
Genes of unknown function	hypothetical chloroplast reading frames (ycf)	ycf1, ycf *, ycf3a, ycf4, ycf15

Note:

aGenes containing introns

bGenes lost in P. delavayi

Duplicated genes

Contraction and expansion of IR regions

The chloroplast genome structure and the junction positions between IR regions among the eight species exhibited several structural variations in the LSC/IRb, IRb/SSC, SSC/IRa, and IRa/LSC borders (Fig. 2). Three different occurrences were observed in the LSC/IRb border. First, in Calanthe ecarinata and C. tricarinata, the rpl22 gene was found in the LSC region 22bp away from the IRb region. Secondly, in 5 species, namely: C. brevicornu, C. alpina, P. flavus, P. delavayi, and C. nipponica, the rpl22 gene overlapped in the LSC/IRb region by 52-60 bp in the IRb region. The third occurrence was observed in C. taibaishanensis whereby the rps19 gene was 24 bp away from the LSC/IRb instead of rpl22. The IRb/SSC junction regions were relatively conserved in 7 species whereby the ndhF gene crossed over to the IRb region by 51-70 bp except in P. delavayi due to its ndhF gene loss. In this regard, the nearest gene trnN in IRb, was 367 bp away from the SSC region in P. delavayi. Both the SSC/IRa and IRa/LSC are well conserved among the 8 Calanthe group genomes whereby the ycf1 gene crossed over the SSC/IRa boundary having 42-1035 bp into the IRa section. Furthermore, in the IRa/LSC junction of 7 species, the psbA gene is found in the LSC region, 106-154 bp away from the IRa. The IRa/LSC junction of C. taibaishanensis is distinct in that the rps19 gene occurs in the IRa, 25 bp away from the LSC.

Fig. 2

Comparison for border positions of LSC, SSC, and IR regions among the 8 Calanthe group species. The boxes denote genes, and the gap between the genes and the boundaries is indicated by the number of bases unless the gene coincides with the boundary. Extensions of genes are shown above the boxes

Comparative genomic analysis

The mVISTA-based identity plot revealed the DNA sequence and gene synteny conservation across the eight plastomes and showed the regions with increased genetic variations (Fig. 3). The number, order, and orientation of genes were relatively conserved. Distinct sequence variations were recorded in several gene regions including psbA-trnK-UUU, rps16-trnQ-UUG, matK-trnK-UUU-rps16, trnS-GCU-trnG-GCC, rpoB-trnC-GCA, petN-psbM, psbM-trnD-GUC, trnE-UUC-trnT-GGU, trnT-GGU-psbD, ndhK-trnM-CAU, atpB-rbcL, rbcL-accD, accD-psaI, petA-psbJ, psbE-petL, trnV-GAC-rps12, ccsA-ndhD, trnL-UAA, trnL-GAU, ndhF, ndhI, rps15, trnP-UGG, rpl33, clpP, psbT, rpl16, rpl14, rps8 and rpl32. Higher genetic variability was observed in the LSC and SSC regions than in the IR regions and in non-coding regions than in the conserved protein-coding regions. The rRNA genes were highly conserved with almost no variation in terms of their numbers among the plastomes. Moreover, greater variation was recorded in the IGS regions than those in the gene regions.

Fig. 3

Global alignment of chloroplast genomes of the 8 Calanthe group species by mVISTA using C. nipponica as the reference. The top line shows the orientation of genes. A cut-off of 70% identity was used for the plots, and the Y-scale represents the percentage identity ranging from 50 to 100%

The sliding window analysis identified three highly variable regions in the 8 Calanthe group plastomes with a nucleotide diversity (Pi) cut-off point set at Pi ≥0.03 (Fig. 4). The highly variable regions were mainly found in the LSC and SSC region compared to IR regions and in non-coding regions than coding regions. The highly variable regions were identified as follows; trnS-GCU-trnG-GCC, rpoB-trnC-GCA, trnE-UCC-trnT-GGU, rpl32-trnL-UAG, ccsA-ndhD and psbL, clpP and rpl32 genes of the chloroplast genomes. These findings were consistent with the mVISTA results, whereby the variation in the IR regions of the chloroplast genomes was relatively lower than that in the LSC and SSC sections.

