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Article

The Complete Chloroplast Genomes of Gynostemma Reveal the Phylogenetic Relationships of Species within the Genus

by
Jiaxia Gan
1,2,†,
Ying Li
2,†,
Deying Tang
3,
Baolin Guo
2,
Doudou Li
2,
Feng Cao
2,
Chao Sun
2,
Liying Yu
4,* and
Zhuyun Yan
1,*
1
State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
2
Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
3
Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong 666100, China
4
Guangxi Botanical Garden of Medicinal Plant, Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Nanning 530023, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2023, 14(4), 929; https://doi.org/10.3390/genes14040929
Submission received: 24 February 2023 / Revised: 6 April 2023 / Accepted: 16 April 2023 / Published: 17 April 2023
(This article belongs to the Special Issue Advances in Chloroplast Genomics and Proteostasis)
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Abstract

:
Gynostemma is an important medicinal and food plant of the Cucurbitaceae family. The phylogenetic position of the genus Gynostemma in the Cucurbitaceae family has been determined by morphology and phylogenetics, but the evolutionary relationships within the genus Gynostemma remain to be explored. The chloroplast genomes of seven species of the genus Gynostemma were sequenced and annotated, of which the genomes of Gynostemma simplicifolium, Gynostemma guangxiense and Gynostemma laxum were sequenced and annotated for the first time. The chloroplast genomes ranged from 157,419 bp (Gynostemma compressum) to 157,840 bp (G. simplicifolium) in length, including 133 identical genes: 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. Phylogenetic analysis showed that the genus Gynostemma is divided into three primary taxonomic clusters, which differs from the traditional morphological classification of the genus Gynostemma into the subgenus Gynostemma and Trirostellum. The highly variable regions of atpH-atpL, rpl32-trnL, and ccsA-ndhD, the repeat unilts of AAG/CTT and ATC/ATG in simple sequence repeats (SSRs) and the length of overlapping regions between rps19 and inverted repeats(IRb) and between ycf1 and small single-copy (SSC) were found to be consistent with the phylogeny. Observations of fruit morphology of the genus Gynostemma revealed that transitional state species have independent morphological characteristics, such as oblate fruit and inferior ovaries. In conclusion, both molecular and morphological results showed consistency with those of phylogenetic analysis.

1. Introduction

Gynostemma Blume is a small genus in the family Cucurbitaceae. Gynostemma has the ability to synthesize saponins and flavonoids. gypenoside II, IV, VIII and XII found in Gynostemma are homologous to ginsenosides Rb1, Rb2, Rd1 and Rf2, respectively in Panax spp. [1] Therefore, Gynostemma have been widely used in traditional medicine, mainly for the treatment of hyperlipidemia [2], diabetes [3] and inflammation [4]. To date, over 300 saponins have been isolated and identified from Gynostemma species [5], and the content and types of saponins, as well as their pharmacological activities, are different among species according to previous studies [6]. Thus, to make better use of Gynostemma plants, it is essential to fully resolve understand the taxonomic identification of this genus.
Due to hybridization, combined with facultative apomixis and polyploidy, Gynostemma is known for the difficulty in delimiting its species among [7]. Gynostemma, which comprises seventeen species and and two varieties, is native to tropical Asia and East Asia, including China, Japan, Malaysia and New Guinea [8]. China (Qinling Mountains and areas south of the Yangtze River) is the main Gynostemma source area, with 14 species and two varieties, including nine species and two varieties endemic to China [8,9]. The plants of this genus can be divided into two subgenera according to their fruit morphology: subgenus Gynostemma with globose or depressed-globose berries and subgenus Trirostellum with campanulate capsules [10]. Interestingly, many investigations of morphological traits have revealed transitional taxa in the wild [11]. Therefore, it is necessary to comprehensively investigate and explore the taxonomy and evolution of species within the Gynostemma genus at the molecular level.
Gynostemma, known as Jiaogulan in China, was first described as a wild edible plant in 1406 by Zhu Su in the book Materia Medica for Famine Relief. The genus name Gynostemma was first published in 1825 by German-Dutch botanist Carl Ludwig won Blume. Since then, species within Gynostemma have been revised many times, mostly based on morphological, ecological and cell taxonomic studies. For example, G. pubescens was once considered a species of the subgenus Gynostemma, but now, G. pubescens is considered a forma of Gynostemma pentaphyllum, not as a separate species, in the Flora of China (2011) because of the similarities in morphology [8]. Currently, DNA sequencing is a popular method for taxonomic studies, and molecular markers can provide new evidence for inter- and intra-species relationships beyond that provided by morphological traits [12]. Only a few studies have explored the phylogenetic relationships of species within Gynostemma based on genes or sequence fragments. By using the nuclear ribosomal internal transcribed spacer (ITS) [7] and chloroplast genes or fragments, Qin (matK, rbcL, and psbA-trnH) [11] and Abid (ycf3, accD, petD and psbB) [13], provided molecular support for the existence of subgenus units in the Gynostemma genus. Meanwhile, the non-monophyletic origin of G. pentaphyllum in the phylogenetic tree indicated the high genetic diversity of this widespread species. Compared with short DNA fragments, the complete chloroplast genome, with a length of approximately 150 kb, can provide more genetic variation information for species classification [14].
Chloroplasts contain their own genome separate from that in the cell nucleus. The chloroplast genome structure of species in different clades is relatively stable, and the genes in the chloroplast genome are fairly similar among land plants [15]. Moreover, chloroplast genomes are characterized by moderate nucleotide substitution rates compared with those of nuclear genomes. These advantages of chloroplast genomes make them an ideal tool for phylogenetic and taxonomic studies [16]. There have been multiple separate reports involving the complete chloroplast genome of a single Gynostemma species [17,18,19,20]. The chloroplast genomes of eight species from the Gynostemma genus were sequenced in Zhang’s study [21]. These studies outlined the phylogenetic relationships among Gynostemma species and provided valuable data for research on the relationships within Gynostemma species. However, for some species in subgenus Gynostemma, chloroplast data are still missing, and subgeneric phylogenetic relationships are also unclear.
In this study, we sequenced and assembled the complete chloroplast genomes of seven subgenus Gynostemma species, providing a full complement to the data on subgenus Gynostemma species distributed in China. We combined these newly obtained chloroplast genomes with data downloaded from GenBank to perform a comparative analysis of Gynostemma chloroplast genomes based on a total of 21 individuals from 14 species in this genus. This study reconstructed the phylogenetic relationships and verified the phylogenetic positions of species within the Gynostemma genus.

