Skip to main content
Download PDF

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

BMC Genomics volume 23, Article number: 716 (2022) Cite this article

Abstract

Background

The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus Gynopodium contains eight species, but six of these species are threatened. No studies to date have characterized the characteristics of the chloroplast genomes (CPGs) within subgenus Gynopodium species. In this study, we compared the structure of CPGs, identified the mutational hotspots and resolved the phylogenetic relationship of subgenus Gynopodium.

Results

The CPGs of six subgenus Gynopodium species ranged in size from 160,027 bp to 160,114 bp. A total of 131 genes were identified, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. We detected neither major expansions or contractions in the inverted repeat region, nor rearrangements or insertions in the CPGs of six subgenus Gynopodium species. A total of 300 large repeat sequences (forward, reverse, and palindrome repeats), 847 simple sequence repeats, and five highly variable regions were identified. One gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG, and ccsA-ndhD) were identified as mutational hotspots by their high nucleotide diversity (Pi) values (≥ 0.004), which were useful for species discrimination. Maximum likelihood and Bayesian inference trees were concordant and indicated that Magnoliaceae consisted of two genera Liriodendron and Magnolia. Six species of subgenus Gynopodium clustered as a monophyletic clade, forming a sister clade with subgenus Yulania (BS = 100%, PP = 1.00). Due to the non-monophyly of subgenus Magnolia, subgenus Gynopodium should be treated as a section of Magnolia. Within section Gynopodium, M. sinica diverged first (posterior probability = 1, bootstrap = 100), followed by M. nitida, M. kachirachirai and M. lotungensis. M. omeiensis was sister to M. yunnanensis (posterior probability = 0.97, bootstrap = 50).

Conclusion

The CPGs and characteristics information provided by our study could be useful in species identification, conservation genetics and resolving phylogenetic relationships of Magnoliaceae species.

Peer Review reports

Background

The genus Magnolia is one of the early diverged angiosperm lineages consisting of approximately 300 species across three subgenera: Gynopodium, Magnolia, and Yulania according to Figlar’s taxonomic system [1, 2]. The extensive changes in chromosome number and rare androdioecious flowers of subgenus Gynopodium make them important materials for studying the evolution and breeding of flowering plants, as they are thought to represent a key transition from bisexual flowers to unisexual flowers [3,4,5]. Furthermore, members of the subgenus Gynopodium are known for their beautiful flowers, leafy branches, and aesthetically appealing shapes having high ornamental, economic, and ecological value [6, 7]. However, over-harvesting coupled with weak regenerative capacity makes the wild populations of subgenus Gynopodium species decreased rapidly [8,9,10]. Six of the eight subgenus Gynopodium species are of conservation concern, including three critically endangered species, two endangered species, and one vulnerable species according to the IUCN Red List [11]. Despite lots of studies on phytocoenological characteristics and breeding of subgenus Gynopodium [8, 9, 12], investigations of the genomic characteristics of this subgenus remain lacking.

Compared with the nuclear genome, the chloroplast genome (CPG) has a small size, low nucleotide substitution rate, single-parental inheritance, and haploid nature, which make it a good option for the analyses of nucleotide diversity and reconstructing phylogenies of closely related species, especially among polyploid taxa [13,14,15]. Although the structure of the CPG is generally conserved consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat regions (IR) [16], some structural rearrangements have been discovered, including the loss of genes or introns, as well as IR expansions and contractions [17, 18]. The comparative and phylogenetic analyses of CPGs have proved an ideal tool for species identification [19], detecting structural variation [20], assessing nucleotide diversity [21], resolving phylogenetic relationships [22], and reconstructing the evolutionary history [23]. Due to the similarity in the morphology of subgenus Gynopodium species and the complexity of their nuclear genomes associated with polyploidy [24], the CPG is suitable for exploring phylogenetic relationships, discriminating species and providing useful information for developing conservation strategies for this subgenus [25].

Here, we used the four newly sequenced CPGs of Magnolia omeiensis, Magnolia nitida, Magnolia sinica, and Magnolia kachirachirai, in addition to two previously published CPGs of Magnolia lotungensis and Magnolia yunnanensis, to (i) characterize the structural features and variations of the CPGs for the six sugenus Gynopodium species, (ii) assessing nucleotide diversity and identify hypervariable regions to developing DNA markers for species discrimination and conservation genetics studies, and (iii) resolve the evolutionary relationships of subgenus Gynopodium species.

Results

Characteristics of the CPGs

In this study, the coverage depth of each organelle genome reached over 100 × (Magnolia omeiensis: 168 × , M. sinica: 102 × , M. nitida: 132 × , M. kachirachirai: 103 ×). The six CPGs within the subgenus Gynopodium ranged in size, from 160,027 bp (M. kachirachirai) to 160,114 bp (M. lotungensis) (Table 1). All CPGs were a typical quadripartite circular structure (Fig. 1) that included a LSC region and a SSC region divided by a pair of IR regions (Fig. 1 and Table 1). The length of the LSC region ranged from 88,130 bp (M. kachirachirai) to 88,170 bp (M. yunnanensis), and the length of the SSC and IR regions ranged from 18,725 bp (M. kachirachirai) to 18,767 bp (M. lotungensis), and from 26,571 bp (M. sinica) to 26,586 bp (M. kachirachirai), respectively (Table 1). The GC-content was similar in all six CPGs. The GC content of the whole plasmid sequence was 39.3%; the GC content of the IR regions was 43.2%, which was higher than that of in LSC and SSC regions (38% and 34.3%) (Table S1). In addition, 131 genes were annotated in all six CPGs, including 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 86 protein-coding genes (Fig. 1 and Table 1). There were two copies for seven of the protein-coding genes, seven of the tRNA genes, and four of the rRNA genes; the other 95 genes were all represented by single copies. Eleven genes possessed introns: rps16, rps12, ropC1, rpl2, rpl16, petB, petD, ndhB, ndhA, clpP1, and atpF (Table 2).

