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Comparative phylogenomic study of East Asian endemic genus, Corchoropsis Siebold & Zucc. (Malvaceae s.l.), based on complete plastome sequences

BMC Genomics volume 25, Article number: 854 (2024) Cite this article

Abstract

Background

Endemic plants are key to understanding the evolutionary history and enhancing biodiversity within their unique regions, while also offering significant economic potential. The East Asian endemic genus Corchoropsis Siebold & Zucc., classified within the subfamily Dombeyoideae of Malvaceae s.l., comprises three species.

Results

This study characterizes the complete plastid genomes (plastomes) of C. crenata var. crenata Siebold & Zucc. and C. crenata var. hupehensis Pamp., which range from 160,093 to 160,724 bp. These genomes contain 78 plastid protein-coding genes, 30 tRNA, and four rRNA, except for one pseudogene, infA. A total of 316 molecular diagnostic characters (MDCs) specific to Corchoropsis were identified. In addition, 91 to 92 simple sequence repeats (SSRs) in C. crenata var. crenata and 75 in C. crenata var. hupehensis were found. Moreover, 49 long repeats were identified in both the Chinese C. crenata var. crenata and C. crenata var. hupehensis, while 52 were found in the South Korean C. crenata var. crenata. Our phylogenetic analyses, based on 78 plastid protein-coding genes, reveal nine subfamilies within the Malvaceae s.l. with high support values and confirm Corchoropsis as a member of Dombeyoideae. Molecular dating suggests that Corchoropsis originated in the Oligocene, and diverged during the Miocene, influenced by the climate shift at the Eocene–Oligocene boundary.

Conclusions

The research explores the evolutionary relationships between nine subfamilies within the Malvaceae s.l. family, specifically identifying the position of the Corchoropsis in the Dombeyoideae. Utilizing plastome sequences and fossil data, the study establishes that Corchoropsis first appeared during the Eocene and experienced further evolutionary divergence during the Miocene, paralleling the evolutionary patterns observed in other East Asian endemic species.

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Background

Biodiversity is an indicator that determines the range of evolutionary and ecological adaptations of species to specific environments [1]. Endemic plants, which are taxa that exclusively grow in specific regions and enhance the biodiversity of those regions, serve as crucial models for studying the evolutionary history of plants. Reports indicate that East Asia, including China, Korea, and Japan, is home to about 600 genera and more than 18,000 species of endemic plants across 31 families [2]. This number is notably higher than that of endemic plants found in the Northern Hemisphere, such as in North America and Europe [3, 4]. The rich diversity of endemic plants in East Asia is attributed to a combination of factors, including varied climatic and geographical changes during the Cenozoic era, a diversity of habitats, and the presence of numerous refugia during the ice ages [5, 6].

The genus Corchoropsis Siebold & Zucc., endemic to East Asia, comprises three annual species within the Malvaceae s.l. It is characterized by simple, alternately arranged leaves, solitary bisexual flowers with five yellow or white petals, 10–15 stamens, the presence of staminodes, a single pistil, and linear fruits [7, 8]. Originally, Corchoropsis was classified within the Tiliaceae by Siebold and Zuccarini in 1843. However, Takeda [9] reclassified it into the tribe Dombeyeae of the Sterculiaceae, based on its floral characteristics. In the current classification, Corchoropsis is placed within the subfamily Dombeyoideae of the Malvaceae s.l. based on its morphological traits [7]. In the initial molecular phylogenetic analyses based on three plastid regions, results indicated that Corchoropsis belongs to the Dombeyoideae and was well-resolved [10]. More recently, Dorr and Wurdack [11] proposed that the morphological similarities and the number of chromosomes shared between the two genera, Corchoropsis and Paradombeya Stapf, justify treating Paradombeya as a synonym of Corchoropsis. However, genomic information for Corchoropsis is not available, and comparative phylogenomic studies on Corchoropsis are lacking.

Of the three types of plant genomes, researchers have prioritised the usage of the plastome sequences due to them being highly conserved and their relatively small size [12]. Given the crucial role of chloroplasts in plant photosynthesis, the plastome has been extensively utilized in recent studies for developing molecular markers, conducting phylogenetic analyses, estimating divergence times, and performing biogeographical analyses [13,14,15]. In this study, we completed the plastomes of Corchoropsis collected from China and South Korea. We compared their genomic structures and reconstructed phylogenomic relationships among related species. Finally, we estimated the divergence times of Corchoropsis, which will aid in understanding the evolutionary patterns of the Malvaceae s.l. and provide essential information for future research on East Asian endemic taxa.

Methods

Taxon sampling, DNA extraction, and plastome assembly

We collected whole individuals of C. crenata var. crenata Siebold & Zucc. in China (N 31°35’51” E 110°52’15”, 857m) and South Korea (N 33°29’47” E 126°39’46”, 157m), as well as C. crenata var. hupehensis Pamp. from South Korea (N 37°25’30” E 127°04’10”, 114m) in the field. Plant collection did not require any specific permits. After collecting the samples, we prepared voucher specimens for each and stored them in the Gachon University Herbarium (GCU), assigning unique accession numbers (Table 1). All voucher specimens were identified by their morphological characters by the authors (Joonhyung Jung and Tao Deng). Total genomic DNA (gDNA) was extracted from fresh leaf material of each taxon employing a modified cetyltrimethylammonium bromide (CTAB) method [16]. This extracted gDNA was then used for next-generation sequencing (NGS) analysis on the Illumina Mi-seq platform (Illumina, Seoul, Korea). The raw sequencing data were then utilized for the de novo assembly of plastome sequences, facilitated by the GetOrganelle toolkit [17]. Subsequently, we conducted a ‘map to reference’ analysis of the plastome sequences to assess coverage, using the Geneious Prime 2023.1.1 program [18]. We annotated the gene content and sequence order with GeSeq [19]. All tRNAs were subjected to a secondary check using tRNAScan-SE web server (http://lowelab.ucsc.edu/tRNAscan-SE/) in its default search mode [20]. Finally, OGDraw [21] was employed to create visual representations of the complete plastome sequences.