Fig. 4

Comparative analysis of the nucleotide diversity values among the 8 Calanthe group chloroplast genomes. The X-axis represents the position of the midpoint of a window (kb), while the Y-axis indicates the nucleotide diversity of each window

Sequence repeats

A total of 507 SSRs were recorded in this study, and the chloroplast genomes of the eight species contained nearly similar numbers of SSRs (57-76) (Fig. 5). Calanthe alpina had the highest number of simple repeats (76), while Phaius delavayi had the least SSRs (57). Additionally, a base preference was recorded in the base composition of the repeating motifs from mononucleotide SSRs to trinucleotide SSRs, mainly A-T rich repeating motifs. Mononucleotide repeats were the most abundant SSRs (28-45), while hexanucleotide repeats were the least (1-2) in the 8 cp genomes (Table S4). A/T repeats were the most abundant mononucleotide repeats (287), followed by dinucleotide repeat sequences (92) which predominantly consisted of AT/AT repeats and all trinucleotide repeats were AAT/ATT. The least abundant repeats were AAG/CTT, AAATAT/ATATTT, AAGTAT/ACTTAT, ACATAT/ATATGT, and AGATAT/ATATCT (Table S4). The LSC of the eight complete genomes had the highest number of SSRs (385). Mononucleotide repeats were the most abundant ranging from 18-33 (LSC), 8-10 (SSC), and (1-2) IR. Hexanucleotides were the least SSRs in all the regions, with none occurring in the IRs of all the species (Figs. 6, 7, 8, and Table S4).

Fig. 5

The total number of SSRs recorded in the cp genomes of 8 Calanthe group species

Fig. 6

The total number of SSRs identified in the LSC regions of 8 Calanthe group species

Fig. 7

The total number of SSRs identified in the SSC regions of 8 Calanthe group species

Fig. 8

The total number of SSRs identified in the IRs regions of 8 Calanthe group species

Tandem repeats were detected and are classified as forward (F), palindrome (P), reverse (R), or complement (C), with each repeat having a length of ≥30 bp sequence similarity of ≥90%. A total of 28-40 repeat sequences were identified, and the highest number of repeats were recorded in P. delavayi (Fig. 9). Palindromic repeats were the most abundant in all the 8 Calanthe group plastomes (17-25), whereas complement repeats were the least abundant (1-5). No complement repeats were found in the chloroplast genomes of C. alpina and P. flavus. The length of the repeat sequences detected predominantly varied between 31 to 50 bp. Additionally, there were no complement repeat sequences in all the eight cp genomes having 51–70 bp in length (Fig. 10 and Table S5). Overall, the SSRs and tandem repeats in the 8 Calanthe group cp genomes showed no significant differences (Kruskal-Wallis, P < 0.05; Table S6). The numbers, types and sizes of SSRs and tandem repeats, however, varied greatly across different structural and functional regions of the cp genomes whereby these repeats were abundant in non-coding regions than in the coding regions (Table S3).

Fig. 9

The total number of tandem repeats recorded in the cp genomes of 8 Calanthe group species

Fig. 10

Different types of tandem repeats identified in the cp genomes of 8 Calanthe group species. A The total number of complement repeats, B the total number of forward repeats, C the total number of palindromic repeats, and D the total number of reverse repeats identified from the cp genomes of 8 Calanthe group species

Codon Usage

The RSCU of the chloroplast genomes of the 8 Calanthe group species was calculated using all protein-coding genes, and a total of 50,035-52,904 codons were recorded. The RSCU values for each species displayed an identical codon preference in the 64 codons of the protein-coding genes. In this regard, 30, 31, 32, and 33 codons from Calanthe taibaishanensis; C. alpina, C. brevicornu, Phaius delavayi, Phaius flavus, and Calanthe ecarinata; C. tricarinata; and C. nipponica respectively exhibited greater preference (RSCU > 1). Two of them, tryptophan (Trp) and methionine (Met), displayed no preferences (RSCU = 1) in all the species. The rest of the codons were least preferred (RSCU < 1). There were no rare codons (RSCU < 0.1) recorded in the CDS genes of the 8 cp genomes of the Calanthe group (Fig. 11).