Table 1 Summary of the CPG features of subgenus Gynopodium
Full size table
Fig. 1
figure 1

Gene map of the CPGs of six subgenus Gynopodium species. The genes inside and outside of the circle are transcribed in the clockwise and counterclockwise directions, respectively. Genes belonging to different functional groups are shown in different colors. The darker gray area in the inner circle indicates the GC content and the lighter gray indicates the AT content of the genome. The thick lines indicate the extent of the inverted repeats (IRa and IRb) that separate the genomes into the small single-copy (SSC) and large single-copy (LSC) regions

Full size image
Table 2 Gene list in the CPGs of six subgenus Gynopodium species
Full size table

Comparative analysis of CPGs

The alignments indicated high sequence similarity among the CPGs of the six subgenus Gynopodium species. However, sequence divergence in non-coding regions was greater than that in coding regions, such as trnH-psbA, rps2-rpoC2, ycf4-cemA, petA-psbJ, and ccsA-ndhD (Fig. 2). The greatest variation among coding regions was observed in ycf1. No major genomic rearrangements or insertions were detected among the six CPGs relative to that of M. omeiensis (Fig. S1).

Fig. 2
figure 2

Sequence alignment of the CPGs of six subgenus Gynopodium species. The alignment was performed using the mVISTA program and the M. omeiensis chloroplast genome was used as a reference. The y-axis indicated the degree of identity ranging from 50 to 100%. Coding and non-coding regions were marked in blue and red, respectively. Black arrows indicated the position and direction of each gene. CNS: conserved non-coding sequences

Full size image

Expansions and contractions in the CPGs of six subgenus Gynopodium species were visualized using IRscope (Fig. 3). The gene rps19 and trnH were located in the LSC region 1 bp from the LSC/IRb border and 11 bp from the IRa/LSC border. The genes rpl2 and ndhF were located in the IRb and SSC regions, respectively, and differed slightly in their proximity to the border between the IRb and SSC regions. The gene ycf1 was located between 4,256 and 4,274 bp in the SSC region, and between 1,270 and 1,279 bp in the IRa region. In all CPGs, significant length variations were detected in the LSC and SSC regions; sequences length was more conserved in the IR regions than those in the LSC and SSC regions (Fig. 3 and Table 1).

Fig. 3
figure 3

Comparisons of the borders of the large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) regions among the CPGs of six subgenus Gynopodium species. Gaps between the ends of boundaries and adjacent genes were indicated in base pairs (bps) above the main line

Full size image

Large repeat sequences and Simple sequence repeats (SSRs) analyses

Large repeat sequences were identified using REPuter software [26]. A total of 300 repeats were identified. Palindromic repeats were the most common repeat sequences, and no complement repeat was found in the CPGs of six subgenus Gynopodium species (Fig. 4). Variation was observed in the number of palindromic repeats and reverse repeats among the six CPGs. The lowest number of palindromic repeats (19) was observed in M. sinica, followed by M. omeiensis (20), M. lotungensis (21). M. nitida (22), M. kachirachirai (22), and M. yunnanensis (22). The number of reverse repeats was less in M. nitida, M. kachirachirai, and M. yunnanensis (9) than in M. lotungensis (10), M. omeiensis (12), and M. sinica (13). Among these repeats, nine were over 30 bp and 24 were 20–29 bp; the longest repeat was 39 bp. Over half of the repeats (60%) were located in non-coding regions, and some of the repeats were located in the coding regions of genes, such as psaA, psaB, ndhC, ycf1, ycf2, rpoB, and rpoC2 (Table S2).

Fig. 4
figure 4

Comparison of the numbers of repeats among the CPGs of six subgenus Gynopodium species: Magnolia omeiensis, Magnolia sinica, Magnolia nitida, Magnolia kachirachirai, Magnolia lotungensis, and Magnolia yunnanensis. (F: Forward, P: Palindromic, and R: Reverse repeats)

Full size image

A total of 847 SSRs were identified in the CPGs of six subgenus Gynopodium species, ranging from 140 to 142 in each species, among which 117–119 were mononucleotides, 9 were dinucleotides, 3–4 were trinucleotides, 9 were tetranucleotides, and 2 were pentanucleotides (Fig. 5a and Table 3). There was no marked variation in the number of SSRs among the six species; however, slight differences were observed in the number of mononucleotides and trinucleotides. Over 80% of SSRs were mononucleotide repeats consisting of 112 A/T repeats and five C/G repeats. All the dinucleotides consisted of multiple copies of AT/TA repeats and AG/CT repeats (Fig. 5b). SSRs were mostly located in intergenic spacer regions (IGS) (69.29%), followed by coding regions (17.86%) and introns (12.86%) (Fig. S2, Table 3). The SSRs in the coding regions were located in 12 protein-coding genes (rpoC1, rpoC2, rpoB, psbC, cemA, rps3, rps19, ndhF, ndhD, ycf1, ycf2, and ycf4) (Table S3). Few SSRs were located in the IR regions (10–12 SSRs); most were located in the LSC region (104–106 SSRs), followed by the SSC region (24–25 SSRs; Table S3).