Table 1 Features of the LSC, SSC, and IR of plastomes in this study
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Comparative plastome analyses

The whole plastome sequences of seven Dombeyoideae, including Corchoropsis, and four Tilioideae taxa were aligned and visualized using the LAGAN mode in mVISTA [22, 23], with Pityranthe trichosperma (Merr.) Kubitzki (Brownlowioideae; GenBank accession No. ON813239) serves as the reference. Additionally, the nucleotide diversity (Pi) of each gene and non-coding regions among the seven Dombeyoideae taxa was examined using a sliding window size of 100 bp and a step size of 25 bp in DnaSP v6.0 [24]. The plastid protein-coding genes were also utilized to identify molecular diagnostic characters (MDCs) specific to Corchoropsis and to each subfamily, employing FastaChar v0.2.4 for the analysis [25].

Repeat and codon usage analyses

The plastomes of Corchoropsis were analysed for simple sequence repeats (SSRs) using the MISA Perl script (MIcroSAtellite Identification Tool) [26]. The analysis established specific thresholds for minimum repeats: at least ten for mononucleotides, five for dinucleotides, four for trinucleotides, and three for tetra-, penta-, and hexanucleotide sequences. Concurrently, the REPuter tool [27] was applied to identify four types of sequence repetitions: forward, reverse, complementary, and palindromic, focusing on sequences at least 30 bp in length with a minimum of 90% similarity.

We employed DAMBE v7.3.11 [28] to determine the RSCU values across 78 plastid protein-coding genes of Corchoropsis.

Phylogenetic analyses

We downloaded 32 complete plastome sequences from NCBI, including one from the Byttnerioideae (Melochia corchorifolia L.), three from the Grewioideae (Colona floribunda (Kurz) Craib, Grewia biloba G.Don, and Microcos paniculata L.) to serve as outgroups. Additionally, for ingroups, we acquired four sequences from the Helicteroideae, seven from the Sterculioideae, two from the Bombacoideae, six from the Malvoideae, one from the Brownlowioideae, four from the Tilioideae, and four from the Dombeyoideae to cover all nine subfamilies in Malvaceae s.l. (Table S1). Then, we extracted 78 plastid protein-coding genes and aligned them using MUSCLE, as embedded in the Geneious Prime 2023.1.1 program. We performed Maximum Parsimony (MP), Maximum Likelihood (ML), and Bayesian Inference (BI) analyses to infer the phylogenetic relationships of Corchoropsis. The MP analysis was performed using PAUP* v4.0a [29], with all characters considered equally important and unordered, and gaps treated as missing data. We carried out searches involving 1,000 random taxon addition replicates with tree-bisection-reconnection (TBR) branch swapping in PAUP*, permitting up to ten trees to be held at each step. To evaluate internal support, we executed bootstrap analyses, termed parsimony bootstrap percentages (PBP), with 1,000 pseudoreplicates, applying the same parameters. For ML analyses, we utilized the IQ-TREE web server (http://iqtree.cibiv.univie.ac.at/) [30], calculating the support value, indicated as mean bootstrap percentage (MBP) and SH-like approximate likelihood ratio test (SH-aLRT), using 1,000 ultrafast bootstrap replicates. Prior to the Bayesian Inference (BI) analysis, we identified the optimal substitution model using the Bayesian Information Criterion (BIC) in MEGA 11 (Table S2) [31]. BI was conducted with MrBayes v3.2.7 [32], initiating two simultaneous runs from random trees for at least 1,000,000 generations, and sampling one tree every 1,000 generations. We discarded 25% of the trees as burn-in samples, and the remainder were used to construct a 50% majority-rule consensus tree. The proportions of bifurcations in this consensus tree were shown as posterior probabilities (PP) to gauge the robustness of the BI tree. We also checked the effective sample size values (ESS) for model parameters to ensure they exceeded 200. Finally, the phylogenetic trees were refined using FigTree v1.4.4 [33].

Molecular dating

In our study, divergence times for Corchoropsis were estimated using BEAST v1.10.4 [34], based on 78 plastid protein-coding genes. Throughout this process, the GTR + I + G model was implemented alongside a Birth and Death speciation tree prior and an uncorrelated lognormal model for molecular clock estimations [35, 36]. The analysis was conducted through a Markov chain Monte Carlo (MCMC) over 100 million generations, with parameter sampling every 1,000 generations. We removed the initial 10,000 (10%) trees as burn-in and utilized TreeAnnotator v1.10.4 to derive a maximum clade credibility tree from the remaining samples. This tree was produced considering a posterior probability threshold of 0.50 and the average node heights. Mean divergence times and 95% higher posterior density (HPD) intervals for these estimates were compiled using Tracer v1.7.2 and subsequently visualized with FigTree v1.4.4.

For our calibration accuracy, we employed five fossils: (1) Wood representing the stem node of the Grewioideae, identified as Grewinium canalisum (Bande & Srivastava) Srivastava & Guleria, was calibrated to an age of 64–67 million years ago (Mya) with a lognormal prior distribution (mean = 1.5, standard deviation = 0.15, and offset = 64; C1) [37]; (2) Leaf corresponding to the stem node of Sterculia, specifically S. washburnii Berry, was assigned ages of 66–72 Mya with a lognormal prior distribution (mean = 3, standard deviation = 0.3, and offset = 66; C2) [38]; (3) Pollen representing the stem node of the Bombacoideae, from Bombacacidites annae (Van der Hammen) Germeraad, was dated to 56–66 Mya with a lognormal prior distribution (mean = 5, standard deviation = 1, and offset = 56; C3) [39, 40]; (4) Leaf indicative of the stem node of the Eumalvoideae, identified as Malvaciphyllum macondicus M.Carvalho, was calibrated to 55.8–61.7 Mya with a lognormal prior distribution, (mean = 3, standard deviation = 0.3, and offset = 55.8; C4) [41]; and (5) Pollen representing the stem node of the Tilioideae, from Tillia sp., was dated to 66–72 Mya with a lognormal prior distribution (mean = 3, standard deviation = 0.3, and offset = 66; C5) [42].