2. Materials and Methods

2.1. Plant Material, DNA Extraction, and Sequencing

Fresh, healthy leaf samples were collected from matured plants of seven species of the genus Gynostemma (Table S1), with vouchers for specimens of G. simplicifolium placed in the Herbarium of Yunnan Branch, Institute of Medicinal Plants, Chinese Academy of Medical Sciences (IMDY), and vouchers for G. burmanicum, G. caulopterum, G. compressum, G. guangxiense, G. laxum, and G. longipes, placed in the Gynostemma Germplasm Nursery of Guangxi Medicinal Plant Garden (GXMG). Chloroplast DNA was extracted using the High Efficiency Plant Gene DNA Kit DP350 (Tiangen Biochemical Technology Co., Beijing, China), and raw reads were obtained on the Illumina NovaSeq6000 platform.

2.2. Chloroplast Genome Assembly and Annotation

Artificial sequences such as sequencing primers and adapters as well as some low-quality regions were removed from the raw data (Table S2), and the quality assessment report of “CleanData” was generated using FastQC v0.11.9 and MultiQC software [22]. “CleanData” was assembled using the GetOrganelle pipeline [23] (https://github.com/Kinggerm/GetOrganelle accessed on 19 January 2022). First, 15 million clean reads were selected from the clean data to filter out possible chloroplast clean reads. Second, the SPAdes splicing program in SOAPdenovo2 [24] was used to assemble the filtered clean reads, the G. pentaphyllum chloroplast genome was used as the reference sequence (GenBank accession No. KX852298), and the relative positions between sequences were obtained using BLAT [25]. Finally, the full-length assembly of the sequences was performed using Bandage [26] software to obtain the full-length circular frame map of the chloroplast, and the LSC, SSC, and IRS region junctions of the full-length frame map were verified using next-generation sequencing. The assembled chloroplast genome sequences were annotated using the GeSeq program [27] and compared to the MPI-MP chloroplast gene library provided by GeSeq Nuclear coding genes (similarity = 65%) and rRNA genes (similarity = 85%) were searched for protein sequences using HMMER [28], and ARAGORN v1.2.38 [29] was used to predict tRNA genes. The annotated results were drawn using OGDRAW v 1.3.1 for the physical maps of the chloroplast genome. The other data downloaded from the NCBI (Table S2) used in this study were reannotated using the same annotation method for the subsequent comparative analysis and phylogenetic analysis in this study.

2.3. Codon Usage Bias and RNA Editing Sites

The codon usage and amino acid frequency in these genes were assessed using the program codon W 1.4.4 [30]. RNA editing sites for the 10 protein-coding sequences of Gynostemma species were predicted by using the online PmtREP program with a cutoff value of 0.8 [31].

2.4. Repeat Analysis

MISA was used to identify SSRs that localizes to the chloroplast genomes of 18 species, defined for microsatellites as a unit size/minimum number of repeats ratio of 1/10, 2/6, 3/4, 4/4, 5/4, or 6/4 [32,33]. REPuter was used to identify forward, palindromic, reverse, and complementary sequences with a minimum repeat size ≥30 bp and sequence identity ≥90% (Hamming distance = 3) [34,35].

2.5. Comparative Analysis, and Identification of Polymorphic Loci

Alignment was visualized in Shuffle-LAGAN mode using mVISTA, using the annotated plasmid of G. burmanicum NC_036141.1 as a reference [36,37]. IRscope was used to analyse the contraction and expansion of the inverse repeat (IR) regions at the chloroplast genome junction [38]. DnaSP v6.12.03 software was used to calculate nucleotide variability (Pi) values and variable sites using matched chloroplast genome sequences with a window length of 600 bp and a step size of 200 bp [39].
To determine the synonymous (ks) and nonsynonymous substitution rates (ka) of 88 protein-coding genes and their ratios (ka/ks) after removing terminators from each protein gene, gene matching was performed in MEGA using MUSCLE, and the resulting data were exported from MEGA X in fasta format [30]. The ka/ks analysis was performed in DnaSP v6.12.03, and the results were interpreted as Ka/Ks > 1 for positive selection, <1 for purifying selection, and Ka/Ks = 1 for neutral selection [39].

2.6. Phylogenetic Analysis

To infer the evolution of the genus Gynostemma, we selected and downloaded chloroplast genome sequences from the NCBI for 46 species and three outgroup species (Table S3), including Begonia guangxiensis (NC_046385.1), Corynocarpus laevigatus (NC_014807.1), and Arabidopsis thaliana (NC_000932.1), and a phylogenetic tree of Cucurbitaceae was constructed based on 86 shared protein-coding genes. We constructed a phylogenetic tree of the chloroplast genome of the genus Gynostemma with Cucumis sativus (NC_007144) as the outgroup based on the complete chloroplast genomes. All protein-coding sequences and the complete chloroplast genome sequence were aligned separately using MAFFT-v 7.490 [40]. Best-fitting models were identified for the 2 datasets using MrModeltest-v3.7 [41]. Maximum likelihood (ML) analysis was performed using the PAUP* procedure [42] with the best-fitting model GTR + G + I and 1000 bootstrap replications. Bayesian inference (BI) was achieved in Mrbayes-v3.2 [43] with the GTR + G + I model. The parameters used are: Markov chain Monte Carlo (MCMC) algorithm run for 1 × 108 generations and extracted once every 1000 generations. The first 25% of samples were discarded as burn-in. Stationarity was considered to be achieved when the average standard deviation of the splitting frequencies remained below 0.001. The phylogenetic trees were visualized by FigTree-v1.4.4. The topological structures of the two phylogenetic trees were consistent, so they were manually combined using AI software.