Fig. 5
figure 5

The number of microsatellite loci with different types of repeats (A) and repeat units (B) detected in the CPGs of six subgenus Gynopodium species

Full size image
Table 3 The number and location of simple sequence repeats (SSRs) in the subgenus Gynopodium species
Full size table

Identification of highly variable regions

The nucleotide diversity within a 600-bp window was calculated for all six CPGs, which ranged from 0 to 0.008 (Fig. 6). There were five highly variable regions with Pi values greater than 0.004, including the ycf1 gene and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG and ccsA-ndhD). Pi was greatest (0.007) for the intergenic region between ccsA and ndhD. Highly variable regions were located in the LSC region (2) and SSC region (3); no highly variable region was detected in the IR region (Fig. 6), which reflects similar patterns with structure variability of CPGs. In addition, we evaluated the potential utility of the five highly variable regions. The rpl32-trnL-UAG marker (π = 0.007) with the highest discriminatory power can discriminate six haplotypes from the six subgenus Gynopodium species (Table 4). The psbA-trnH-GUG marker (π = 0.006) with high haplotype diversity can discriminate five haplotypes. Similarly, the marker petA-psbJ (π = 0.005), ccsA-ndhD (π = 0.007), and ycf1 (π = 0.004) can discriminate three haplotypes from the six subgenus Gynopodium species (Table 4).

Fig. 6
figure 6

Sliding window test of nucleotide diversity (Pi) in the multiple alignments of six subgenus Gynopodium species (window length: 600 bp; step size: 200 bp). The X-axis indicates the position of the midpoint of the window; the Y-axis indicates the nucleotide diversity of each window

Full size image
Table 4 Nucleotide diversity and discriminatory power of the subgenus Gynopodium chloroplast markers
Full size table

Phylogenetic relationships

Phylogenetic relationships were reconstructed using both ML and BI approaches, based on the whole CPGs of 22 species covering all known sections within Magnoliaceae. Topologies of the ML and BI trees were concordant and confirmed that Magnoliaceae comprised two subfamilies (Liriodendroideae and Magnolioideae), each with one genus (Liriodendron and Magnolia). Within Magnolia, subgenus Gynopodium was sister to the subgenus Yulania (BS = 100%, PP = 1.00) (Fig. 7). However, due to the non‐monophyly of subgenus Magnolia, three previously established subgenera in Magnolia were not supported (Fig. 7). Subgenus Gynopodium should be treated as a section of genus Magnolia following Wang et al. (2021) [27]. Within Subgenus Gynopodium, M. sinica diverged first (PP = 1, BS = 100), followed by M. nitida, M. kachirachirai, and M. lotungensis (albeit with relatively low support values), and M. omeiensis was sister to M. yunnanensis (PP = 0.97, BS = 50) (Fig. 7, Fig. S3).

Fig. 7
figure 7

Phylogenetic relationship of Magnoliaceae based on the CPGs of 20 Magnolia species and two Liriondendron species. The phylogeny was inferred by Bayesian inference. Numbers above the lines indicate the posterior probabilities from the Bayesian inference

Full size image

Discussion

Characteristics of the CPGs

The CPGs of most angiosperms varied in size from 120 to 160 kb [16]. Our results indicated that the CPGs of six subgenus Gynopodium species are similar in size (ca. 160 kb) and structure (quadripartite circular structure) to other Magnolia species [28,29,30] as well as other higher plants [31]. The total number, order, and composition of genes in the CPGs were highly conserved within subgenus Gynopodium, which is also consistent with most Magnolia species [32, 33], suggesting a very conserved structure of CPGs of subgenus Gynopodium.

The overall GC content has been reported to be associated with the phylogenetic position; specifically, the GC content tends to be higher in early diverged lineages, such as magnoliids [34]. Our results are consistent with these previous findings. Of the six subgenus Gynopodium species, the overall GC content of CPGs was approximately 39.3%, which is similar to that of other Magnolia species, such as M. shiluensis [32], M. grandiflora [35], and M. zenii [36] but higher than the average GC content (35%) of most angiosperms [37]. The GC content also varies among different regions of the CPG [34, 38]. IR region (43.2%) contains significantly higher GC content than that of the LSC (38%) and SSC regions (34.3%) (Table S1), which can attribute to the high GC content in the ribosomal RNA (rRNA) genes in IR region (Fig. 1). Identical findings have been reported in other species, such as Magnolia polytepala [39], Magnolia delavayi [40] and Datura stramonium [41].

Conservatisms of the CPGs

We compared the CPGs of six species within the subgenus Gynopodium. The results indicated that the SSC and LSC regions were more divergent than IR regions, and sequences in non-coding regions were more divergent than that in coding regions, which were consistent with previous findings in Magnolia species [29] and other flowering plants [42, 43] In this study, we identified six regions presenting significant variations in the CPGs of subgenus Gynopodium species, such as five intergenic regions: trnH-psbA, rps2-rpoC2, ycf4-cemA, petA-psbJ, and ccsA-ndhD, and one gene ycf1 (Fig. 2). No major genomic rearrangements or insertions were detected among the six CPGs, which further corroborated the results of recently published studies about Magnoliaceae [27]. Previous studies also found that variation in the size of angiosperms CPGs might be largely driven by length variation in IR regions, intergenic regions, and the number of gene copies [44,45,46]. The structure of the six CPGs within subgenus Gynopodium species was highly conserved; no major expansions or contractions were observed in the IR regions. However, variations in sequence length have been observed in both the LSC and SSC regions, which may drive variations in the size of CPGs within the subgenus Gynopodium species, as reported in other species [29, 47, 48].