Results

Plastome features of Corchoropsis

A total of 116,672 to 1,084,633 reads were assembled, accounting for 1.6–5.0% of the total 7,371,166 to 24,724,830 reads (Table S3). The plastid genome of Corchoropsis is characterized by a quadripartite structure, which consists of a large single copy (LSC) region (88,770–89,379 bp), a small single copy (SSC) region (20,496–20,505 bp), and two inverted repeats (IRs) regions (25,413–25,420 bp) (Fig. 1 and Table 1). A comparison of the plastome sequences from two individuals of C. crenata var. crenata, collected respectively from China and South Korea, revealed a difference of 164 bp (0.2%). Additionally, we identified 889 and 937 difference (0.9–1.0%) between C. crenata var. crenata and C. crenata var. hupehensis, respectively. The genetic composition of Corchoropsis was found to encompass 129 genes, among infA gene is identified as a pseudogene, and 17 genes are repeated in the IR regions (Table 2). These genes comprise nine protein-coding genes (atpF, ndhA, ndhB, petB, petD, rpl2, rpl16, rpoC1, and rps16) and five tRNAs (trnK-UUU, trnG-UCC, trnL-UAA, trnI-GAU, and trnA-UGC), each with a single intron. In addition, three protein-coding genes (clpP1, rps12, and pbf1) are noted for having two introns (Table 2). Notably, the rps12 gene undergoes trans-splicing; its 5’ exon is found in the LSC region, whereas the 3’ exon along with an intron are located within the IR regions.

Fig. 1
figure 1

Complete plastome map of Corchoropsis and their gene contents. The colored boxes represent conserved plastid genes. Genes located inside the circle are transcribed clockwise, while those outside the circle are transcribed counterclockwise. The grey bar graphs in the inner circle indicate the GC content of the plastome

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Table 2 Features of the LSC, SSC, and IR of Corchoropsis
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Comparative plastome analyses

Based on mVISTA results, we found that the plastomes exhibited high similarity, particularly in the coding and IR regions, which were more conserved compared to the non-coding, LSC, and SSC regions (Fig. 2). We analysed nucleotide divergences of plastid protein-coding genes, tRNA, rRNA, and non-coding regions to elucidate variant characteristics among the seven Dombeyoideae taxa (Fig. 3 and Table S4). The nucleotide diversity (Pi) for each plastid protein-coding gene ranged from 0 (pbf1, petL, petN, psaJ, and rps7) to 0.04202 (rpl32), with an average of 0.00962. In the tRNA and rRNA regions, variations in only nine genes were observed, ranging from 0.0002 (rrn23) to 0.01299 (trnS-GCU). In the non-coding regions, two intergeneric spacers (trnR-UCU–atpA and rpl22–rps19) showed remarkably high values (Pi > 0.1).

Fig. 2
figure 2

Plots of percent sequence identity of the plastomes of seven Dombeyoideae and four Tilioideae taxa with Pityranthe trichosperma (Brownlowioideae; GenBank accession No. ON813239) as a reference. The percentage of sequence identities was estimated, and the plots were visualised in mVISTA. Superscript abbreviations; C : China individual, K : South Korea individual

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Fig. 3
figure 3

Nucleotide diversity (Pi) values of the plastomes in seven Dombeyoideae taxa

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From the alignment data of 78 plastid protein-coding genes within members of the Malvaceae s.l., we identified 316 MDCs specific to Corchoropsis (Fig. 4 and Table S5). Notably, both two individuals of C. crenata var. crenata exhibit 122 unique MDCs, in comparison to C. crenata var. hupehensis. Within the members of the Malvaceae s.l., the individual from China exhibited nine MDCs, including six deletions in the psbK gene, whereas the individual from South Korea displayed ten MDCs, all characterized as single nucleotide polymorphisms (SNPs). Moreover, we calculated the number of MDCs unique to each genus and subfamily within the Malvaceae s.l., with the range for genera extending from 63 (Tilia L.) to 707 (Melochia L.), and for subfamilies from 45 (Helicteroideae) to 707 (Byttnerioideae).

Fig. 4
figure 4

The number of MDCs in 78 plastid protein-coding genes across 35 Malvaceae s.l. taxa. The red bar represents more than 500 MDCs, the yellow bar shows 200 to 500 MDCs, and the grey bar indicates fewer than 200 MDCs among the subfamilies

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Repeat and codon usage of Corchoropsis

In total, 91 to 92 SSRs were identified in C. crenata var. crenata and 75 in C. crenata var. hupehensis (Fig. 5). Both exhibited a high number of mono-nucleotide repeats. The number of dinucleotide repeats ranged from 13 in C. crenata var. hupehensis to 16–17 in C. crenata var. crenata. There were four instances of trinucleotide repeats. The number of tetranucleotide repeats varied, with eight observed in the C. crenata var. crenata individual from China and seven in both C. crenata var. crenata individual from South Korea and C. crenata var. hupehensis. Pentanucleotide repeats were less common, with two identified in C. crenata var. crenata and one in C. crenata var. hupehensis. The majority of SSRs consisted of the A/T motif, in contrast to the G/C motif, as detailed in Table S6.

Fig. 5
figure 5

Types and numbers of SSRs and long repeats in the plastomes of Corchoropsis. The number at the top of each stack represents the total count of both SSRs and long repeats

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Further analysis of longer repeats indicated a higher prevalence of forward and palindromic repeats over reverse and complementary ones across the Corchoropsis. Specifically, 49 long repeats were identified in both the C. crenata var. crenata individual from China and C. crenata var. hupehensis, and 52 in the C. crenata var. crenata individual from South Korea (Fig. 5). Only one complementary repeat was found in both C. crenata and its variety. The specific locations and the number of occurrences of these long repeats are detailed in Table S7.