Fig. 11

The codon usage distribution in all the protein-coding genes of the complete chloroplast genome of the 8 Calanthe group species

Leucine (Leu), encoded by UUA, UUG, CUU, CUC, CUA, and CUG was the most abundant amino acid, with a proportion of 9.70-10.56 %, which consist 4,993-5,374 of the total number of codons. Serine (Ser), encoded by UCU, UCC, UCA, UCG, AGU, and AGC was the second most plentiful amino with a proportion of 8.93-9.81 % (4,661-5,187codons), whereas tryptophan (Trp), encoded by UGG was the least abundant amino acid encoded, with a proportion of 1.22-1.47 % (641-759 codons) (Table S7). Statistical analysis of the RSCU values in the 8 Calanthe group cp genomes did not vary significantly (Kruska-Wallis, P < 0.05; Table S8).

Phylogenetic analysis

The application of high-throughput sequencing technology has enhanced the availability of whole plastid genomes, leading to the resolution of closely related taxa using plastome sequences [24]. The phylogenetic positions of the eight newly sequenced Calanthe and Phaius species were inferred using a matrix of 64,593 characters (nucleotides). These characters represent the 73 protein-coding genes shared among the eight species in the Calanthe group, combined with 14 species of the Calanthe alliance, for which their complete chloroplast genome sequences had been officially published in the NCBI database. The ML and BI trees exhibited similar phylogenetic topologies with high bootstrap values and posterior probabilities (Fig. 12; Figure S1). Phaius species (excluding P. delavayi) form two clades in the phylogenetic tree (Fig. 12; Figure S1). The first clade includes P. tankervilleae, and P. hainanensis [BP(ML) = 100%, PP = 1.00]. The second clade consists of only P. flavus [BP(ML) =75.6/57%, PP =0.9851], closely related to Cephalantheropsis, and Styloglossum. The third clade was composed of two sister groups: Cephalantheropsis (C. obcordata) and Styloglossum (C. lyroglossa) [BP(ML) = 100%, PP = 1.00]. The fourth clade consisted of two species, P. delavayi/C. delavayi [BP(ML) = 100%, PP = 1.00], while the last clade was made of the rest of the species of section Calanthe. All the species of sect. Calanthe clustered together in a super clade [BP(ML) = 100%, PP = 1.00], consisting of three lineages and includes 14 Calanthe group species. The first lineage includes only C. alpina [BP(ML) = 98.2/95%, PP = 1.00], and this taxon is sister to a clade containing the remaining species of this section. The rest of the species formed the other two lineages of this section which include (C. triplicata, C. sylvatica, C. davidii) and (C. taibaishanensis, C. nipponica, C. arcuata) [BP(ML) = 98.9/96%, PP = 1.00] as well as (C. grifithii, C. tricarinata, C. ecarinata, C. brevicornu) and (C. henryi, C. bicolor and C. aristulifera) [BP(ML) = 100%, PP = 1.00].

Fig. 12

Maximum likelihood tree of the Calanthe group reconstructed based on 73 protein-coding genes. The bootstrap proportion values are indicated on the respective nodes. The different sections of the Calanthe group are also indicated. The species names colored blue represent our sequenced species plastomes and the species in black represent the species plastome sequences downloaded from the NCBI

Discussion

Comparison of the chloroplast genomes of the 8 Calanthe group species

Complete chloroplast sequencing and genomic analyses have revealed that orchid plastomes are highly conserved in terms of size, structure, gene order and content [28-31]. These findings are congruent with results from our study on the 8 plastomes of the Calanthe group which revealed that the cp genome of the 8 Calanthe group species is a quadripartite structure that varied in size among the species ranging between 150,105 bp (P. delavayi) and 158,714 bp (C. nipponica). The plastome is divided into four regions consisting of an LSC (83,364bp-87,450bp), IRs (25,222bp-26,430bp), and an SSC (16,297-18,586bp). The inferred structure and contents are consistent with previous research on orchids [32, 33]. The chloroplast genome in angiosperms has a conserved genome structure [34], including two inverted repeats (IRs) which separate a large single-copy section (LSC) and a small single-copy section (SSC). Furthermore, when compared to nuclear and certain plant mitochondrial genomes, chloroplast genomes are smaller and less prone to recombination, providing unique data for studying genome size variation and evolutionary status [35, 36]. These characteristics are useful for comparative studies because they allow researchers to investigate genome divergences across a wide range of evolutionary time, from early land plants [37] to recently domesticated plants, and to detect selection signals of genome size evolution [38].