Large repeats and simple sequence repeats

Knowledge of genetic diversity within subgenus Gynopodium is necessary to develop sustainable conservation management that ensures long-term maintenance of the genetic diversity within these species [3, 49]. Repeat sequences, which are dispersed in CPGs, are an important source of structural variation and play a significant role in genomic evolution [16, 50]. In our study, 300 repeats were identified, of which palindromic repeats were the most common, while complement repeats were missing in CPGs of the subgenus Gynopodium. The different number of forward repeats, palindromic repeats and reverse repeats generated the variations of CPGs [41]. Therefore, genetic variation in large repeats can provide useful information for phylogenetic research and population genetics. Previous studies have indicated that repeat sequences are mostly located in the intergenic spacer regions, followed by the coding regions [14, 32]. Our findings are consistent with this general pattern; 61.22-65.31% of the repeats were located in IGS regions, followed by coding regions and introns (34.69-38.38%) (Table S2).

SSRs are useful molecular markers that have been widely used in species discrimination, breeding and conservation, and phylogenetic studies [51,52,53,54]. In the CPGs of six subgenus Gynopodium species, the number of SSRs located in the LSC and SSC regions accounted for 92.86% of all SSRs, and only ten SSRs were located in the IR region (Table S3). Our findings were consistent with the general pattern of angiosperm that most of the repeats were located in the LSC and SSC regions of CPGs [36, 48]. The SSRs of the CPGs of six subgenus Gynopodium species identified in our study provided valuable sources for developing primers of specific SSR loci and a useful tool for species identification.

Highly variable regions

Highly variable regions provide abundant phylogenetic information and can be used as potential molecular markers to delimit closely related taxa [55]. The Pi of highly variable regions within subgenus Gynopodium species was lower (< 0.008) compared with previously published values of other species [56, 57] and some of Magnolia species [29, 30]. The low genetic diversity of subgenus Gynopodium species and other Magnolia species, e.g., Magnolia ashei may relate to their limited habitat and small populations as threatened species [54, 58, 59].

In the Magnoliaceae, several highly variable regions, such as, matk, ycf1, psbA-trnH and atpB-rbcL have been recognized as potential sites for DNA barcoding [39, 60]. In this study, we recognized five highly variable regions with Pi values greater than 0.004, including one gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG and ccsA-ndhD). The highly variable regions identified here have high discriminatory power to distinguish 6 (rpl32-trnL-UAG), 5 (psbA-trnH-GUG), 3 (petA-psbJ), 3 (ccsA-ndhD), and 3 (ycf1) plastid haplotypes from six subgenus Gynopodium species (Table 4). These regions could be considered as potential barcoding markers for species identification of subgenus Gynopodium.

Phylogenetic relationship

CPGs have shown substantial power in solving phylogenetic relationships among angiosperms [61]. However, it is still controversial regarding the boundaries of the genera of Magnoliaceae [1, 6]. Based on the whole CPGs of 22 species covering all known sections of Magnoliaceae, topologies of the ML and BI trees all supported that Magnoliaceae consisted of two subfamilies Magnolioideae and Liriodendroideae, each with one genus, Magnolia and Liriodendron, respectively. However, due to the non‐monophyly of subgenus Magnolia, three previously established subgenera in Magnolia were not supported. Our results supported the infrageneric circumscriptions reported by Wang et al. that classified Magnolia into 15 clades corresponding to 15 sections and subgenus Gynopodium treated as a section of Magnolia [27, 62]. And our results also supported merging section Manglietiastrum into section Gynopodium as reported previously [62, 63].

Although we recovered the phylogenetic relationship within subgenus Gynopodium, some of the nodes were poorly supported (Fig. 7). The low nucleotide diversity and nucleotide substitution rate in the CPGs of subgenus Gynopodium species and other Magnolia species might contribute to the lack of phylogenetic resolution in Magnoliaceae [62, 64, 65]. Consequently, genetic markers from the mitochondrial and nuclear genomes should be developed to reconstruct more robust phylogenies of subgenus Gynopodium species.

Conclusions

We compared the complete CPGs of six subgenus Gynopodium species (four newly sequenced and two obtained from previous studies). All CPGs exhibited the typical quadripartite structure of most angiosperms. The number, composition, and order of genes in the CPGs of subgenus Gynopodium species were similar to those of other species in the Magnoliaceae. We detected neither major expansions or contractions in the IR region, nor rearrangements or insertions. We identified large repeats, SSRs, and highly variable regions within subgenus Gynopodium, getting knowledge of the extremely low genetic diversity in these species. The six highly variable regions identified here will be useful for species delimitation within the subgenus Gynopodium. Overall, our findings and genetic resources presented here will facilitate future studies of subgenus Gynopodium and aid in species discrimination and conservation strategy development for threatened species in this subgenus.

Materials and methods

Plant material, DNA extraction and sequencing

Leaf samples of M. omeiensis were collected from mature trees from wild populations on Emei Mountain (Sichuan, China). Leaf samples of M. nitida were collected from Nanjing Botanical Garden. Leaf samples of M. kachirachirai and M. sinica were collected from South China Botanical Garden. The plant materials were identified by Dr. Lei Zhang and the voucher specimens (collection numbers: LiuJQ-2019–123, LiuJQ-2019–168, LiuJQ-2019–050, and ZC-1906–7) were deposited in the herbarium of Sichuan University. The CPGs of 20 species spanning all sections within Magnoliaceae were obtained from the National Center of Bio-technology Information (NCBI, https://www.ncbi.nlm.nih.gov/). Liriodendron chinense and Liriodendron tulipifera were used as outgroups, and the two CPGs for these species were downloaded from NCBI (Table S4).

Total genomic DNA was extracted from silica gel‐dried leaves using a modified CTAB method [66] and treated with RNase (TransGen, China). The DNA samples were indexed by tags and pooled together in a single lane of a Genome Analyzer (Illumina HiSeq 2000) for sequencing at BGI-Shenzhen. Paired‐end reads (2 × 150 bp) were sequenced, and more than 4.0 Gb of reads were obtained for each sample.

