Comprehensive Analysis of Chloroplast Genome of Hibiscus sinosyriacus: Evolutionary Studies in Related Species and Genera

Abstract

The Hibiscus genus of the Malvaceae family is widely distributed and has diverse applications. Hibiscus sinosyriacus is a valuable ornamental tree, but it has not been extensively researched. This study aimed to complete the chloroplast genome of H. sinosyriacus and elucidate its evolutionary relationship with closely related species and genera. The complete chloroplast genome of H. sinosyriacus was found to be 160,892 bp in length, with annotations identifying 130 genes, including 85 coding genes, 37 tRNAs, and 8 rRNAs. Interspecific variations in the Hibiscus spp. were explored, and H. sinosyriacus has species-specific single-nucleotide polymorphisms in four genes. Genome structure analysis and visualization revealed that in the Abelmoschus genus, parts of the large single-copy region, including rps19, rpl22, and rps3, have been incorporated into the inverted repeat region, leading to a duplication and an increase in the number of genes. Furthermore, within the Malvales order, the infA gene remains in some genera. Phylogenetic analysis using the whole genome and coding sequences established the phylogenetic position of H. sinosyriacus. This research has further advanced the understanding of the phylogenetic relationships of Hibiscus spp. and related genera, and the results of the structural and variation studies will be helpful for future research.

1. Introduction

The Hibiscus genus of the Malvaceae family encompasses approximately 220–250 species that are widely distributed across tropical, subtropical, and temperate climates in the form of trees, shrubs, and herbs [1]. Historically, this genus has been utilized for ornamental, culinary, and medicinal purposes [2,3]. With technological advancements and the rise of high-value industries, the applications of Hibiscus spp. have expanded to include indoor decoration, functional foods, cosmetics, and medicinal research [4,5,6,7,8]. Among the various Hibiscus species, Hibiscus sinosyriacus L. H. Bailey is a deciduous shrub native to the subtropical and tropical regions of southern China [9]. In the previous study, this species is morphologically most similar to H. syriacus, but with some differences, including broader leaves, elongated epicalyx tubes, and larger growth. Moreover, through an amplified fragment length polymorphism analysis, two species were clearly differentiated [10]. In the Republic of Korea, novel cultivars of H. syriacus have been developed by interbreeding with H. sinosyriacus to enhance their ornamental value, flower quality, and growth habit [11,12,13].

Chloroplast (cp), one of the cell organelles in plants, is integral to photosynthesis, plant immunity, and other vital biological functions, including amino acid synthesis and nitrogen metabolism [14,15]. As a symbiotic entity within cells, cp possesses ancestral genomic DNA and is predominantly maternally inherited from angiosperms [16]. The cp genome of angiosperms is highly conserved and typically presents a quadripartite structure comprising a large single-copy (LSC), a small single-copy (SSC), and a pair of inverted repeat (IR) regions [15]. Although the cp genome remains largely intact, genetic events such as insertions, deletions, rearrangements, and copy number variations have led to plant divergence and evolution [17]. Consequently, cp genomes have been used in diverse research areas, including species differentiation, evolutionary distance estimation, parameter determination, and cultivar identification [18,19,20].

The evolutionary relationship between species or genera has typically been analyzed by selecting various regions within the cp genome, such as protein-coding sequences (CDSs) and mutational hotspots. Generally, well-conserved CDS regions have been primarily used for phylogenetic classification [21]. Restricted regions showing extensive variations, such as ycf1, ycf3, and matK-trnK, known as mutational hotspots, have been emphasized more for developing markers to identify species, cultivars, or subspecies rather than for studies determining broad evolutionary relationships between genera or between species [22,23,24]. Recent studies have also focused on utilizing regions outside the CDS that are well conserved but still exhibit variations for phylogenetic analysis [25].

In this study, we aimed to elucidate the complete cp genome of H. sinosyriacus for the first time. Additionally, by comparing in-depth the genome structure and variations with its closely related species, we hope to help in future research such as marker development. Furthermore, by clarifying the phylogenetic relationship with closely related species and genera, we aimed to confirm the evolutionary position of H. sinosyriacus.