An examination of 78 plastid protein-coding genes was conducted across Corchoropsis taxa to evaluate their relative synonymous codon usage (RSCU), excluding the stop codons UAA, UAG, and UGA (Fig. 6). There were slight differences in codon counts among the species, with C. crenata var. crenata presenting 22,729–22,731 codons and C. crenata var. hupehensis having a slightly higher figure of 22,732 (Table S8). Regarding amino acids, leucine (L) was identified as the most frequently occurring, constituting 10.47–10.49% of the total amino acids, whereas cysteine (C) was found to be the least common, representing only 1.14–1.15%.

Fig. 6
figure 6

Relative synonymous codon usage (RSCU) analysis of 20 amino acids in protein-coding genes of the complete plastomes of Corchoropsis. The values at the top of each stack indicate the frequency of use of each amino acid. The order of each three columns from left to right is C. crenata var. crenataC, C. crenata var. crenataK, and C. crenata var. hupehensis

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Phylogenetic analyses

We conducted MP, ML, and BI analyses and observed consistent topologies across the phylogenetic trees, which strongly supported the monophyly of the nine subfamilies of Malvaceae s.l. (Fig. 7). The sequence matrix encompassed 68,010 characters, with 57,869 (85.1%) being constant and 5,729 (8.4%) being parsimony informative. We derived the most parsimonious tree with a tree length of 14,303, consistency index (CI) of 0.802, and retention index (RI) of 0.837, as depicted in Fig. 7. Subsequently, two distinct clades were identified diverging with moderate support values: one comprising the Malvoideae and Bombacoideae, and the other including the Brownlowioideae, Dombeyoideae, and Tilioideae (PBP = 71/SH-aLRT = 78/MBP = 77/PP = 0.938). Within this framework, the subfamily Tilioideae was identified as the sister group to the Dombeyoideae, supported by high values (PBP = 86/SH-aLRT = 100/MBP = 100/PP = 1). In the Dombeyoideae, Pterospermum Schreb. formed the basal clade, and Eriolaena DC. was determined to be the sister to Corchoropsis (PBP = 100/SH-aLRT = 100/MBP = 100/PP = 1).

Fig. 7
figure 7

The Maximum Likelihood (ML) tree derived from 78 plastid protein-coding genes includes 35 Malvaceae s.l. taxa. Numbers indicate support values, represented as parsimony bootstrap percentages (PBP)/SH-aLRT support/mean bootstrap percentages (MBP)/posterior probability (PP). Only support values with PBP ≤ 85%, MBP ≤ 95%, and PP ≤ 0.95 are displayed. The bold names indicate genomes obtained in this study, while the boxes represent the subfamily within the Malvaceae s.l

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Molecular dating

Mean divergence age estimates and their corresponding 95% HPD intervals for key phylogenetic nodes, derived from BEAST analysis, are presented in Fig. 8 and Table 3. This analysis indicates that the crown node of Malvaceae s.l. occurred during the Lower Cretaceous period, approximately 108.36 Mya, with a 95% HPD interval of 85.04–139.93 Mya (node 1). The Helicteroideae is estimated to have diverged around 96.59 Mya, with a 95% HPD interval of 81.05–119.44 Mya (node 2). The Sterculioideae is estimated to have diverged around 87.49 Mya, with a 95% HPD interval of 76.55–101.42 Mya (node 3). The Bombacoideae + Malvoideae clade is estimated to have diverged approximately 86.25 Mya, with a 95% HPD interval of 75.67–99.86 Mya (node 4), with further divergence occurring in the Paleocene. Within the Brownlowioideae + Tilioideae + Dombeyoideae clade (node 5), Dombeyoideae + Tilioideae is diverged around 79.27 Mya, with a 95% HPD interval of 70.54–90.12 Mya (node 6). Additionally, within the Dombeyoideae, the genus Corchoropsis is estimated to have originated in the Oligocene, approximately 32.84 Mya, with a 95% HPD interval of 16.09–49.19 Mya (node 8).

Fig. 8
figure 8

Chronogram of Malvaceae s.l. based on 78 plastid protein-coding genes estimated from BEAST. The nodes represent posterior mean ages, with blue bars indicating 95% HPD intervals. Numbers 1–9 correspond to nodes of interest (Table 3). Nodes labeled C1–C5 with red star are calibration points used in the analysis. The geological epoch is displayed below the tree

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Table 3 The estimated age of interested nodes of Malvaceae s.l
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Discussion

Complete plastomes of Corchoropsis and its comparison

The plastome, well known for its photosynthetic functions, is highly conserved and small in size compared to the two other types of plant genomes [12]. With growing interest in biodiversity across various countries, genomic research focused on endemic plants has seen significant advancement [43, 44]. Here, we have completed plastome sequences of the East Asian endemic genus, Corchoropsis, noted for its highly conserved structure based on our comparative genomic analyses. It was observed that the infA gene, encoding translation initiation factor 1, has undergone pseudogenization, a common occurrence in many members of Malvaceae s.l [45,46,47]. In the Dombeyoideae, Pterospermum also exhibits a pseudogenized infA gene. In contrast, Eriolaena, which is identified as the sister to Corchoropsis in this study, possesses an intact form of the gene, suggesting it is not a synapomorphic character (not shown).

Through mVISTA and nucleotide diversity analyses, we identified higher nucleotide variations in non-coding regions than in coding regions, a pattern found in most angiosperms [48, 49]. Two non-coding regions, rpl22–rps19 and trnR-UCU–atpA, located in the LSC region, exhibit high diversity (Pi > 0.1, Fig. 3). Additionally, two coding regions, rpl32 and ycf1, located in the SSC region, also show high diversity (Pi > 0.03). Generally, the IR region has lower diversity due to its importance in replication initiation, structural stability, and gene conservation, thus remaining well-conserved [50,51,52]. Despite its duplicated form affecting gene composition through IR expansion and contraction, we identified no differences among seven members of the Dombeyoideae in this study.