The genome sizes of the 8 Calanthe group species varied in size among the species between 150,105 bp (P. delavayi) and 158,714 bp (C. nipponica). Previous studies on seed plants have proposed three important factors that cause variation in chloroplast genome size: (1) intergenic region variations, which mainly affects variation in chloroplast genome size within a genus [39, 40]; (2) variation of an IR region [41, 42]; and (3) gene loss, which is an important reason for the shrinking of chloroplast genome size in some plants [41, 42]. The length corresponds to the size range of the cp genomes of most angiosperms [43]. However, the variation in size among cp genomes in orchids been linked to the contraction and expansion of both the inverted repeat regions [4, 28, 44].

Angiosperm plastomes have comparatively little variation in gene content, despite their differences in size range [45], similar to findings from our study which displayed sequence similarity in gene order and arrangement across the 8 Calanthe group plastomes. The plastomes’ characteristics and sequence variabilities have been linked species phylogenetic relationships and evolution; thus, closely related species are more likely to have similar plastome sizes and characteristics [46]. A previous study on the evolution of flowering plants plastome architecture revealed that the cumulative influence of transposable elements proliferation greatly dwarfs the impacts of tandem or dispersed gene duplication in increasing genomic DNA content, and the process of long-term genomic fractionation, which is associated with the loss of most gene duplications after whole genome duplication [47]. Transposable elements have been implicated as important factors in gene regulation and adaptation, particularly because gene content is fairly consistent across plants and transposable elements accumulate and degrade rapidly [48-50]. Although this pattern is now known, the underlying causes of constancy of genic content in related orchid genera despite the rapid diversification rate in the family Orchidaceae are far less well understood.

Additionally, the GC contents of the LSC and SSC regions in the 8 Calanthe group species were lower compared to that of the IR regions. This occurrence was possibly due to the four rRNA genes, rrn16, rrn23, rrn4.5, and rrn5 sequences in the IR regions [33].

A few differences were recorded in the protein-coding genes of the complete cp genome of the 8 Calanthe group species, despite land plants being generally considered highly conserved [51]. We revealed that protein-coding genes in the ndh family differed between Calanthe group species. The genes ndhC, ndhF, and ndhK were lost in P. delavayi but they were retained in the other species. The loss of these three NADH dehydrogenase subunits is common in orchids and was first reported in this species by Chen in 2020 [4]. In higher plants, the cp genomes contain 11 ndh genes (ndhA-ndhK) that encode nicotinamide-adenine dinucleotide (NADH) dehydrogenase subunits that associate with nuclear-encoded subunits to form the NADH dehydrogenase-like (NDH) complex, which is involved in cyclic electron flow around photosystem I (PSI) and chlororespiration [52, 53]. Although the chloroplast NDH complex mediates cyclic electron transport in PSI, no negative effects in ndh-deficient mutants or transgenics have been observed under suitable growing conditions [29], suggesting that chloroplast ndh genes may be unnecessary in autotrophic plants. Evidently, loss or pseudogenization of plastid ndh genes has been observed in a variety of photoautotrophic seed plant lineages [54, 55] including Cymbidium, Dendrobium, Phalaenopsis, and Ophrys [29, 56–58]. These studies also showed that different orchid species exhibited a variable loss or retention of the genes; for instance, Cymbidium encodes the ndhE, ndhJ,and ndhC genes [59] while Oncidium only encodes the ndhB gene [31]. The loss of the ndh genes has been linked to evolutionary processes whereby several studies inferred that orchids' ancestral protein-coding ndh genes might have been transferred to the nucleus [28, 60]. Fungal symbionts have also been attributed to the lack of functional ndh genes; thus, homologous genes from these resources have been presumed to perform the functions of the lost chloroplast-encoded ndh genes in some orchids [32, 60]. Nevertheless, this hypothesis is yet to be tested, and the mechanisms underlying the variable loss or retention of ndh genes in orchid species are worthy of further research.

Comparative analysis

DNA barcode technology has been widely used in identifying species, resource management, and phylogenetic and evolutionary studies [61, 62]. The comparative analysis of the 8 Calanthe group chloroplast genomes using mVISTA revealed the DNA sequence similarities among related species. No definitive rearrangements or gene inversions were recorded, indicating that the Calanthe group plastome was highly conserved [28]. The size of the genome and organization of the intergenic spacers correspond to previously observed variations in the size of the Calanthe chloroplast genomes [4].