3. Results

3.1. Characterization of the Chloroplast Genomes of the Gynostemma Genus

To gain some insight into the phylogenetic positions of species within Gynostemma, it is important to obtain chloroplast genome data for as many species as possible in the genus under study. To this end, seven Gynostemma species, namely, G. burmanicum, G. caulopterum, G. compressum, G. guangxiense, G. laxum, G. longipes, and G. simplicifolium, were sampled for the chloroplast genome sequencing. The chloroplast genomes ranged in size from 157,419 bp to 157,840 bp (Table S4). The chloroplast genomes of all Gynostemma species are typically quadripartite in structure with a large single-copy region (LSR: 85,831–86,470 bp), a small single-copy regions (SSR: 18,510–18,636 bp) and two inverted repeat regions (IRA and IRB: 26,114–26,295 bp) (Figure 1). The GC contents of the chloroplast genomes of all seven species were quite similar (36.96–36.98%), of which the GC contents of the IR, LSC and SSC regions were 42.74–42.80%, 34.75–34.87% and 30.64–30.84%, respectively (Table S4). This high GC percentage in the IR regions was caused by the rRNA genes distributed in these regions. A total of 133 genes were identified in each chloroplast genome, including 87 protein-coding genes, eight rRNA genes, 37 tRNA genes and one pseudogene (Table S4). These genes were classified into three groups according to their functions, including photosynthesis, self-replication and others (Table 1). The gene distributions in these seven chloroplasts were the same: the LSC and SSC regions encoded 83 and 12 genes, respectively, and the IR regions contained 19 duplicate genes. There were 22 intron-containing genes, of which 20 genes had one intron and two genes had two introns (Table 1). The basic information and gene contents of 14 previously reported chloroplast genomes of Gynostemma species are presented in Supplementary Table S4. By comparing all sequenced chloroplast genomes generated in this study with 14 other previously reported chloroplast genomes of Gynostemma species (Table S4), we found that they had a highly conserved gene content, gene number, orientation and intron number.

3.2. Analysis of Codon Usage Bias and Prediction of RNA Editing Sites

The relative synonymous codon usage (RSCU) value was calculated to show the codon usage frequency based on protein-coding genes of seven Gynostemma chloroplast genomes. The chloroplast genome protein-coding genes of each Gynostemma species were composed of 26,614–26,723 codons. Except for methionine (Met) and tryptophan (Trp), which were encoded by a single codon, the amino acids were encoded by two to six synonymous codons and displayed a preference for certain codons. Among these amino acids, leucine (Leu, 10.5%) was the most abundant amino acid, whereas cysteine (Cys, 1.2%) was the least universal amino acid in these chloroplast genomes. The RSCU values of all codons are shown in Figure 2 (Table S5). Approximately half of the codons were used more frequently, with RSCU values greater than 1 (32/64), and almost all biased codons ended with A/U (29/32). The most and least commomly used codons were AUU (M), encoding leucine, and UGC (N), encoding cysteine, respectively. According to the codon usage bias analysis, the RSCU values were very similar in all Gynostemma chloroplast genomes, and the frequency of different codons coding for the same amino acid was almost the same in all Gynostemma species.
RNA editing is an important post-transcriptional modification process and has been observed in many published chloroplast genomes. To reveal the composition and characteristic of RNA editing of the Gynostemma chloroplast genome, RNA editing sites in seven newly sequenced chloroplast genomes were predicted. For each chloroplast genome, approximately 15–17 RNA editing sites distributed in 10 protein-coding genes were predicted (Table S6). The RNA editing site in the rps11 gene (nucleotide position 91) was predicted from the chloroplast genomes of G. burmanicum, G. caulopterum, G. compressum, G. guangxiense, and G. longipes, but was not present in the G. laxum and G. simplicfolium chloroplast genomes. Three interspecies differential RNA editing sites were predicted in the rps4 gene of the Gynostemma chloroplast genome. In G. burmanicum, G. guangxiense, G. laxum and G. simplicifolium, the editing site occurred at nucleotide position 602, causing ACT(T) to ATT(I) conversion, whereas in G. caulopterum, G. compressum and G. longipes, the editing sites occurred at the nucleotide positions 496 and 503 causing CTT (L) to TTT (F) and CCA (P) to CTA (L) conversions, respectively. Unfortunately, these interspecies differences in RNA editing sites did not exhibit clear subgenus specificity. In addition, two identified RNA editing sites were found at the start codons of psbL and ndhD.

3.3. Repeat Analysis

The characteristics of SSR copy number polymorphism make it a valuable molecular metric for genetic diversity research and evolution research. The repeat analysis of chloroplast SSRs plays a crucial role in taxonomic and phylogenetic studies of plant species. MISA was used to identify SSRs of 21 Gynostemma chloroplast genomes (Figure 3A,B). For the seven newly sequenced chloroplast genomes involved in this study, we identified 64, 67, 57, 59, 59, 71, and 56 SSRs in G. burmanicum, G. caulopterum, G. compressum, G. guangxiense, G. laxum, G. longipes, and G. simplicifolium, respectively. Mononucleotide, dinucleotide, trinucleotide, and tetranucleotide repeat units were identified in all Gynostemma species, but no pentanucleotide repeat units or hexanucleotide repeat units were found (Figure 3B). The A/T and AT/TA repeat units were the most abundant mononucleotide and dinucleotide types, respectively, in all Gynostemma chloroplast genomes, accounting for approximately 81–87% of the total number of SSRs. In contrast, C/G repeats were very rare. This result is consistent with the phenomenon that most abundant SSRs consist of polyA or polyT repeats in most chloroplast genomes [44]. The composition of trinucleotide repeats varied among different species, with G. guangxiense, G. compressum, G. caulopterum, and G. longipes having one ATC/ATG motif and no AAG/CTT motifs, and G. laxum, G. burmanicum, and G. simplicifolium having an AAG/CTT motif and no ATC/ATG motifs (Figure 3A). Most of the identified SSRs were within the intergenic region (IGS), while fewer SSRs were located in the intron region or the protein-coding region (CDS) (Table S7).
REputer, another repeat analysis tool, was also used to detect four types of long repeat sequences in the Gynostemma chloroplast genomes, including forward, palindromic, reverse, and complementary repeats (Figure 3C,D), which are thought to play an important role in genome rearrangements. There are certain differences in the types and numbers of repeats in chloroplast genomes of different species of Gynostemma. For all Gynostemma chloroplast genomes, forward and palindromic repeats were the most common repeat types. Only zero to four reverse or complementary repeats are present in most Gynostemma chloroplast genomes. Compared with the chloroplast of most species in this genus, which contains approximately 40 repeats, the G. caulopterum chloroplast contains 90 repeats, more than twice as many as the numbers of other species. The size of repeats varies among 21 species, and most of the repeats exist in the range of 35–34 bp (Figure 3D). G. caulopterum chloroplast contains more long length repeats (>45 bp) than other species chloroplasts. These SSRs and the long repeats identified in the Gynostemma chloroplast genome can be used as significant molecular markers to explore the genetic diversity and phylogeny of Gynostemma in future studies.