Assembly and annotation

The raw Illumina reads were first filtered by removing paired-end reads that contained (i) adapter sequences, (ii) more than 10% N bases, and (iii) more than 50% of bases with a Phred quality score less than ten. The filtered reads were then assembled using NOVOPlasty version 4.0 [67] and the complete plastome sequence of Magnolia biondii Pamp. (KY085894) as a reference. These assemblies were manually inspected using Geneious Prime version 9.1.8 [68]. The genome was automatically annotated using Plann version 1.1 [69] based on the well-annotated plastome of M. insignis Wall. (KY921716). All annotated CPGs were submitted to GenBank (accession numbers: OL631157, OL631158, OL631159, and OL631160). The chloroplast genomes map was generated by OGDRAW version 1.2 [70].

Comparative analysis of the CPGs of subgenus Gynopodium species

The results of the comparative analysis of the CPGs of the six subgenus Gynopodium species were visualized using online mVISTA software [71] with the annotated CPG of M. omeiensis as the reference in Shuffle-LAGAN mode. Detection of structural variation was conducted using Mauve software [72] with M. omeiensis as the reference. The borders of the four different regions among the six CPGs were visualized using IRscope [73].

Repeat structure and highly variable regions analysis

The online software REPuter [26] was used to identify repeat sequences (forward, reverse, complement, and palindromic) in CPGs with default parameters. Simple sequence repeats were examined using MISA-web [74] with minimal repeat numbers of 8, 5, 4, 3, 3, and 3 for mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, respectively. To identify highly variable regions, polymorphic sites and nucleotide diversity (Pi) in the six MAFFT-aligned CPGs were assessed using a sliding window analysis in DNAsp v6.12.03, with a 200-bp step size and a 600-bp window length [75]. Regions in the CPGs with numbers of polymorphic sites greater than the sum of the average and double the standard deviation were considered highly variable regions [76]. Then we estimated the number of haplotypes, haplotype diversity, parsimony informative sites, and singleton sites to detect the discriminatory power of highly variable regions using DnaSP v6.12.03 [75].

Phylogenetic analysis

Phylogenies were reconstructed using maximum likelihood (ML) and Bayesian inference (BI) analyses with the complete CPGs of 20 Magnolia species and two Liriodendron species (Table S4). ML analysis was conducted in RAxML [77] using the GTRGAMMA model and 1000 bootstrap (BS) replicates. BI analysis was conducted in Mrbayes v 3.2.6 [78], with four independent Markov chain Monte Carlo analysis runs for 1,000,000 generations each. PartitionFinder was used to determine the optimal partitioning scheme [79]. Priors were set to default values, and trees were sampled every 1,000 generations, with the first 25% discarded as burn-in. The consensus tree was calculated from trees sampled after reaching likelihood convergence, and the posterior probabilities (PPs) of the tree nodes were calculated.

Availability of data and materials

All annotated chloroplast genomes have been deposited in GenBank (https://www.ncbi.nlm.nih.gov/genbank/), and accession numbers are provided in Additional file 7. Other data generated or analyzed in our study are included in the additional files.

Abbreviations

CPG:

Chloroplast genome

IGS:

Intergenic spacer regions

IR:

Inverted repeat

LSC:

Large single-copy

SSC:

Small single-copy

CDS:

Coding sequence

SSRs:

Simple sequence repeats

GC:

Guanine-cytosine

PCG:

Protein-coding gene

BI:

Bayesian inference

ML:

Maximum Likelihood

IUCN:

International Union for the Conservation of Nature

References

  1. Figlar RB. Taxonomy topics—a new classification for Magnolia. In: Royal Horticultural Society ed. Rhododendrons with Camellias and Magnolias. Cornwall: MPGBooks Ltd. 2006:69–82.

  2. Figlar RB. A brief taxonomic history of Magnolia. Version April 2012 Available from https://www.magnoliasociety.org/ClassificationArticle. 2012 [and more or less continuously updated since]. [Accessed 2 January 2020].

  3. Li JM, Li QQ, Xiao LQ. Development of microsatellite markers in Parakmeria nitida (Magnoliaceae). Am J Bot. 2012;99(6):e234–6.

    Article  PubMed  Google Scholar 

  4. Xiao LQ, Li QQ. Phylogeography and allopolyploidization of Magnolia sect. Gynopodium (Magnoliaceae) in subtropical China. Plant Syst Evol. 2017;303(7):957–67.

    Article  CAS  Google Scholar 

  5. Liu YH, Xia NH, Yang QH. The origin, evolution and phytogeography of Magnoliaceae. Trop Subtrop Bot. 1995;3(4):1–12.

    Google Scholar 

  6. Xia NH, Liu YH, Nooteboom HP. Flora of China - Magnoliaceae. Beijing: Science press & St. Louis: Missouri Botanical Garden Press. 2008;8.

  7. Zhao N, Liu L, Zhang YQ, Yan HF, Liu TJ, Huang HR. The complete plastid genome of Magnolia omeiensis (Magnoliaceae). Mitochondrial DNA B. 2019;4(1):1837–8.

    Article  Google Scholar 

  8. Zhang P, Liu RY, Liang KH. A preliminary study on phytocoenological characteristics of Parakmeria omeiensis community. Guihaia. 1993;13(1):61–9.

    CAS  Google Scholar 

  9. Chen J, Fan JC, Lu CT, Zhao B. Biological characteristics and conservation measures of an threatened species Magnolia omeiensis. Sci tech Sichuan agric. 2015;4:22–5.

    Google Scholar 

  10. Yu DP, Wen XY, Li CH. The reintroduction of Parakmeria omeiensis Cheng, a Critically Endangered endemic plant. In: Ren H, editor. southwest China, in Conservation and reintroduction of rare and endangered plants in China. Singapore: Springer; 2020. p. 151–8.