In line with findings from other studies [63] and those from mVISTA, the LSC and SSC regions were more variable than the IR regions. The mVISTA results revealed the following highly variable regions across the 8 plastomes: psbA-trnK-UUU, rps16-trnQ-UUG, matK-trnK-UUU-rps16, trnS-GCU-trnG-GCC, rpoB-trnC-GCA, petN-psbM, psbM-trnD-GUC, trnE-UUC-trnT-GGU, trnT-GGU-psbD, ndhK-trnM-CAU, atpB-rbcL, rbcL-accD, accD-psaI, petA-psbJ, psbE-petL, trnV-GAC-rps12, ccsA-ndhD, trnL-UAA, trnL-GAU, ndhF, ndhI, rps15, trnP-UGG, rpl33, clpP, psbT, rpl16, rpl14, rps8 and rpl32. Interestingly, these highly variable regions were mostly similar to the mutational hotspots identified in other species of the Calanthe alliance [4], suggesting that these variable loci can be used as important references for future studies on the evolution and diversity in the Calanthe alliance. The nucleotide diversity was higher in the LSC and SSC compared to SSC regions and identified the following hypervariable regions across the Calanthe group plastome: trnS-GCUtrnG-GCC, rpoBtrnC-GCA, trnE-UCCtrnT-GGU, rpl32trnL-UAG, ccsA-ndhD and protein-coding genes psbL, clpP and rpl32. The markedly high divergence observed in these genes and intergenic regions is similar to that observed in other angiosperms [4, 64, 65] and may be attributed to rapid genome evolution due to higher mutation rates compared to other regions [66].

The IR regions are relatively conserved compared to the SSC and LSC regions in the Calanthe group plastomes. Significant variation was only observed in the LSC/IRb junction, which displayed three occurrences in the eight species. At the same time, the remaining three (IRb/SSC, SSC/IRa, and IRa/LSC) are conservative and stable. Contraction in the IR was detected due to the loss of the ndhF gene in P. delavayi. Previous studies have highlighted that the loss of ndh genes significantly contributes to the instability of the IR/SSC borders in orchids [58, 67]. The variation in size and evolutionary events in different plants may also be linked to the expansion and contraction of the junctions in the different regions of the chloroplast plastomes [23, 68, 69]. The location of the boundary, particularly the expansion and contraction, has been successfully used to infer phylogenetic relationships and provide insights on the evolution of the lineages in Apiaceae [70], ferns [71], Poaceae [72], Pinaceae [28], and many monocots [73]. Nevertheless, even though overall genomic structures and gene orders are highly conserved, orchid plastomes exhibited clear differences at the IR/SSC boundaries, which cannot readily be used in a phylogenetic study. Furthermore, the ndh genes in SSC regions have been lost independently across orchid genera [58, 67], corroborating the findings by Kim et al. (2015) [30] which proposed that the instability of orchid IR/SSC junctions was highly related to the loss of the ndhF gene. Even so, the mechanism underlying the variations in the sequences flanking the IR/SSC junctions of orchid plastomes remains unknown. Therefore, our findings from the present study on the IR boundary does not provide the necessary information to elucidate the evolutionary relationships within the Calanthe group, thus, additional sampling of Calanthe spp. and related genera will allow for clear and specific tests [74].

Molecular Markers

Simple sequence repeats have distinct features that make them efficient genetic markers such as abundance in number, highly repetitive, a simple structure, maternal inheritance of chloroplast genomes, and relatively conserved [75]. SSRs and repeat sequences have been extensively used in identifying species, phylogenetic analysis, population evolution studies, and system geography of various species [76]. In this regard, the variation in the number and distribution of SSRs and tandem repeats in all the 8 Calanthe group genomes and different regions of the whole plastomes were detected. Repeats were widespread in the non-coding regions compared to the coding regions, consistent with previous reports on other species [30, 77]. The chloroplast genome rearrangement and nucleotide substitution can be attributed to the differential distribution of these repeats [78].

Additionally, the SSRs were mainly distributed in LSC, compared to the SSC and IR regions illustrating that the distribution of SSRs was dependent on their locations in the chloroplast genome [79]. These repeats can therefore be used to develop genetic markers for phylogenetic studies. The identified SSR and tandem repeats can also be used to investigate the genetic structure, diversity, phylogeny, and differentiation of species in the Calanthe alliance and other orchid species.