3.4. Comparative Analysis and Selection Pressure Analysis

To elucidate the chloroplast genome divergence of different Gynostemma species, we used mVISTA to perform a comparative analysis based on all available chloroplast genome data for this genus (14 samples downloaded from the NCBI and seven newly sequenced samples in this study) (Figure 4). The comparison revealed that the chloroplast genomes of different species of Gynostemma were highly similar. The IR regions were less divergent than the LSC and SSC regions. Furthermore, it was observed that protein-coding regions showed higher conservation than noncoding regions. The greatest divergence was found in intergenic regions, including trnK-rps16, trnS-trnG, trnR-atpA, atpH-atpI, rpoB-trnC, petN-psbM, trnT-psbD, psaA-pafI, trnT-trnL, trnF-ndhJ, ndhC-trnV, rpl32-trnL, ccsA-ndhD and trnH-psbA. In addition, high sequence divergence was found only in three protein-coding regions, rps16, ndhF and ycf1.
To quantify differences in chloroplast genomes from different Gynostemma species, the DNA polymorphism analysis was performed to detect highly variable sites by calculating the nucleotide diversity (Pi) value (Figure 5). The average Pi value was 0.0072. The IR regions showed much lower variability in Pi values than the LSC and SSC regions. Pi values higher than twice the median (Pi > 0.0124) were used to identify mutational hotspots. The region that showed the highest Pi value was petN-psbM (Pi ~ 0.04), and the top 10 regions with pi values are marked, included nine intergenic regions and one protein-coding region. Due to their high variability, these regions can be used as candidate molecular markers for plant identification and phylogenetic analysis in Gynostemma.
The ratio of synonymous substitutions (Ks) to nonsynonymous substitutions (Ka) is an important reference for determining whether a mutation is neutral, detrimental, or beneficial, with Ka/Ks > 1 indicating a beneficial mutation, Ka/Ks < 1 indicating a detrimental mutation, and Ka/Ks = 1 indicating a neutral mutation. We compared the chloroplast genomes of 21 individuals of the genus Gynostemma to calculate their Ks, Ka, and Ka/Ks (Table S8). We calculated Ks and Ka and their ratios for a total of 87 genes, 10 of which could not be determined due to a lack of information (Ks = 0). After removing these 10 genes, a total of 10 genes had Ka/Ks > 0.5, of which only rpl14 had Ka/Ks > 1 and was positively selected.

3.5. IR Region Contraction and Expansion

The IR region is considered as the most conserved region in the chloroplast genome. The variation in chloroplast genome size is generally thought to be caused by expansion/contraction of the IR region. The IR expansion/contraction of Gynostemma chloroplast genomes was analysed by performing collinearity analysis of the genomes (Figure S1) and comparing the boundary structure of LSC, SSC, and IRs regions among the Gynostemma chloroplast genomes (Figure 6). The collinearity analysis was conducted by using MAUVE. The entire chloroplast genome sequence was a homologous region without large fragment rearrangements or loss. The perfect collinearity indicated that the chloroplast genomes within this genus were relatively conserved. In all species, rps19 flanks the LSC/IRb junction, with part of the sequence present in the IR and the rest in the LSC. Although the length of the rps19 gene in IRb varied among species, the results did not suggest subgenus specificity. For the widespread species G. pentaphyllum, the length of the rps19 gene to the LSC/IRb boundary was different among samples (2 bp, 20 bp and 51 bp). Except in G. microspermum and G. burmanicum, the ycf1 fragment and ndhF genes were located at the boundary of SSC/IRb. In both G. microspermum and G. burmanicum, the ndhF gene was not situated at the SSC/IRb boundary; however, the reasons were different. In G. microspermum, which has the shortest IR region length in the Gynostemma genus, the contraction of the IR region caused the loss of approximately 60 bp of the ycf1 fragment and the ndhF gene to move away from the SSC/IRb boundary. In our newly sequenced G. burmanicum, the frameshift mutation and premature termination caused by the 2 bp deletion of the ndhF gene resulted in the absence of the ndhF gene at the SSC/IRb boundary. However, this deletion mutation was not observed in the other two published samples of G. burmanicum. In all Gynostemma species, the ycf1 genes were located at the boundary of SSC/IRa. The length of the overlapping regions of the ycf1 gene and SSC showed clear subgenus differences. The overlapping region of all Gynostemma subgenus species is 4499 bp in length, while that of Trirostellum subgenus species is slightly longer ranging from 4508 to 4653 bp. No gene stretches across the boundary between the LSC and IRa regions of all Gynostemma species. The trnH gene is 25–44 bp away from the LSC/IRa boundary. Interestingly, the length from the trnH gene to the LSC/IRa boundary was different among different individuals of G. burmanicum, G. pentaphyllum and G. longipes. Overall, the IR boundaries in the nine Gynostemma species showed similar characteristics with only slight differences in the flanking region or distance from the boundary in the organized genes, including rps19, ycf1, ndhF and trnH.