2. Materials and Methods

2.1. DNA Extraction, Sequencing, Assembly, and Annotation

Fresh leaves of H. sinosyriacus (“Melmauve”) were obtained from the Hibiscus Clonal Archive of the National Institute of Forest Science (37.15° N, 126.57° E), Suwon, Republic of Korea. Total DNA was extracted using a GeneAll^® Exgene™ Genomic DNA Purification Kit (GeneAll Biotechnology, Seoul, Republic of Korea). Next-generation sequencing library construction was performed by Macrogen (Seoul, Republic of Korea) using a TruSeq™ Nano DNA Kit (Illumina, San Diego, CA, USA). Genome sequencing was performed using a NovaSeq™ 6000 platform (Illumina). The cp genome sequence was assembled using NOVOPlasity 4.3.1, an organelle assembler based on the cp genome of H. syriacus (KR_259989), with k-mers of 27, 29, and 35 [26]. Genes, rRNAs, tRNAs annotations, and circular maps were drawn using GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html, accessed on 15 March 2023) containing annotators blatN, blatX, and Chlorom [27]. Error correction was manually conducted using Sanger sequencing, by designing primers around the nucleotides where the errors occurred.

2.2. Comparative Analyses of cp Genome Sequences

To comprehensively compare the cp sequences of the 17 species of the Malvaceae family, we used the mVISTA program. To observe the positional changes in genes at the boundaries of each compartment structure, including hibiscus and its close relatives, we used the GeSeq annotation program to identify the boundaries of each structure.

2.3. Simple Sequence Repeats (SSRs) Analysis

MISA version 2.1 was used to identify SSRs in the cp genomes of H. sinosyriacus and 16 other species, including H. syriacus, H. coccineus, H. mutabilis, H. sabdariffa, H. rosa-sinensis, H. trionum, H. cannabinus, H. taiwanensis, Gossypium gossypioides, G. herbaceum, G. hirsutum, G. raimondii, A. esculentus, A. manihot, A. moschatus, with Tilia amurensis as the outgroup [28]. The analysis was performed using parameters set at 8/mono, 3/di, 3/tri, 3/tetra, and 3/penta. Statistical analyses of average SSRs across the three genera, excluding T. amurensis, were conducted using R version 4.3.1 (The R Foundation, Vienna, Austria). To evaluate the significance among group means that did not adhere to a normal distribution, we used the non-parametric Kruskal–Wallis test [29]. Subsequently, Dunn’s test with Bonferroni correction was conducted for post hoc analysis [30].

2.4. Detection of Variants and Statistical Analyses

To compare the overall count of single-nucleotide polymorphisms (SNPs) and indels in the complete cp genomes of 16 species, using H. sinosyriacus as a reference, sequences were aligned using Clustal Omega version 1.2.4 [31]. Subsequently, the alignment results were subjected to pairwise comparison analysis using CLC main workbench version 23.0.2, to determine the gaps, differences, distances, percent identities, and identities of each species [32]. These metrics were calculated separately for the whole cp genome, CDSs, and specific regions, including LSC, IRa, SSC, and IRb. For the identification of SNPs and indels within the CDSs of nine species from the Hibiscus genus, the ClustalW alignment tool embedded in the Vector NTI Advanced 10 software was used [33]. All genes were annotated using BLAST X and Chlorom annotation engines within the GeSeq. Statistical methods were used to determine whether there were significant differences in variation across cp genomes between species and genera of the 17 species belonging to the Malvaceae family. Given that the species within each genus did not follow a normal distribution, as determined using the Shapiro–Wilk test in R version 4.3.1, we utilized the non-parametric Kruskal–Wallis test for statistical analysis. For post hoc analysis, the Dunn’s test with Bonferroni correction was applied. Two methods were used to extract samples from the 17 species. The first method utilized the pairwise averages of species within each genus, whereas the second method used H. sinosyriacus as a reference.

2.5. Phylogenetic Tree Analysis

Alignment analyses of the complete cp genomes were performed using the same species as those included in the SSR analysis—nine species of Hibiscus, including H. sinosyriacus, three species of Abelmoschus, and four species of Gossypium, with T. amurensis as the outgroup—using Clustal Omega version 1.2.4. The following are the scientific names of the plants used for phylogenetic analysis, along with their respective GenBank accession numbers: H. sinosyriacus (MZ_367751), H. syriacus (KR_259989), H. mutabilis (MK_820657), H. coccineus (OK_336487), H. sabdariffa (MZ_522720), H. rosa-sinensis (NC_042239), H. trionum (OL_628829), H. cannabinus (NC_045873), H. taiwanensis (MK_937807), A. esculentus (NC_035234), A. manihot (NC_053353), A. moschatus (NC_053355), G. gossypiodes (NC_017894), G. herbaceum (JK_317353), G. hirsutum (NC_007944), G. raimondii (NC_016668), and T. amurensis (MH_169573). Phylogenetic analyses were performed separately for each region, including the whole cp genome, LSC, SSC, IR, and CDS regions. The analysis was performed using the neighbor-joining method in the CLC genomics workbench program version 23.1, with 1000 bootstraps.