Relative Synonymous Codon Usage

The RSCU value is the ratio of the usage frequency of a specific codon to the expected frequency and can eradicate the influence of amino acid composition on the codon usage [80]. Additionally, RSCU promotes the detection of synonymous codons [81]. Most codons with RSCU values greater than 1 ended with A or U, whereas those ending with a C or G had RSCU values of less than 1. These findings are consistent with previous studies [82, 83].

Compositional constraints and translational selection are presumed as the main factors that result in the codon usage variation among protein-coding genes in and across the plastomes [84]. Moreover, compositional bias has been shown to determine the codon usage variation amidst genes in most AT or GC-rich organisms [85]. Analysis of RSCU may provide a basis for studying specific mechanisms causing biased preference of synonymous codons in different species [86]. In addition, it plays a crucial role in both practical and theoretical studies on the basics of molecular biology [87].

Phylogenetic and taxonomic implications

Phylogenetic analyses using chloroplast genome data have been used successfully to infer the evolutionary relationships among angiosperms [30, 81, 83]. Phylogenetic studies of Orchidaceae using complete plastomes are in a rather early stage due to paucity of plastome sequences. However, the relationships among major orchid lineages determined using whole plastomes (species tree) agree well to the large-scale phylogenetic studies of Orchidaceae using two or three genes (gene tree). Therefore, by sequencing more Orchidaceae complete plastomes can help resolve the pressing phylogenetic problem. Molecular datasets comprising of protein-coding genes, non-coding regions, and hypervariable regions have been used to infer major phylogenetic relationships between major orchids clades [88]. However, there are numerous uncertainties about the phylogenetic placement of several subtribes and genera. This knowledge gap is caused by a lack of both taxonomic and genomic sampling efforts required to cover all major orchid clades (subtribes/groups of genera) [89]. In this study the relationships among the Calanthe alliance genera included in our phylogenetic assessment are generally consistent with recent studies [6, 15], although there are a few differences.

Previous studies on the Calanthe group based on morphological characteristics (adnation of the lip to the column) recognized Calanthe and Phaius as paraphyletic [21, 90, 91]. In addition, P. delavayi, which was previously included in genus Phaius based on its floral morphology by Pridgeon [14], was later classified as a member of genus Calanthe based on molecular evidence (ITS and cpDNA) by Zhai [15]. These findings are in agreement with results from our study as further discussed in the subsequent section.

In the present study, Phaius species (excluding P. delavayi) form two clades. The first clade includes Phaius: P. tankervilleae and P. hainanensis, while the second divergent clade comprised only one species of Phaius: P. flavus. These results are consistent with those of Zhai [15], who were the first to report the divergence within Phaius, excluding C. delavayi/ P. delavayi based on ITS and cpDNA data. Therefore, we strongly support the proposal by Zhai’s study that Phaius is restricted to the lineage that includes species such as P. tankervilleae and P. hainanensis. The clade consisting of P. tankervilleae and P. hainanensis is characterized by caducous floral bracts and eight pollinia in two groups separated from each other. In contrast, the second clade, which includes species such as P. flavus, has distinct features, including persistent floral bracts, pollinia which occur in two categories attached to a sticky substance by caudicles [21, 92]. Zhai’s study suggested the inclusion of a new genus, Paraphaius, to encompass the lineage consisting of P. flavus. Results from our study on the phylogenetic position of P. flavus [BP(ML) =75.6/57%, PP =0.9851] are consistent with Zhai's in 2014. This species was clustered together with the clade supporting Calanthe lyroglossa of Calanthe sect. Styloglossa and Cephalantheropsis obcordata of Calanthe sect. Cephalantheropsis, supporting Zhai’s proposal of recognizing subsection Paraphaius to encompass P. flavus. However, more sampling is required to help further resolve the phylogeny of this species adequately.