Recent advancements in species identification have been achieved through the use of MDCs. These developments enhance traditional barcoding methods and focus on refining species identification across various taxonomic categories [25, 53]. We counted MDCs from 78 plastid protein-coding genes, which enhances the possibility of species identification due to their conservation for specific functions (Fig. 4 and Table S5). In Corchoropsis, a total of 316 MDCs were identified, including one independent insertion encoding ‘IC’. Additionally, two independent deletions encoding ‘NNHK’ and ‘FLN’ were found. All these genetic variations were observed in the ycf1 gene, which exhibits high diversity.

Repeat and codon usage of Corchoropsis

SSRs, highly regarded for their polymorphism, are particularly suited for phylogenetic and population genetic studies [54, 55]. In our study, the identified SSRs predominantly exhibited a high A/T content. Consequently, the majority of repeats in the C. crenata var. crenata individuals from China (67.03%), South Korea (67.39%), and C. crenata var. hupehensis (66.67%) were composed of A/T. Additionally, our study uncovered long repeats within Corchoropsis, showing slight variations across different types. The data on SSRs and long repeats collected here offer valuable insights for the selection of effective molecular markers for distinguishing C. crenata and its variety.

An examination of codon usage within plastid protein-coding genes can yield insights into mutation trends, the influences of selection, and genetic drift at the species level. Typically, most amino acids are encoded by two to six synonymous codons, with the exceptions of methionine (M) and tryptophan (W). Our analysis revealed that 29 codons exhibited elevated RSCU values (greater than 1), predominantly terminating in A or U. Conversely, codons with lower RSCU values (less than 1) frequently ended in G or C (Table S8). Notably, the codon AUU, which encodes for isoleucine (Ile), was found to be the most prevalently used, aligning with observations in other studies within the Malvaceae s.l. group [45, 56].

Phylogenetic relationships and divergence times of Corchoropsis

Historically, the Bombacaceae, Malvaceae s.s., Sterculiaceae, and Tiliaceae constituted the core Malvales, renowned for their close interrelationships [57, 58]. Phylogenetic analyses, employing morphological, anatomical, palynological, and chemical characteristics, have revealed that within these families, only the Malvaceae s.s. are monophyletic. The other three families demonstrate paraphyletic or polyphyletic relationships, led to the recommendation to unify these groups under a single family, Malvaceae s.l [59]. In previous studies on the subfamiliar relationships within the Malvaceae s.l., Alverson et al. [60] utilized the ndhF gene to group the Dombeyoideae with Tilioideae, revealing polytomy among the subfamilies. Hernandez-Gutierrez and Magallon [61] later reconstructed the Malvaceae s.l. using six plastid, one mitochondrial, and one nuclear region, suggesting that the Dombeyoideae is closely related to Brownlowioideae, although with low support. Conover et al. [62] examined the Malvaceae s.l. based on 67 plastid genes and identified the Dombeyoideae as sister to a group comprising the Bombacoideae, Malvoideae, Sterculioideae, and Tilioideae. Wang et al. [63] and Li et al. [64], focusing on plastome sequences, indicated that the Tilioideae as a sister group to the Dombeyoideae, notably excluding the Brownlowioideae from this relationship. Subsequently, the phylogenetic positions of nine subfamilies were clearly resolved based on plastome sequences with robust support values, following the resolution of the plastome of the Brownlowioideae [56, 65]. Notably, the Dombeyoideae, which includes the genus Corchoropsis, emerged as a sister group to the Tilioideae, and these two subfamilies formed a cluster with the Brownlowioideae. Our phylogenetic analyses further validated the monophyly of the nine subfamilies of the Malvaceae s.l., corroborating these recent findings (Fig. 7) [56, 65].

Currently, Corchoropsis shows a close association with other Asian genera like Eriolaena and Pentapetes L. within the Dombeyoideae of the Malvaceae s.l., a relationship supported by morphological characteristics [7]. Within the genus, C. crenata var. hupehensis is distinguished from C. crenata var. crenata by its glabrous ovary and capsule, featuring a red stigma, whereas the latter features a yellow stigma. The distinctive color of the stigma is influenced by the apocarotenoids crocetin and crocin, which are products of the oxidative cleavage of zeaxanthin and play a significant role in attracting pollinators [66, 67]. Both having the same distribution suggests that this may be an example of adaptive evolution and may necessitate a discussion regarding recognition as a separate species.

The initial molecular phylogenetic analysis of Corchoropsis, utilizing three plastid protein-coding genes, substantiated its placement within the Dombeyoideae and its close relationship with related genera [10]. In this study, plastome sequences have confirmed Corchoropsis as a member of the Dombeyoideae, however, there is still a lack of genomic data for this subfamily to clarify intergeneric relationships. Additionally, further studies are needed to examine the recent taxonomic synonymization of members from Paradombeya with Corchoropsis [11], although recent study supported their monophyly with high support values based on six molecular markers [68].

Numerous studies have been conducted to estimate the divergence times of the Malvaceae s.l. and its members, with fossil data suggesting that the crown node age of the Malvaceae s.l. ranges from 70.7 to 110.47 Mya [61, 63, 65, 68, 69]. These results varied due to differences in taxon sampling, the fossils used, and the tree prior model, which are sensitive factors for the analyses. Our results support the findings of Cvetković et al. [65], setting the oldest fossil, Bombacoxylon langstoni Wheeler & Lehman, for the crown node of Malvales [70]. Our analysis, based on plastome sequences and clearly defined relationships among the nine subfamilies, indicated that the stem ages of the subfamilies range between 62.20 Mya (Bombacoideae and Malvoideae) and 96.59 Mya (Helicteroideae). These ages are slightly higher than previous reports [61, 63, 65, 68, 69], however, the corresponding geological periods and the phylogenetic relationships align with Cvetković et al. [65]. Notably, their study incorporated the Dipterocarpaceae taxa into their data matrix, and the use of different taxa from each subfamily could influence the discrepancies observed in molecular dating. Our study suggests that the Dombeyoideae originated in the Upper Cretaceous (79.27 Mya) and further diverged in the Eocene (51.65 Mya). The crown node age of the Dombeyoideae is similar to that suggested by Skema et al. [68], which involved a broad ancestral range encompassing major areas including Asia, Africa, and Madagascar.