3. Results

3.1. Cp Genome Assembly and Annotation of H. sinosyriacus Genes

The assembly process utilized 121,987,386 total reads, 2,315,382 of which aligned with the reference genome; 2,300,724 of these were used for assembly, with an average organelle coverage of 2173×. The complete cp genome of H. sinosyriacus was sequenced and assembled, resulting in a circular genome 160,892 bp in length (Figure 1). This genome was then deposited in GenBank, under the accession number MZ_367751. The genome comprised four distinct regions: LSC, IRs (IRa and IRb), and SSC. The LSC region was 89,747 bp in length, the IRa and IRb regions were 25,742 bp each, and the SSC region was 19,661 bp in length. The GC content of H. sinosyriacus was 36.85%. The total annotation included 130 genes, including 85 CDSs, 37 tRNAs, and 8 rRNAs (

Table 1. Summary of the complete cp genomes of 17 species of the Malvaceae family.

	Genome Size (bp)	LSC	IRB	SSC	IRA	Number of Genes	Protein Coding Genes	tRNA	rRNA	GC Contents (%)
H. sinosyriacus	160,892	89,747	25,742	19,661	25,742	130	85	37	8	36.85
H. syriacus	161,022	89,701	25,745	19,831	25,745	130	85	37	8	36.83
H. mutabilis	160,879	89,353	26,300	18,926	26,300	130	85	37	8	36.92
H. coccineus	160,280	89,121	26,243	18,673	26,243	130	85	37	8	36.92
H. sabdariffa	162,428	90,327	26,100	19,901	26,100	130	85	37	8	36.74
H. rosa-sinensis	160,951	89,511	25,597	20,246	25,597	130	85	37	8	36.99
H. trionum	160,530	89,272	26,152	18,954	26,152	130	85	37	8	36.90
H. cannabinus	162,903	90,351	26,533	19,486	26,533	130	85	37	8	36.65
H. taiwanensis	161,056	89,538	25,419	20,680	25,419	130	85	37	8	36.89
G. gossypiodes	159,959	88,779	25,588	20,004	25,588	129	84	37	8	37.31
G. herbaceum	160,140	88,711	25,604	20,221	25,604	129	84	37	8	37.31
G. hirsutum	160,301	88,817	25,602	20,280	25,602	129	84	37	8	37.24
G. raimondii	160,161	88,654	25,651	20,205	25,651	129	84	37	8	37.31
A. esculentus	163,121	88,091	27,999	19,032	27,999	133	88	37	8	36.74
A. manihot	163,428	88,214	28,140	18,934	28,140	133	88	37	8	36.70
A. moschatus	163,430	88,263	28,118	18,931	28,118	133	88	37	8	36.71
T. amurensis	162,564	91,100	25,493	20,478	25,493	129	84	37	8	36.51

). Of the 85 CDSs, there were 12 genes in the cp genome of H. sinosyriacus: petD, petB, atpF, ycf3, ndhB, ndhA, rpoC1, rps16, rps12, rpl16, rpl2, and clpP1. Among these, ycf3 had three introns and clpP1 had two introns, whereas the remaining 10 genes contained one intron each. Among the 37 tRNAs, eight tRNAs—trnK-UUU, trnS-UCC, trnL-UAA, trnV-UAC, two copies of trnE-UUC, and two copies of trnA-UGC—each contained one intron (

Table 2. Gene contents in the cp genome of H. sinosyriacus.