    Google Scholar 

  11. Rivers MC, Beech E, Murphy L, Oldfield SF. The red list of Magnoliaceae- revised and extended, Richmond. UK: Botanic Gardens Conservation International; 2016.

    Google Scholar 

  12. Chen Y, Chen G, Yang J, Sun WB. Reproductive biology of Magnolia sinica (Magnoliaecea), a threatened species with extremely small populations in Yunnan. China Plant Divers. 2016;38(5):253–8.

    Article  PubMed  Google Scholar 

  13. Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S. Plant DNA barcoding: from gene to genome. Biol Rev Camb Philos Soc. 2015;90(1):157–66.

    Article  PubMed  Google Scholar 

  14. Hong Z, Wu ZQ, Zhao KK, Yang ZJ, Zhang NN, Guo JY, et al. Comparative analyses of five complete chloroplast genomes from the genus Pterocarpus (Fabacaeae). Int J Mol Sci. 2020;21(11):1–18.

    Article  Google Scholar 

  15. Xue S, Shi T, Luo WJ, Ni XP, Iqbal S, Ni ZJ, et al. Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina. Hortic Res. 2019;6(89):1–13.

    CAS  Google Scholar 

  16. Wicke S, Schneeweiss GM, dePamphilis CW, Muller KF, Quandt D. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol. 2011;76(3–5):273–97.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 2016;17(1):134.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Raman G, Park KT, Kim JH, Park S. Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications. BMC Genomics. 2020;21(1):855.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kim GB, Lim CE, Kim JS, Kim K, Lee JH, Yu HJ, et al. Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications. BMC Genomics. 2020;21(1):415.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Xiong Q, Hu YX, Lv WQ, Wang QH, Liu GX, Hu ZY. Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution. BMC Genomics. 2021;22(1):707.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Yang YX, Zhi LQ, Jia Y, Zhong QY, Liu ZL, Yue M, et al. Nucleotide diversity and demographic history of Pinus bungeana, an endangered conifer species endemic in China. J Syst Evol. 2020;58(3):282–94.

    Article  Google Scholar 

  22. Zhang FJ, Wang T, Shu XC, Wang N, Zhuang WB, Wang Z. Complete chloroplast genomes and comparative analyses of L. chinensis, L. anhuiensis, and L. aurea (Amaryllidaceae). Int J Mol Sci. 2020;21(16):5729.

  23. Li HT, Yi TS, Gao LM, Ma PF, Zhang T, Yang JB, et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nat Plants. 2019;5(5):461–70.

    Article  PubMed  Google Scholar 

  24. Parris JK, Ranney TG, Knap HT, Baird WV. Ploidy levels, relative genome sizes, and base pair composition in Magnolia. J Am Soc Hortic Sci. 2010;135(6):533–47.

    Article  Google Scholar 

  25. Yang JX, Hu GX, Hu GW. Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales. BMC Genomics. 2022;23(1):27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic acids res. 2001;29(22):4633–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Wang YB, Liu BB, Nie ZL, Chen HF, Chen FJ, Figlar RB, et al. Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming. J Syst Evol. 2020;58(5):673–95.

    Article  Google Scholar 

  28. Zhang M, Guo S, Yin YP, Zhou LJ, Ren B, Wang L, et al. Chloroplast genome and historical biogeography of the three Magnolias. Preprint, ;available at Research Square. 2021. (https://doi.org/10.21203/rs.3.rs-284868/v1).

  29. Shen YM, Chen K, Gu CH, Zheng SY, Ma L. Comparative and phylogenetic analyses of 26 Magnoliaceae species based on complete chloroplast genome sequences. Can J For Res. 2018;48(12):1456–69.

    Article  CAS  Google Scholar 

  30. Guzman-Diaz S, Nunez FAA, Veltjen E, Asselman P, Larridon I, Samain MS. Comparison of Magnoliaceae plastomes: Adding neotropical Magnolia to the discussion. Plants (Basel). 2022;11(3):1–29.

    Google Scholar 

  31. Asaf S, Khan AL, Khan A, Al-Harrasi A. Unraveling the chloroplast genomes of two Prosopis species to identify its genomic information, comparative analyses and phylogenetic relationship. Int J Mol Sci. 2020;21(9):3280.

    Article  CAS  PubMed Central  Google Scholar 

  32. Deng YW, Luo YY, He Y, Qin XS, Li CG, Deng XM. Complete chloroplast genome of Michelia shiluensis and a comparative analysis with four Magnoliaceae species. Forests. 2020;11(3):267.

    Article  Google Scholar 

  33. Chen S, Wu T, Fu Y, Hao J, Ma H, Zhu Y, et al. Complete chloroplast genome sequence of Michelia champaca var. champaca Linnaeus, an ornamental tree species of Magnoliaceae. Mitochondrial DNA B. 2020;5(3):2839–41.

    Article  Google Scholar 

  34. Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, et al. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol. 2006;6:77.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Li XW, Gao HH, Wang YT, Song JY, Henry R, Wu HZ, et al. Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related species. Sci China Life Sci. 2013;56(2):189–98.

    Article  CAS  PubMed  Google Scholar 

  36. Li YF, Sylvester SP, Li M, Zhang C, Li X, Duan YF, et al. The complete plastid genome of Magnolia zenii and genetic comparison to Magnoliaceae species. Molecules. 2019;24(2):261.