Presently, Phaius delavayi has become a vital species in the taxonomic studies of the Calanthe alliance due to its complex taxonomic history between Calanthe and Phaius [1, 17]. Previous studies have identified Phaius delavayi as a link between Calanthe and Phaius [16]. It is Morphologically identical to Calanthe due to its relatively small individual, basal leaves, elongated column, and inconspicuous pseudobulbs [22]. Nevertheless, it has similar morphological features characterized in Phaius because of its long labellum embracing its column (Fig. 13) [15]. Previously, based on morphological characteristics, Chen in 1999 [21], treated this species as a member of the sect. Calanthe, although in their work, the Flora of China project in 2009 [91], they accepted a taxonomic placement of this species within Phaius as earlier proposed by Perner and Cribb [90]. However, Zhai’s study on the phylogenetic relationships in the Calanthe alliance in China suggested that P. delavayi should be retained within Calanthe rather than within Phaius. In addition, this study proposed the inclusion of a new section, Alpinocalanthe, to accommodate this unique taxon due to its phylogenetic placement and distinct morphological characteristics, namely: small plants, persistent bracts in flowers; labellum adnate to column wings at the basal area, a slender column; a somewhat 3-lobed labellum, circumjacent column and a disk-shaped labellum having three shortly hairy ridges. Based on the ML and BI trees using coding sequences, our results indicate P. delavayi [BP(ML) = 100%, PP = 1.00], is closely related to Calanthe than to Phaius, consistent with findings by Zhai [15]. In this regard, we also support the use of the name Calanthe delavayi instead of Phaius delavayi.

Fig. 13

Morphological characteristics of the Calanthe group species. Photos taken by Guangwan Hu. The picture of P. flavus was taken by Lourens Grobler (http://www.orchidspecies.com/phaiusflavus.html)

Calanthe sect. Calanthe is the largest infrageneric group of the genus Calanthe, including approximately 140 species worldwide, out of which 50 species occur in China [15, 93]. In the current study, an independent super clade encompassing all the 14 Calanthe group species of this section was identified. The results revealed that the primary relationship was consistent with other studies among the Calanthe section Calanthe group [4, 5, 94]. The results obtained from the Maximum Likelihood (ML)/Bayesian Inference (BI) analyses revealed that the genus Calanthe forms a high support clade as a paraphyletic group [BP(ML) = 100%, PP = 1.00].

Our conclusion, however, on the paraphyly of the Calanthe group differs from that of the latest study by Chen et al. (2020) on the plastome structure and adaptive evolution of Calanthe s.l. which revealed the monophyly of Calanthe s.l. species [4]. This rigorous but taxonomically under-sampled study completely distinguished the seven species of the Calanthe group in their phylogenetic inference with high bootstrap support values. The discrepancies noted between this study and our present study is most likely due to large variation in the number of characters and taxa included [95]. Regardless of the fact that our matrix is character-rich and thus less prone to error caused by individual genes [96], we must highlight that our taxon sampling is highly fragmentary, and supplementary plastome sequences from poorly sampled and/or unsampled genera in the Calanthe alliance may result in topological changes.

Based on protein coding genes shared among all the target Calanthe group species, our study on the calanthe group chloroplast genome provides valuable genetic information on the eight newly sequenced species, highlights the power of using plastome data to resolve phylogenetic relationships between closely related species, and will facilitate future phylogenetic studies on orchids.

Conclusions

In conclusion, the complete plastomes can provide relevant information for resolving evolutionary disputes between closely related taxa. In this study, the complete chloroplast genome of 8 Calanthe group species were sequenced and compared. In addition, phylogenetic relationships in the Calanthe group were resolved with high or moderate support values. The highly divergent genes and regions of cp genomes identified in this study can be used as effective DNA barcodes in genetic diversity studies and in phylogenetic analyses. Further chloroplast genome sequencing of orchids is necessary to clarify the diversity of complete plastomes and to facilitate species identification, phylogenic analysis, and elucidate evolutionary relationships within orchid species.

Materials and methods

Sample collection

Collection permits for sample collection were granted by the Sichuan Forestry and Grassland Administration Sichuan province, China and Yunnan Forestry and Grassland Administration, Yunnan province, China. Fresh leaves from 8 Calanthe group species were collected from the Sichuan and Yunnan provinces of China (Table S1). Guang-Wan Hu, Jiaxin Yang and Xiang Dong performed formal identification of the samples after collection whereby the leaf samples of Calanthe tricarinata, Calanthe alpina, Calanthe nipponica, Calanthe taibaishanensis, Calanthe ecarinata, Calanthe brevicornu, Phaius delavayi, and Phaius flavus and stored in seal-bags containing silica gel before DNA extraction. The sample specimen of each species was then deposited at the Herbarium of Wuhan Botanical Garden (HIB) with specific voucher numbers (Table S1).