The Eocene–Oligocene boundary, around 34 Mya, had a significant impact on global biodiversity due to notable climatic shifts [71,72,73]. These changes led to increased dispersal events, especially pronounced during the Miocene, which in turn facilitated the diversification and emergence of new genera [74]. Specifically, within the Dombeyoideae, Corchoropsis crenata originated in this boundary and its variety further diversified during the Miocene. Other East Asian endemic angiosperms, especially Dobinea Buch.-Ham. ex D.Don (Anacardiaceae) and Chimonanthus Lindl. (Calycarthaceae), originated in the Eocene–Oligocene and further diversified in the Miocene, supporting speciation during that period [75, 76].

Conclusions

Endemic plants, characterized by their restricted distribution, are crucial for biodiversity conservation and provide an essential foundation for investigating phylogenetic relationships, biogeographical histories, and genetic diversity. This study offers insights into the plastomes of the genus Corchoropsis, which is endemic to East Asia. The analysis of whole plastome sequences is instrumental in understanding structural variations, providing super-barcoding information, elucidating phylogenetic relationships, and estimating divergence times. We have gathered fundamental genomic data, especially regarding MDCs, SSRs, and long repeats, which are invaluable for future studies in super-barcoding, population genetics, and phylogenetics. Our research delineates the phylogenetic relationships among nine subfamilies of the Malvaceae s.l. and clarifies the phylogenetic position of Corchoropsis within the Dombeyoideae. Based on plastome sequences and fossil data, we have determined that Corchoropsis originated in the Eocene and further diverged in the Miocene, similar to other East Asian endemic angiosperms.

Data availability

The three plastome sequences we obtained from this study were archived in NCBI. The accession numbers are presented in Table 1 (PP840627-PP840629).

References

  1. Myers N, Mittermeier RA, Mittermeier CG, Da Fonseca GA, Kent J. Biodiversity hotspots for conservation priorities. Nature. 2000;403(6772):853–8.

    Article  CAS  PubMed  Google Scholar 

  2. Manchester SR, CHEN ZD, LU AM, Uemura K. Eastern Asian endemic seed plant genera and their paleogeographic history throughout the Northern Hemisphere. J Syst Evol. 2009;47(1):1–42.

    Article  Google Scholar 

  3. Huang JH, Chen JH, Ying JS, Ma KP. Features and distribution patterns of Chinese endemic seed plant species. J Syst Evol. 2011;49(2):81–94.

    Article  Google Scholar 

  4. Chung GY, Jang H-D, Chang KS, Choi HJ, Kim Y-S, Kim H-J, Son D-C. A checklist of endemic plants on the Korean Peninsula II. Korean J Plant Taxonomy. 2023;53(2):79–101.

    Article  Google Scholar 

  5. Milne RI, Abbott RJ. The origin and evolution of Tertiary relict floras. 2002.

  6. Qiu Y-X, Fu C-X, Comes HP. Plant molecular phylogeography in China and adjacent regions: tracing the genetic imprints of quaternary climate and environmental change in the world’s most diverse temperate flora. Mol Phylogenet Evol. 2011;59(1):225–44.

    Article  PubMed  Google Scholar 

  7. Bayer C, Kubitzki K. Malvaceae. Flowering Plants· Dicotyledons: Malvales, Capparales and Non-betalain Caryophyllales. Springer; 2003. pp. 225–311.

  8. Tang Y. The systematic position of Corchoropsis Sieb. & Zucc. Cathaya. 1992;4:131–50.

  9. Takeda H. The genus Corchoropsis. Bull Misc Inf Kew 1912, 365.

  10. Won H. Phylogenetic position of Corchoropsis Siebold & Zucc.(Malvaceae sl) inferred from plastid DNA sequences. J Plant Biology. 2009;52:411–6.

  11. Dorr LJ, Wurdack KJ. Indo-Asian Eriolaena expanded to include two Malagasy genera, and other generic realignments based on molecular phylogenetics of Dombeyoideae (Malvaceae). Taxon. 2021;70(1):99–126.

    Article  Google Scholar 

  12. Dobrogojski J, Adamiec M, Luciński R. The chloroplast genome: a review. Acta Physiol Plant. 2020;42(6):98.

    Article  CAS  Google Scholar 

  13. Kim T-H, Kim J-H. Molecular phylogeny and historical biogeography of Goodyera R. Br.(Orchidaceae): a case of the vicariance between East Asia and North America. Front Plant Sci. 2022;13:850170.

    Article  PubMed  PubMed Central  Google Scholar 

  14. Feng Z, Zheng Y, Jiang Y, Pei J, Huang L. Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes. Sci Rep. 2024;14(1):9783.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Li J, Du Y, Xie L, Jin X, Zhang Z, Yang M. Comparative plastome genomics and phylogenetic relationships of the genus Trollius. Front Plant Sci. 2023;14:1293091.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Doyle J. DNA protocols for plants. Molecular techniques in taxonomy. Springer; 1991. pp. 283–93.

  17. Jin J-J, Yu W-B, Yang J-B, Song Y, DePamphilis CW, Yi T-S, Li D-Z. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020;21:1–31.

    Article  Google Scholar 

  18. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–9.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017;45(W1):W6–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Chan PP, Lowe TM. tRNAscan-SE: searching for tRNA genes in genomic sequences. Gene Prediction: Methods Protocols 2019:1–14.