    Article  PubMed Central  Google Scholar 

  37. Schmid P, Flegel WA. Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations. J Transl Med. 2011;9(1):87.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Cai XL, Landis JB, Wang HX, Wang JH, Zhu ZX, Wang HF. Plastome structure and phylogenetic relationships of Styracaceae (Ericales). BMC Ecol Evol. 2021;21(1):103.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Sun LY, Jiang Z, Wan XX, Zou X, Yao XY, Wang YL, et al. The complete chloroplast genome of Magnolia polytepala: Comparative analyses offer implication for genetics and phylogeny of Yulania. Gene. 2020;736: 144410.

    Article  CAS  PubMed  Google Scholar 

  40. Xu XD, Wu SS, Xia JJ, Yan B. The complete chloroplast genome of Magnolia delavayi, a threatened species endemic to Southwest China. Mitochondrial DNA B. 2020;5(3):2734–5.

    Article  Google Scholar 

  41. Yang Y, Dang YY, Li Q, Lu JJ, Li XW, Wang YT. Complete chloroplast genome sequence of poisonous and medicinal plant Datura stramonium: organizations and implications for genetic engineering. PLoS ONE. 2014;9(11): e110656.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Li L, Wu QP, Fang L, Wu KL, Li MZ, Zeng SJ. Comparative chloroplast genomics and phylogenetic analysis of Thuniopsis and closely related genera within Coelogyninae (Orchidaceae). Front Genet. 2022;13: 850201.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Luo C, Huang WL, Sun HY, Yer H, Li XY, Li Y, et al. Comparative chloroplast genome analysis of Impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications. BMC Genomics. 2021;22(1):571.

    Article  PubMed  PubMed Central  Google Scholar 

  44. Zheng XM, Wang JR, Feng L, Liu S, Pang HB, Qi L, et al. Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants. Sci Rep. 2017;7(1):1555.

    Article  Google Scholar 

  45. Bedoya AM, Ruhfel BR, Philbrick CT, Madrinan S, Bove CP, Mesterhazy A, et al. Plastid genomes of five species of Riverweeds (Podostemaceae): structural organization and comparative analysis in Malpighiales. Front Plant Sci. 2019;10:1035.

    Article  PubMed  PubMed Central  Google Scholar 

  46. Chang H, Zhang L, Xie HH, Liu JQ, Xi ZX, Xu XT. The conservation of chloroplast genome structure and improved resolution of infrafamilial relationships of Crassulaceae. Front Plant Sci. 2021;12: 631884.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Gu CH, Dong B, Xu L, Tembrock LR, Zheng SY, Wu ZQ. The complete chloroplast genome of Heimia myrtifolia and comparative analysis within Myrtales. Molecules. 2018;23(4):846.

    Article  PubMed Central  Google Scholar 

  48. Zhao JT, Xu Y, Xi LJ, Yang JW, Chen HW, Zhang J. Characterization of the chloroplast genome sequence of Acer miaotaiense: comparative and phylogenetic analyses. Molecules. 2018;23(7):1740.

    Article  PubMed Central  Google Scholar 

  49. Wang L, Xiao AH, Ma LY, Chen FJ, Sang ZY, Duan J. Identification of Magnolia wufengensis (Magnoliaceae) cultivars using phenotypic traits, SSR and SRAP markers: insights into breeding and conservation. Genet Mol Res. 2017;16(1):gmr16019473.

    Article  Google Scholar 

  50. Marechal A, Brisson N. Recombination and the maintenance of plant organelle genome stability. New Phytol. 2010;186(2):299–317.

    Article  CAS  PubMed  Google Scholar 

  51. Mohammad-Panah N, Shabanian N, Khadivi A, Rahmani M-S, Emami A. Genetic structure of gall oak (Quercus infectoria) characterized by nuclear and chloroplast SSR markers. Tree Genet Genomes. 2017;13(3):70.

    Article  Google Scholar 

  52. Bi Y, Zhang MF, Xue J, Dong R, Du YP, Zhang XH. Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria. Sci Rep. 2018;8(1):1184.

    Article  PubMed  PubMed Central  Google Scholar 

  53. Yan XK, Liu TJ, Yuan X, Xu Y, Yan HF, Hao G. Chloroplast genomes and comparative analyses among thirteen taxa within Myrsinaceae s.str. clade (Myrsinoideae, Primulaceae). Int J Mol Sci. 2019;20:4534.

    Article  CAS  PubMed Central  Google Scholar 

  54. von Kohn C, Conrad K, Kramer M, Pooler M. Genetic diversity of Magnolia ashei characterized by SSR markers. Conserv Genet. 2018;19(4):923–36.

    Article  Google Scholar 

  55. Xu KW, Lin CX, Lee SY, Mao LF, Meng KK. Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships. BMC Genomics. 2022;23(1):203.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Pacheco TG, Lopes AS, Welter JF, Yotoko KSC, Otoni WC, Vieira LDN, et al. Plastome sequences of the subgenus Passiflora reveal highly divergent genes and specific evolutionary features. Plant Mol Biol. 2020;104:21–37.

    Article  CAS  PubMed  Google Scholar 

  57. Hishamuddin MS, Lee SY, Ng WL, Ramlee SI, Lamasudin DU, Mohamed R. Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships. Sci Rep. 2020;10(1):13034.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Yao Z, Guo J, Jin CZ, Liu YB. Endangered mechanisms for the first-class protected wild plants with extremely small populations in China. Biodiv Sci. 2021;29(3):394–408.

    Article  Google Scholar 

  59. Rico Y, Gutierrez Becerril BA. Species delimitation and genetic structure of two endemic Magnolia species (section Magnolia; Magnoliaceae) in Mexico. Genetica. 2019;147(1):57–68.

    Article  CAS  PubMed  Google Scholar 

  60. Shi SH, Jin H, Zhong Y, He XJ, Huang YL, Tan FX, et al. Phylogenetic relationships of the Magnoliaceae inferred from cpDNA matK sequences. Theor Appl Genet. 2000;101:925–30.