3.6. Phylogenetic Relationships among the Gynostemma Species

At present, although the phylogenetic tree shows that Gynostemma belongs to the basal group of Cucurbitaceae (Figure S2), the phylogenetic relationships of species within this genus are still controversial. According to the Flora of China (2011) [8], two subgenera, Gynostemma (eight species and two variants) and Trirostellum (six species), are included within this genus. To obtain better resolution of the phylogenetic relationships within the Gynostemma genus, we constructed a phylogenetic tree using 21 whole chloroplast genome sequences from nine subgenus Gynostemma and five subgenus Trirostellum species. To explore the taxonomic relationships of different populations within a species, multiple sequencing datasets of the same species were used for phylogenetic analysis. The Bayesian inference (BI) and maximum likelihood (ML) analyses yielded phylogenetic relationships with the same topology. The phylogenetic tree with supporting values is presented in Figure 7 Gynostemma formed four clades, supported by Bayesian posterior probabilities of 1 and maximum likelihood bootstrap support of 100%. Clade I included G. microspermum of subgenus Trirostellum, which occupied the most basal position in this genus. The three other species of subgenus Trirostellum (G. cardiospermum, G. laxiflorum and G. yixingense) clustered on one branch as Clade II, the closest clade to Clade I. The members of Clade IV, the clade farthest from the base, contained species all belonging to subgenus Gynostemma, including G. laxum, G. pubescens, G. simplicifolium, G. burmanicum, G. pentaphyllum, and G. longipes. Clade III appeared to be a transitional clade whose members included G. caulopterum, G. longipes, G. compressum, G. pentaphyllum, and G. guangxiense of subgenus Gynostemma and G. pentagynum of subgenus Trirostellum. Interestingly, different samples of the widespread species G. pentaphyllum and G. longipes existed in both Clades III and IV.

3.7. Morphological Analysis

The classification within the genus Gynostemma is mainly based on the morphological characteristics of the fruits. Here, we summarize the morphological characteristics of Gynostemma species through literature review, specimen observation and field investigation (Table 2). Obviously, in the taxonomic literature of Gynostemma, the fruit types of G. pentagynum, G. guangxiense, G. compressum and G. caulopterum are confused or not indicated. According to our field investigation, G. caulopterum, G. guangxiense and G. compressum from the subgenus Gynostemma and G. pentagynum from the subgenus Trirostellum share some common morphological characteristics, such as oblate fruit shape (2–5 ribs), persistent perianth and style, and inferior ovary. The typical subgenus Gynostemma fruits are globose berries, while typical subgenus Trirostellum fruits are campanulate capsules. Therefore, the fruit shapes of oblate distinguishing the group from the rest of the species are shared by this group. The genus Gynostemma is divided into two subgenera in traditional morphology Gynostemma and Trirostellum, but phylogenetic analysis shows that the genus Gynostemma is mainly divided into three independent branches. Therefore, we propose the existence of intermediate transitional branches. The typical subgenus Gynostemma fruits are globose berries, while the typical subgenus Trirostellum fruits are campanulate capsules. The species of Clade III, G. pentagynum, G. guangxiense, G. compressum and G. caulopterum, share a particular fruit shape, the oblate fruit, which is different from both of the subgenera Gynostemma and Trirostellum (Figure 8). Interestingly, the species in the transitional branch happen to be those with oblate fruit morphology. The perfect correspondence between the three fruit shapes and the phylogenetic tree suggested possible subgenus taxon reformation.

4. Discussion

4.1. General Characteristics of the Chloroplast Genomes of the Genus Gynostemma

Gynostemma is an economic plant genus in Southeast Asia, with saponin components that vary among species or populations [5,47]. Obtaining information about the intragenus and infraspecific variation of the chloroplast genomes is an important step in genetic research on this genus and a basis for the development and application of Gynostemma resources [48]. To date, comparative analyses of complete chloroplast genomes have made significant contributions to reconstructing phylogenies at different taxonomic levels in plants, including species of the genus Gynostemma [21,49]. However, in lower taxonomic units, for example, at the intraspecies or within-genus level, there is probably less variation in the chloroplast genome, which is mainly observed in hotspot regions [50].
In this study, we sequenced and assembled the complete chloroplast genome of seven Gynostemma species, three of which were reported for the first time, including those of G. simplicifolium, G. laxum and G. guangxiense. Furthermore, we downloaded all the available chloroplast genomes for this genus and performed a comprehensive analysis of the chloroplast genomes of this basal group of Cucurbitaceae. The chloroplast genomes of different species of Gynostemma are highly conserved, and the gene compositions, structures and GC contents are similar, RNA editing sites and condon usage bias showing close species relationships within the genus Gynostemma [13,17,18,19,20,21,51]. Our newly sequenced chloroplast genomes of Gynostemma species revealed differences between the two subgenera, despite the low chloroplast polymorphism in this genus.

4.2. Analysis of Codon Usage Bias and Prediction of RNA Editing Sites

Codon usage bias is closely associated with gene expression. Therefore, the origin, mutation and evolutionary patterns of species or genes are usually reflected by the use of codons. The most enriched amino acid within the Gynostemma species was leucine, and this result was frequently reported in other angiosperms [52]. The frequently used codons (RSCU > 1) usually end in A/U, which is consistent with reports from other plants [51]. The occurrence of base addition, loss, or conversion in the coding region after transcription is known as RNA editing. C-to-U RNA editing occurs mostly in angiosperms [53]. Two RNA editing events were detected in this study. psbL and ndhD could be translated normally because of the conversion of ACG (Thr) to the start codon AUG. The unconventional codon phenomenon in psbL and ndhD is common in Cucurbitaceae [54] and is also present in plants such as Betula platyphylla [55] and Nicotiana tabacum [53].