  21. Greiner S, Lehwark P, Bock R. OrganellarGenomeDRAW (OGDRAW) version 1.3. 1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019;47(W1):W59–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S, Program NCS. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 2003;13(4):721–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS. Dubchak I: VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 2000;16(11):1046–7.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  25. Merckelbach LM, Borges LM. Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species. Mol Ecol Resour. 2020;20(6):1761–8.

    Article  PubMed  Google Scholar 

  26. Beier S, Thiel T, Münch 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 

  27. 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 

  28. Xia X. DAMBE7: New and improved tools for data analysis in molecular biology and evolution. Mol Biol Evol. 2018;35(6):1550–2.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Swofford DL. Phylogenetic analysis using parsimony (* and other methods). Version. 2002;4:b10.

    Google Scholar 

  30. Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016;44(W1):W232–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 2021;38(7):3022–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 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 

  33. Rambaut A. FigTree, a graphical viewer of phylogenetic trees (Version 1.4. 4). Institute of evolutionary biology. University of Edinburgh; 2018.

  34. Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018;4(1):vey016.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006;4(5):e88.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Gernhard T. Using birth-death model on trees. J Theor Biol. 2008;253(769–778):1066.

    Google Scholar 

  37. Wheeler EA, Srivastava R, Manchester SR, Baas P. Surprisingly modern latest cretaceous–earliest paleocene woods of India. IAWA J. 2017;38(4):456–542.

    Article  Google Scholar 

  38. Berry EW. Tertiary flora from the Rio Pichileufu, Argentina. Volume 12. Geological Society of America; 1938.

  39. Jaramillo CA, Dilcher DL. Middle Paleogene palynology of Central Colombia, South America: a study of pollen and spores from tropical latitudes; Middle Paleogene palynology of Central Colombia, South America: a study of pollen and spores from tropical latitudes. Palaeontographica Abteilung B. 2001;258(4–6):87–259.

    Article  Google Scholar 

  40. Graham A. Late Cretaceous and Cenozoic history of Latin American vegetation and terrestrial environments; 2010.

  41. Carvalho MR, Herrera FA, Jaramillo CA, Wing SL, Callejas R. Paleocene Malvaceae from northern South America and their biogeographical implications. Am J Bot. 2011;98(8):1337–55.

    Article  PubMed  Google Scholar 

  42. Rouse GE, Hopkins W, Piel K. Palynology of some late Cretaceous and early Tertiary deposits in British Columbia and adjacent Alberta. 1970.

  43. Koepfli K-P, Paten B, Scientists GKCo, O’Brien SJ. The genome 10K project: a way forward. Annu Rev Anim Biosci. 2015;3(1):57–111.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Ghazal H, Adam Y, Idrissi Azami A, Sehli S, Nyarko HN, Chaouni B, Olasehinde G, Isewon I, Adebiyi M, Ajani O. Plant genomics in Africa: present and prospects. Plant J. 2021;107(1):21–36.

    Article  CAS  PubMed  Google Scholar 

  45. Mehmood F, Shahzadi I, Waseem S, Mirza B, Ahmed I, Waheed MT. Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): comparative analyses and identification of mutational hotspots. Genomics. 2020;112(1):581–91.

    Article  PubMed  Google Scholar 

  46. Yang JY, Lee W, Pak J-H, Kim S-C. Complete chloroplast genome of Ulleung Island endemic basswood, Tilia insularis (Malvaceae), in Korea. Mitochondrial DNA Part B. 2018;3(2):605–6.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Lu Q, Luo W. The complete chloroplast genome of two Firmiana species and comparative analysis with other related species. Genetica. 2022;150(6):395–405.

    Article  CAS  PubMed  Google Scholar 

  48. Kim T-H, Ha Y-H, Setoguchi H, Choi K, Kim S-C, Kim H-J. First Record of Comparative Plastid Genome Analysis and phylogenetic relationships among Corylopsis Siebold & Zucc.(Hamamelidaceae). Genes. 2024;15(3):380.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Hu K, Sun X-Q, Chen M, Lu R-S. Low-coverage whole genome sequencing of eleven species/subspecies in Dioscorea sect. Stenophora (Dioscoreaceae): comparative plastome analyses, molecular markers development and phylogenetic inference. Front Plant Sci. 2023;14:1196176.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Palmer JD, Thompson WF. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell. 1982;29(2):537–50.

    Article  CAS  PubMed  Google Scholar 

  51. Heinhorst S, Cannon GC. DNA replication in chloroplasts. J Cell Sci. 1993;104(1):1–9.

    Article  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  53. Jiang Y, Yang J, Folk RA, Zhao J, Liu J, He Z, Peng H, Yang S, Xiang C, Yu X. Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes. BMC Plant Biol. 2024;24(1):181.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Yang H, Li X, Liu D, Chen X, Li F, Qi X, Luo Z, Wang C. Genetic diversity and population structure of the endangered medicinal plant Phellodendron amurense in China revealed by SSR markers. Biochem Syst Ecol. 2016;66:286–92.

    Article  CAS  Google Scholar 

  55. Zhang Z, Xie W, Zhao Y, Zhang J, Wang N, Ntakirutimana F, Yan J, Wang Y. EST-SSR marker development based on RNA-sequencing of E. sibiricus and its application for phylogenetic relationships analysis of seventeen Elymus species. BMC plant biology 2019, 19:1–18.

  56. Wu M, He L, Ma G, Zhang K, Yang H, Yang X. The complete chloroplast genome of Diplodiscus trichospermus and phylogenetic position of Brownlowioideae within Malvaceae. BMC Genomics. 2023;24(1):571.

  57. Bentham G. Notes on Malvaceae and Sterculiaceae. Bot J Linn Soc. 1862;6(23):97–123.

    Google Scholar 

  58. Cronquist A. An integrated system of classification of flowering plants. Columbia university; 1981.

  59. Judd WS, Manchester SR. Circumscription of Malvaceae (Malvales) as determined by a preliminary cladistic analysis of morphological, anatomical, palynological, and chemical characters. Brittonia. 1997;49:384–405.