    Article  CAS  Google Scholar 

  61. Li HT, Luo Y, Gan L, Ma PF, Gao LM, Yang JB, et al. Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol. 2021;19(1):232.

    Article  PubMed  PubMed Central  Google Scholar 

  62. Dong SS, Wang YL, Xia NH, Liu Y, Liu M, Lian L, et al. Plastid and nuclear phylogenomic incongruences and biogeographic implications of Magnolia s.l. (Magnoliaceae). J Syst Evol. 2021;60:1–15.

    Article  Google Scholar 

  63. Kim S, Park CW, Kim YD, Suh Y. Phylogenetic relationships in family Magnoliaceae inferred from ndhF sequences. Am J Bot. 2001;88(4):717–28.

    Article  CAS  PubMed  Google Scholar 

  64. Kim S, Suh Y. Phylogeny of Magnoliaceae based on ten chloroplast DNA regions. J Plant Biol. 2013;56(5):290–305.

    Article  Google Scholar 

  65. Azuma H, Chalermglin P, Nooteboom HP. Molecular phylogeny of Magnoliaceae based on plastid DNA sequences with special emphasis on some species from continental Southeast Asia. Thai Forest Bulletin (botany). 2011;39:148–65.

    Google Scholar 

  66. Allen GC, Flores-Vergara MA, Krasnyanski S, Kumar S, Thompson WF. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Protoc. 2006;1(5):2320–5.

    Article  CAS  PubMed  Google Scholar 

  67. Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2017;45(4):1–9.

    Google Scholar 

  68. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28:1647–9.

    Article  PubMed  PubMed Central  Google Scholar 

  69. Huang DI, Cronk QC. Plann: a command-line application for annotating plastome sequences. Appl Plant Sci. 2015;3(8):1500026.

    Article  Google Scholar 

  70. Lohse M, Drechsel O, Kahlau S, Bock R. OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013;41:575–81.

    Article  Google Scholar 

  71. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004;32(Web Server issue):273–9.

    Article  Google Scholar 

  72. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394–403.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Amiryousefi A, Hyvnen J, Poczai P. IRscope: An online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 2018;34(17):3030–1.

    Article  CAS  PubMed  Google Scholar 

  74. Beier S, Thiel T, Munch T, Scholz U, Mascher M. MISA-web: a web server for microsatellite prediction. Bioinformatics. 2017;33(16):2583–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 2017;34(12):3299–302.

    Article  CAS  PubMed  Google Scholar 

  76. Wang W, Yang T, Wang HL, Li ZJ, Ni JW, Su S, et al. Comparative and phylogenetic analyses of the complete chloroplast genomes of six Almond species (Prunus spp. L.). Sci Rep. 2020;10(1):10137.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61(3):539–42.

    Article  PubMed  PubMed Central  Google Scholar 

  79. Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 2017;34(3):772–3.

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank TopEdit for providing linguistic assistance during the preparation of this manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (#31770566, 31770232), National Key Research and Development Program of China (#2017YFC0505203), Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences (CI2021A03908), Biodiversity Survey, and Observation and Assessment Program of the Ministry of Ecology and Environment of China.

Author information

Author notes

  1. Huanhuan Xie, and Lei Zhang contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China

    Huanhuan Xie, Hong Chang, Zhenxiang Xi & Xiaoting Xu

  2. Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan, 750021, China

    Lei Zhang

  3. Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China

    Cheng Zhang

Authors
  1. Huanhuan Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lei Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cheng Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hong Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zhenxiang Xi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xiaoting Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

XZX and XXT conceived and designed the study. XHH and ZC performed the analyses. XHH, CH, and ZL collected the data. XHH wrote the manuscript. All authors reviewed and revised the manuscript. The author(s) read and approved the final manuscript.

Corresponding authors

Correspondence to Zhenxiang Xi or Xiaoting Xu.

Ethics declarations

Ethics approval and consent to participate

We have complied with the relevant institutional, national, and international guidelines in collecting leaf materials for this study. The collection of these leaf materials was permitted by the staff of Emei Mountain, Nanjing Botanical Garden, and South China Botanical Garden. Our study will contribute to the studies in population genetics and conservation biology of these species.

Consent for publication

Not applicable.

Competing interests

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Additional file 1: Figure S1.

Alignment of the CPGs of sixsubgenus Gynopodium species by Mauve. The Magnolia omeiensis genome (the reference genome) is shown at the top. Color bars indicate locally collinear blocks, and connecting lines indicate correspondingblocks across genomes.

Additional file 2: Figure S2.

Proportion of simplesequence repeats in the inverted repeat (IR), large single-copy (LSC), and small single-copy (SSC) regions (A) and in the intergenic spacer (IGS),coding (CDS), and intron regions(B).

Additional file 3: Figure S3.

Phylogenetic relationship of the family Magnoliaceae (20 Magnolia species and two Liriondendron species) based on the CPGs.Phylogenies were inferred by maximum likelihood analysis. Numbers above thelines indicate the bootstrap values from the maximum likelihood analysis.

Additional file 4: Table S1.

 GC content of the CPGs of the six subgenus Gynopodium species.

Additional file 5: Table S2.

List of large repeat sequences in the CPGs of six subgenus Gynopodium species.

Additional file 6: Table S3.

 List of SSRs in the CPGs of six subgenus Gynopodium species.

Additional file 7: Table S4.

Accession numbers of the CPGs used in the phylogenetic analysis.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Xie, H., Zhang, L., Zhang, C. et al. Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species. BMC Genomics 23, 716 (2022). https://doi.org/10.1186/s12864-022-08934-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12864-022-08934-6

Keywords

BMC Genomics

ISSN: 1471-2164

Contact us