Chloroplast Genome Sequencing and Assembly

The genomic DNA was extracted from about 100 micrograms of the leaves using a modified cetyltrimethylammonium bromide (CTAB) method [97]. Genome sequencing was performed using the Illumina platform at Novo gene Company (Beijing, China), followed by filtration of low-quality data and adaptors and assembly of the clean data was obtained using GetOrganelle-1.6.2 software [98], using Calanthe triplicata (NC_024544) as the reference genome. Bandage software was then used to check the final results of the assembled genome after manual corrections. The optimal result was selected, after which manual adjustment of these results was also made. Lastly, inverted repeat regions were identified using Geneious Prime 2019.2.1 (https://www.geneious.com).

Genome annotation

The annotation of the assembled genomes was performed using GeSeq online tool with default settings [99], followed by confirmation of tRNAs annotations using the tRNAscan-SE [100]. The Plastid Genome Annotator (PGA), a standalone command-line annotation tool, validated the Calanthe cp genomes [101]. The gene map of the complete cp genomes was drawn using OrganellarGenome DRAW software [102] (Fig. 1). The annotated complete chloroplast genomes were submitted to the GenBank database with accession numbers as follows: Calanthe alpina (OL322023), C. brevicornu (OL348396), C. ecarinata (OL348397), C. nipponica (OL348398), C. taibaishanensis (OL351366), C. tricarinata (OL351367), Phaius delavayi (OL351368), and P. flavus (OL351369).

Genome comparison and sequence divergence

The IRscope [103] was used in the comparison of the border junctions of inverted repeat (IR), small single copy (SSC), and large single copy (LSC) regions. Using Shuffle-LAGAN mode, the mVISTA software [104] was used to compare and visualize the complete chloroplast genomes of the eight species with C. nipponica as the reference. Additionally, all the 8 Calanthe alliance cp genome sequences were aligned using MAFFT v7.409 [105]. Further, we performed a sliding window analysis to evaluate the variability (Pi) over the plastomes using DnaSP v5.10 [106] at 600 base pairs window length and 200 base-pair step size.

Repeat structure and Simple Sequence Repeats (SSRs) analysis

The visualization of forward, palindrome, reverse, and complement repeats in the Calanthe group genome was conducted using REPuter [107], with the minimum repeat size being set at 30 bp, maximum at 50 bp and sequence identity of no less than 90% (hamming distance= 3). Identification of simple sequence repeats (SSRs) was performed using MISA (https://webblast.ipk-gatersleben.de/misa/index.php) [108], with the minimum number of repeats as follows: 10 for mono-, 5 for di-, 4 for tri-, and 3 for tetra-, 3 for penta-, and 3 for hexanucleotide SSRs.

Relative synonymous codon usage

All the protein-coding genes for the combined genomes were extracted using MEGA 7 [109] software which was then used to calculate the relative synonymous codon usage (RSCU) ratio. RSCU values >1 represent frequently used codons than expected, while values <1 signify the opposite. Codons having no preference value are set to 1.00.

Phylogenetic relationship analysis was conducted using 73 PCGs extracted from the complete cp genome sequences of the 8 Calanthe group taxa mentioned above, with one outgroup, Preptanthe rubens (NC_050869) and thirteen previously sequenced members of the Calanthe alliance downloaded from the NCBI database (Table S2). Multiple sequence alignment of the 22 complete cp genome sequences was performed using MAFFT with default parameters. The best fit model was identified using the Model Finder program [110] integrated into Phylosuite. The best-fit models for the phylogenetic analysis were GTR GTR+G, GTR+I+G, and setting (rcluster) for the concatenated alignment as implemented in ModelFinder. Phylogenetic reconstructions were performed using the maximum likelihood (ML) method using the IQ-Tree integrated in Phylosuite [111]: a GUI-based software written in python 3.6.7. The analyses were run with 1000 bootstrap replicates. Phylogenies were then inferred by Bayesian Inference using MrBayes 3.2.6 [112] under the GTR+G+F model (2 parallel runs, 10,000,000 generations and sampled at a frequency of 1000 generations), in which the first 25% of the sampled trees were discarded as burn-in. The remaining trees were used to build a majority rule consensus tree and establish posterior probability values for each branch. Finally, the trees were refined and visualized using FigTree v1.4.4 and later combined using AI software.

Additional file 1.

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