4.3. Phylogenetic Relationships

At present, phylogenetic relationships and interspecific taxonomic relationships can be demonstrated by complete chloroplast genomes and protein-coding genes based on a large number of literature reports [54,56]. The phylogenetic tree of Cucurbitaceae was established using the protein CDS region, and this phylogenetic tree indicated with a high bootstrap value that the genus Gynostemma is clearly related among the genera of Cucurbitaceae, which is consistent with the results of Zhang’s study [57]. The phylogenetic tree shows that the genera Gerrardanthus, Cyclantheropsis, Hemsleya and Gynostemma constitute the earliest divergent lineages of Cucurbitaceae, which is consistent with the APG IV classification system [58]. As in previous studies [18], the phylogenetic tree within the genus Gynostemma indicated that G. microspermum was the earliest divergent lineage of Gynostemma. In addition, two interesting phenomena occurred in the third branch: First, in contrast to previous studies, G. pentaphyllum and G. longipes were found to occur in the Clade III, which may be due to the hybridization and maternal inheritance of plastids [59]. The phylogenetic tree constructed by gene fragments similarly indicated that G. pentaphyllum is nonmonophyletic in origin [11,13]. Second, the phylogenetic tree of the genus Gynostemma is divided into three primary taxonomic clusters, which differs from the traditional morphological classification of the genus Gynostemma into the subgenus Gynostemma and Trirostellum [8,10]. Clade III has species of both subgenus Trirostellum and subgenus Gynostemma, defined as a transitional branch. Studies on the microstructural characteristics of the seed coat of the genus Gynostemma showed the existence of transitional forms between the two subgenera [60], and a strict concordance tree was obtained based on the sequences of the ITS, matK, and rpcL genes of Gynostemma, which also revealed that the two genera did not form two independent branches [7]. Evolutionary correlations within the genus Gynostemma are better revealed by a sufficient sample sizes of chloroplast genomes [61].

4.4. Identification of Suitable Polymorphic Loci at the Subgenus and Species Levels

The chloroplast genome is abundant in phylogenetic information [62], and visualization of this information in this research revealed gene fragments with consistent patterns of phylogenetic relationships with Gynostemma. The fragments obtained from the mVISTA analysis are trnR-atpA, atpH-atpL, rpoB-psbD, psbZ-rps14, trnP-psaJ, rpl32-trnL, ccsA-ndhD, and trnV-ocf70, of which atpH-atpL, rpl32-trnL, and ccsA-ndhD are polymorphic regions. These hypervariable polymorphic regions are considered to provide valuable markers for elucidating phylogenetic relationships among Gynostemma species. Microsatellites (SSRs) are widely present in plant chloroplast genomes and have properties such as polymorphism, codominant inheritance and multiallelism [63]. Therefore, SSR molecular markers are often applied in genotype identification, genetic analysis, population structure detection and biogeographic analysis [64,65]. When we investigated the SSRs of the chloroplast genome of the genus Gynostemma, interestingly, we found that trinucleotide repeat units were associated with phylogenetic position. Clades I and II lacked AAG/CTT and ATC/ATG repeats; Clade III included ATC/ATG repeats but lacked AAG/CTT repeats except in G. pentagynum; and Clade IV included AAG/CTT repeats but lacked ATC/ATG repeats. The pattern was basically consistent with the pattern of phylogenetic tree branching. This consistency is not a coincidence, instead suggesting the important role of SSRs for gene rearrangement and phylogenetic studies. In addition, analysis of the IR boundaries revealed that the lengths of the overlapping regions of rps19 and IRb and of ycf1 and SSC have clear subgenus differences. Polymorphic loci in the chloroplast genomes at the subgenus and species levels enable clear visualization of the evolutionary process of the species. For example, G. microspermum forms an independent branch in the most basal position of the genus Gynostemma, and its IR contraction and expansion are different from those of other species. G. pentagynum occupies the most basal position of Clade III, and its polymorphic fragments and SSR fragment variation regularity are more similar to those of Clade II.

4.5. Association of Fruit Shapes with the Phylogenetic Tree

Based on extensive field observations of Gynostemma fruit morphology and a comprehensive review of the Gynostemma taxonomic literature (Figure 8), we found that the morphology-based classification supported the chloroplast genome-based phylogenetic tree well. In other words, there may be a transitional group between the subgenus Gynostemma and Trirostellum. In summary, our study is the most comprehensive taxonomic and molecular evolutionary study of the Gynostemma genus based on chloroplast genomes.
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Figure 8. Fruit morphology of some Gynostemma species. (A): G. microspermum (capsule with a persistent perianth and style); (B): G. compressum, (C): G. caulopterum, (D): G. guangxiense and (E): G. pentagynum (oblate fruit with an inferior ovary and a persistent perianth and style); (F): G.longipes (berry without a persistent perianth and style).
Figure 8. Fruit morphology of some Gynostemma species. (A): G. microspermum (capsule with a persistent perianth and style); (B): G. compressum, (C): G. caulopterum, (D): G. guangxiense and (E): G. pentagynum (oblate fruit with an inferior ovary and a persistent perianth and style); (F): G.longipes (berry without a persistent perianth and style).
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5. Conclusions

In this study, the seven chloroplast genomes of the genus Gynostemma were sequenced, assembled, analyzed, and compared with 14 other published chloroplast genomes of Gynostemma species. Phylogenetic analysis was performed to clarify the phylogenetic relationships within the genus Gynostemma. The taxonomic relationships of subgenera were inferred from the results of the phylogenetic tree, chloroplast genome fragments, and morphology. The mVISTA, SSR and IR boundary results revealed differences at the subgenus level. By discovering the correlation between fruit morphology and the phylogenetic tree, a new hypothesis for the subgenus level classification of Gynostemma was proposed. In addition, molecular markers for highly polymorphic regions at the subgenus level were provided for further taxonomic and DNA barcode studies.