    Article  Google Scholar 

  60. Alverson WS, Whitlock BA, Nyffeler R, Bayer C, Baum DA. Phylogeny of the core Malvales: evidence from ndhF sequence data. Am J Bot. 1999;86(10):1474–86.

    Article  CAS  PubMed  Google Scholar 

  61. Hernandez-Gutierrez R, Magallon S. The timing of Malvales evolution: incorporating its extensive fossil record to inform about lineage diversification. Mol Phylogenet Evol. 2019;140:106606.

    Article  PubMed  Google Scholar 

  62. Conover JL, Karimi N, Stenz N, Ané C, Grover CE, Skema C, Tate JA, Wolff K, Logan SA, Wendel JF. A Malvaceae mystery: a mallow maelstrom of genome multiplications and maybe misleading methods? J Integr Plant Biol. 2019;61(1):12–31.

    Article  PubMed  Google Scholar 

  63. Wang J-H, Moore MJ, Wang H, Zhu Z-X, Wang H-F. Plastome evolution and phylogenetic relationships among Malvaceae subfamilies. Gene. 2021;765:145103.

    Article  CAS  PubMed  Google Scholar 

  64. Li R, Cai J, Yang J, Zhang Z, Li D, Yu W. Plastid phylogenomics resolving phylogenetic placement and genera phylogeny of Sterculioideae (Malvaceae sl). 2022.

  65. Cvetković T, Areces-Berazain F, Hinsinger DD, Thomas DC, Wieringa JJ, Ganesan SK, Strijk JS. Phylogenomics resolves deep subfamilial relationships in Malvaceae sl. G3 2021, 11(7):jkab136.

  66. Castillo R, Fernández J-A, Gómez-Gómez L. Implications of carotenoid biosynthetic genes in apocarotenoid formation during the stigma development of Crocus sativus and its closer relatives. Plant Physiol. 2005;139(2):674–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Lv Y, Gao P, Liu S, Fang X, Zhang T, Liu T, Amanullah S, Wang X, Luan F. Genetic mapping and QTL analysis of stigma color in melon (Cucumis melo L). Front Plant Sci. 2022;13:865082.

    Article  PubMed  PubMed Central  Google Scholar 

  68. Skema C, Jourdain-Fievet L, Dubuisson J-Y, Le Péchon T. Out of Madagascar, repeatedly: the phylogenetics and biogeography of Dombeyoideae (Malvaceae sl). Mol Phylogenet Evol. 2023;182:107687.

    Article  CAS  PubMed  Google Scholar 

  69. Richardson JE, Whitlock BA, Meerow AW, Madriñán S. The age of chocolate: a diversification history of Theobroma and Malvaceae. Front Ecol Evol. 2015;3:120.

    Article  Google Scholar 

  70. Wheeler E, Lehman T. Late cretaceous woody dicots from the Aguja and Javelina Formations, Big Bend National Park, Texas, USA. Iawa J. 2000;21(1):83–120.

    Article  Google Scholar 

  71. Bowen GJ. When the world turned cold. Nature. 2007;445(7128):607–8.

    Article  CAS  PubMed  Google Scholar 

  72. Katz ME, Miller KG, Wright JD, Wade BS, Browning JV, Cramer BS, Rosenthal Y. Stepwise transition from the Eocene greenhouse to the Oligocene icehouse. Nat Geosci. 2008;1(5):329–34.

    Article  CAS  Google Scholar 

  73. Liu Z, Pagani M, Zinniker D, DeConto R, Huber M, Brinkhuis H, Shah SR, Leckie RM, Pearson A. Global cooling during the Eocene-Oligocene climate transition. Science. 2009;323(5918):1187–90.

    Article  CAS  PubMed  Google Scholar 

  74. Buerki S, Forest F, Stadler T, Alvarez N. The abrupt climate change at the eocene–oligocene boundary and the emergence of South-East Asia triggered the spread of sapindaceous lineages. Ann Botany. 2013;112(1):151–60.

    Article  Google Scholar 

  75. Liu C, Yang J, Jin L, Wang S, Yang Z, Ji Y. Plastome phylogenomics of the east Asian endemic genus Dobinea. Plant Divers. 2021;43(1):35–42.

    Article  PubMed  Google Scholar 

  76. Jamal A, Wen J, Ma Z-Y, Ahmed I, Abdullah, Chen L-Q, Nie Z-L, Liu X-Q. Comparative chloroplast genome analyses of the winter-blooming eastern Asian endemic genus Chimonanthus (Calycanthaceae) with implications for its phylogeny and diversification. Front Genet. 2021;12:709996.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Funding

This work was supported under the framework of international cooperation program managed by the National Research Foundation of Korea (NRF-2020K2A9A2A06069516), the Key Projects of the Joint Fund of the National Natural Science Foundation of China (U23A20149), the National Natural Science Foundation of China (32322006), and the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0502).

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  1. Department of Life Sciences, Gachon University, 1342, Seongnam-daero, Seongnam-si, 13120, Republic of Korea

    Joonhyung Jung, Yu Gyeom Kim & Joo-Hwan Kim

  2. State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China

    Tao Deng & Hang Sun

  3. Department of Island and Coast Biodiversity, Honam National Institute of Biological Resources, 99, Gohadoan-gil, Mokpo-si, 58762, Republic of Korea

    Changkyun Kim

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JJ and TD have contributed equally to this work. They performed the experiments, analysed the data, prepared figures and tables, and wrote the initial draft. CK and YGK collected the plant materials, designed the species sampling, and co-wrote the manuscript. HS and JHK designed the experiments and revised the manuscript. All authors agree with the content of the manuscript. All authors have contributed to the manuscript and approved the submitted version.

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Jung, J., Deng, T., Kim, Y.G. et al. Comparative phylogenomic study of East Asian endemic genus, Corchoropsis Siebold & Zucc. (Malvaceae s.l.), based on complete plastome sequences. BMC Genomics 25, 854 (2024). https://doi.org/10.1186/s12864-024-10725-0

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