Supplementary Materials

The following supporting information can be down loaded at: https://www.mdpi.com/article/10.3390/genes14040929/s1, Figure S1. MAUVE alignment of chloroplast genomes of 21 individuals of the genus Gynostemma. The differently coloured squares represent different types of genes. Black represents transfer RNAs (tRNAs), and green repersents tRNAs with introns (rRNAs). Red represents ribosomal RNA, while white represents protein-coding genes; Figure S2. Phylogenetic trees were generated using maximum likelihood (ML) and Bayesian (BI) methods on the basis of 53 Cucurbitaceae chloroplast genomic CDS regions.ML trees and BI trees have the same topology.Bayesian posterior probabilities/ML bootstrap values are shown on the nodes and values of 1/100 are unlabelled. Different colours indicate as different tribes according to the APG IV classification system; Table S1: Sample collection information; Table S2: Sequencing quality of seven species of the genus Gynostemma; Table S3: List of species and their accession numbers in GenBank included in this study; Table S4: Basic characteristics of the chloroplast genomes of 21 individuals of the genus Gynostemma; Table S5: Number of codons and RSCU values of the chloroplast genomes of seven genus Gynostemma; Table S6: Prediction of RNA editing sites of the chloroplast genomes of seven Gynostemma genus; Table S7: Seven newly sequenced simple repeat sequences (SSRs) of the Gynostemma chloroplast genome; Table S8 Ka, Ks and Ka/Ks values of genes of the genus Gynostemma.

Author Contributions

Conceptualization, B.G., J.G. and F.C.; methodology, J.G.; software, J.G. and Y.L.; validation, Y.L. and B.G.; formal analysis, J.G.; investigation, J.G. and F.C.; resources, D.T. and L.Y.; data curation, J.G.; writing—original draft preparation, J.G. and Y.L.; writing—review and editing, Y.L. and J.G.; visualization, J.G. and Y.L.; supervision, D.L. and B.G.; project administration, Z.Y. and B.G.; funding acquisition, C.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported by the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (Grant No. 2021-I2M-1-032).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

This seven complete chloroplast genomes have been deposited at GenBank with accession numbers ON872370 (G. burmanicum), ON872371 (G. caulopterum), ON872372 (G. compressum), ON872373 (G. guangxiense), ON872374 (G. laxum), ON872375 (G. longipes) and ON872376 (G. simplicifolium).

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Chloroplast genome maps of Gynostemma. Genes transcribed counterclockwise are present inside of the circle. Genes transcribed clockwise are present outside of the circle. The colour of the genes corresponds to the function of the genes. The dashed area of the inner circle indicates the GC content of the genome. * Genes with intron.
Figure 1. Chloroplast genome maps of Gynostemma. Genes transcribed counterclockwise are present inside of the circle. Genes transcribed clockwise are present outside of the circle. The colour of the genes corresponds to the function of the genes. The dashed area of the inner circle indicates the GC content of the genome. * Genes with intron.
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Figure 2. Comparative analysis plots of RSCU values of seven species in the genus Gynostemma. The bar chart above each amino acid shows RSCU values within Gynostemma species. Each bar represents a species, from left to right: G. burmanicum, G. caulopterum, G. compressum, G. guangxiense, G. laxum, G. longipes and G. simplicifolium.
Figure 2. Comparative analysis plots of RSCU values of seven species in the genus Gynostemma. The bar chart above each amino acid shows RSCU values within Gynostemma species. Each bar represents a species, from left to right: G. burmanicum, G. caulopterum, G. compressum, G. guangxiense, G. laxum, G. longipes and G. simplicifolium.
Genes 14 00929 g002
Genes 14 00929 g003 550
Figure 3. Repeat sequence signature map. (A): SSRs for repeated unit classification. (B): comparison of mononucleotide to tetranucleotide repeat sequence types. (C): palindromic, forward, reverse, and complementary repeat sequence types; (D): Repeat length classification of long repeat sequences. * Represents a newly sequenced species of the genus Gynostemma.
Figure 3. Repeat sequence signature map. (A): SSRs for repeated unit classification. (B): comparison of mononucleotide to tetranucleotide repeat sequence types. (C): palindromic, forward, reverse, and complementary repeat sequence types; (D): Repeat length classification of long repeat sequences. * Represents a newly sequenced species of the genus Gynostemma.
Genes 14 00929 g003
Genes 14 00929 g004 550
Figure 4. Comparison of the chloroplast genomes of Gynostemma. Global Shuffle-LAGAN alignment was performed on the mVISTA website. Grey arrows above the alignment represent the genes. In each plot, the vertical scale represents the percent identity (50 to 100%). Genome regions are colour-coded as protein-coding exon (blue), rRNA or tRNA (sky blue), and conserved noncoding sequences (CNS, red). * Represents a newly sequenced chloroplast genome of Gynostemma species in this study.
Figure 4. Comparison of the chloroplast genomes of Gynostemma. Global Shuffle-LAGAN alignment was performed on the mVISTA website. Grey arrows above the alignment represent the genes. In each plot, the vertical scale represents the percent identity (50 to 100%). Genome regions are colour-coded as protein-coding exon (blue), rRNA or tRNA (sky blue), and conserved noncoding sequences (CNS, red). * Represents a newly sequenced chloroplast genome of Gynostemma species in this study.
Genes 14 00929 g004
Genes 14 00929 g005 550
Figure 5. Comparative analysis of nucleotide diversity (Pi) values among chloroplast genomes of Gynostemma species. The pink line is twice the median Pi value (Pi = 0.0124).
Figure 5. Comparative analysis of nucleotide diversity (Pi) values among chloroplast genomes of Gynostemma species. The pink line is twice the median Pi value (Pi = 0.0124).
Genes 14 00929 g005
Genes 14 00929 g006 550
Figure 6. Comparison of SC/IR junctions among the chloroplast genomes of Gynostemma species. JLB (junction of LSC/IRb), JSB (junction of SSC/IRb), JSA (junction of SSC/IRa), JLA (junction of LSC/IRa). * Represents newly sequenced chloroplast genomes of Gynostemma species in this study.
Figure 6. Comparison of SC/IR junctions among the chloroplast genomes of Gynostemma species. JLB (junction of LSC/IRb), JSB (junction of SSC/IRb), JSA (junction of SSC/IRa), JLA (junction of LSC/IRa). * Represents newly sequenced chloroplast genomes of Gynostemma species in this study.
Genes 14 00929 g006
Genes 14 00929 g007 550
Figure 7. Phylogenetic tree of complete chloroplast genomes of the genus Gynostemma based on maximum likelihood (ML) and Bayesian inference (BI) methods. The Bayesian posterior probabilities/ML bootstrap support values are displayed at the nodes. The colour of the species name indicates the subgenus: blue—subgenus Gynostemma, yellow—subgenus Trirostellum. branch length representative substitutions per site. * Represents newly sequenced chloroplast genomes of Gynostemma species in this study.
Figure 7. Phylogenetic tree of complete chloroplast genomes of the genus Gynostemma based on maximum likelihood (ML) and Bayesian inference (BI) methods. The Bayesian posterior probabilities/ML bootstrap support values are displayed at the nodes. The colour of the species name indicates the subgenus: blue—subgenus Gynostemma, yellow—subgenus Trirostellum. branch length representative substitutions per site. * Represents newly sequenced chloroplast genomes of Gynostemma species in this study.
Genes 14 00929 g007
Table
Table 1. Genes encoded in common among seven species of the genus Gynostemma.
Table 1. Genes encoded in common among seven species of the genus Gynostemma.
Gene FunctionsBiological FunctionGene ListNumber
PhotosynthesisATP synthase relatedatpA atpF atpH atpI atpE atpB6
Photosystem IpsaB psaA psaI psaJ psaC5
Photosystem IIpsbA psbK psbI psbM psbD psbC psbZ psbJ psbL
psbF psbEpsbB psbT psbH		14
Cytochrome b/f complexpetN petA petG petL petB * petD *6
NADH dehydrogenasendhJ ndhK ndhC ndhB * ndhF ndhD ndhE ndhG
ndhI ndhA * ndhH ndhB *		12
Photosystem biogenesis factor 1pbf11
Photosystem I assembly proteinpafI ** pafII2
Self-replicationRibosomal Structural RNAsrrn16 rrn23 rrn4.5 rrn5 rrn5 rrn4.5 rrn23 rrn168
Translation-related genetrnK-UUU * trnQ-UUG trnS-GCU trnR-UCU
trnC-GCA trnD-GUC trnY-GUA trnE-UUC
trnT-GGU trnS-UGA trnG-GCC trnfM-CAU
trnG-UCC trnS-GGA trnT-UGU trnL-UAA *
trnF-GAA trnV-UAC * trnM-CAU trnW-CCA
trnP-UGG trnl-CAU trnL-CAA trnV-GAC
trnE-UUC * trnA-UGC * trnR-ACG trnN-GUU
trnL-UAG trnN-GUU trnR-ACG trnA-UGC *
trnE-UUC * trnV-GAC trnL-CAA trnl-CAU
trnH-GUG		37
Ribosomal Proteins (small subunit)rps16 * rps2 rps14 rps4 rps18 rps12 * rps12 * rps11 rps8 rps3 rps19 rps7 rps15 rps714
Ribosomal Proteins (large subunit)rpl33 rpl20 rpl36 rpl14 rpl16 * rpl22 rpl2 * rpl23 rpl32 rpl23 rpl2 *11
RNA polymeraserpoC2 rpoC1 rpoB rpoA4
Other genesRuBisCO large subunitrbcL1
Translation relatedinfA1
Acetyl-CoA carboxylase geneaccD1
RNA SplicingmatK1
Carbon metabolism cemA1
c-type Cytochrome biogenesisccsA1
ATP-dependent protease subunitclpP1 **1
Unknownycf2 orf70 ycf1 ycf1 orf70 ycf26
* Genes with one intron. ** Genes with two introns.
Table
Table 2. Gynostemma species information summary.
Table 2. Gynostemma species information summary.
SubgenusSpeciesFruitPersistenceInformation Source
TypeMature PerformanceShapePerianthStyle
Trirostellum
[10]		G. microspermumcapsulesplitcampanulate-Yes[8] and Substance
G. cardiospermumcapsulesplitcampanulate-Yes[8]
G. yixingensecapsulesplitcampanulate-Yes[8]
G. laxiflorumcapsulesplitcampanulate-Yes[8]
G. pentagynum--5-angled-oblateYesYes[8] and Substance
Gynostemma
[10]		G. guangxiense--3-angled-oblateYesYes[8,45] and Substance
G. compressum--compressed, obtriangularYesYes[8] and Substance
G. caulopterum--compressed globoseYesYes[8,46] and Substance
G. pentaphyllumberrynot splitglobose--[8]
G. longipesberrynot splitglobose--[8]
G. burmanicumberrynot splitglobose--[8]
G. simplicifoliumberrynot splitglobose--[8]
G. laxumberrynot splitglobose--[8]
Species font color corresponds to the clade of phylogenetic tree.
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MDPI and ACS Style

Gan, J.; Li, Y.; Tang, D.; Guo, B.; Li, D.; Cao, F.; Sun, C.; Yu, L.; Yan, Z. The Complete Chloroplast Genomes of Gynostemma Reveal the Phylogenetic Relationships of Species within the Genus. Genes 2023, 14, 929. https://doi.org/10.3390/genes14040929

AMA Style

Gan J, Li Y, Tang D, Guo B, Li D, Cao F, Sun C, Yu L, Yan Z. The Complete Chloroplast Genomes of Gynostemma Reveal the Phylogenetic Relationships of Species within the Genus. Genes. 2023; 14(4):929. https://doi.org/10.3390/genes14040929

Chicago/Turabian Style

Gan, Jiaxia, Ying Li, Deying Tang, Baolin Guo, Doudou Li, Feng Cao, Chao Sun, Liying Yu, and Zhuyun Yan. 2023. "The Complete Chloroplast Genomes of Gynostemma Reveal the Phylogenetic Relationships of Species within the Genus" Genes 14, no. 4: 929. https://doi.org/10.3390/genes14040929

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