Role	Group of Gene	Name of Gene	No.
Photosynthesis	Photosystem I	psaA, psaB, pasC, psaI, psaJ	5
	Photosystem II	psbA, psbK, psbI, psbM, psbD, psbF, psbC, psbH, psbJ, psbL, psbE, psbN, psbB	13
	Cytochrome b/f complex	psbT, psbZ, petN, petA, petL, petG, petD 1, petB 1	8
	ATP synthase	atpI, atpH, atpA, atpF 1, atpE, atpB	6
	Cytochrome c-type synthesis	ccsA	1
	Assembly/stability of photosystem I	ycf3(pafI) 3, ycf4(pafII)	2
	NADPH dehydrogenase	ndhB *1, ndhH, ndhA 1, ndhI, ndhG, ndhJ, ndhE, ndhF, ndhC, ndhK, ndhD	12
	Rubisco	rbcL	1
Transcription and translation	Small subunit of ribosome	rpoA, rpoC2, rpoC1 1, rpoB, rps16 1, rps2, rps14, rps4, rps18, rps12 ***1, rps11, rps8, rps3, rps19, rps7 *, rps15	18
	Large subunit of ribosome	rpl33, rpl20, rpl36, rpl14, rpl16 1, rpl22, rpl2 *1, rpl23 *, rpl32	11
	Translational initiation factor	infA	1
	Ribosomal RNA	rrn16 *, rrn4.5 *, rrn5 *, rrn23 *	8
	Transfer RNA	trnH-GUG, trnK-UUU 1, trnQ-UUG, trnS-GCU, trnS-UCC 1, trnR-UCU, trnC-GCA, trnD-GUC, trnY-GUA, trnE-UUC 1**, trnI-GGU, trnS-UGA, trnG-UCC, trnfM-CAU **, trnS-GGA, trnT-UGU, trnL-UAA 1, trnF-GAA, trnV-UAC 1, trnW-CCA, trnP-GGU, trnL-CAA *, trnV-GAC *, trnA-UGC 1*, trnR-ACG *, trnN-GUU *, trnL-UAG, trnI-CAU	37
Other	RNA processing	matK	1
	Carbon metabolism	cemA	1
	Fatty acid synthesis	accD	1
	Proteolysis	clpP1  2	1
	Component of TIC complex	ycf1	1
	Hypothetical proteins	ycf2 *	2
Total number of genes			130

¹ Contained one intron in the gene. ² Contained two introns in the gene. ³ Contained three introns in the gene. * There are two copies in the genome. ** There are three copies in the genome. *** Trans-spliced gene.

).

3.2. Comparative Structural Analysis

The positions of the genes at the boundaries of each quadripartite structure of the cp genome play a crucial role in observing insertions, deletions, and structural transformations in large frames [34,35]. The structural differences in 17 species, including 9 species of the genus Hibiscus, were analyzed to determine the gene loci at the beginning and end of the structural boundaries (Figure 2). The average sizes of the cp genomes were 161,216 bp for the Hibiscus genus, 163,326 bp for the Abelmoschus genus, 160,140 bp for the Gossypium genus, and 162,564 bp for T. amurensis. Among them, the Abelmoschus genus had the largest genome, whereas Gossypium had the smallest. The average sizes of the LSC region in the genera Hibiscus and Gossypium were 89,268 and 89,658 bp, respectively, whereas that in the genus Abelmoschus was 88,189 bp, with a difference of 1079–1469 bp. Conversely, the genus Abelmoschus exhibited an expansion in the IR region by 1849–2593 bp, compared with the other two genera, which was due to the presence of rps19, rpl22, and rps3 genes. In the LSC region, the rps19 gene (excluding the genus Abelmoschus) spanned the boundary of seven species: H. sinosyriacus, H. syriacus, H. sabdariffa, H. cannabinus, G. gosyspioides, G. herbaceum, and G. raimondii. Additionally, the rps16 gene in the three species of the Abelmoschus genus also crossed the boundary line. In contrast, there were seven species for which no genes were located across the boundary: H. mutabilis, H. coccineus, H. rosa-sinensis, H. trionum, H. taiwanensis, G. hirsutum, and T. amurensis. Notably, H. rosa-sinensis exhibited the largest distance between the gene and the boundary (103 bp). In the IRb structure, three species from the Abelmoschus genus began with the rps3 gene, whereas in the other species, the rpl2 gene appeared after the boundary with the LSC region. Within the Hibiscus genus, the end of the ycf1 fragment in H. sabdariffa was 489 bp before the start of the small SSC region, a pattern similar to that observed in the Abelmoschus genus. The ycf1 fragment of H. coccineus showed a 116 bp difference from the SSC boundary. All other ycf1 fragments of Hibiscus species crossed the SSC boundary. In most cases, the last gene of the IRa, rpl2, was located 57–137 bp before the LSC boundary, whereas in the case of the Abelmoschus genus, the rpl16 gene was present.

The GC content of H. sinosyriacus was 36.85%, and the average GC content of the genus Hibiscus was ~36.85%. The average GC content of the genus Abelmoschus was 36.72%, which was lower than that of the genus Hibiscus, whereas that of the genus Gossypium was 37.29%, which was much higher. The GC content of T. amurensis was the lowest (36.51%) (Table 1). Differences were observed in the number of genes in the cp genome among the genera. The genus Abelmoschus had three additional genes compared with other genera, as the IR region included rps19, rpl22, and rps3. Unlike other genera, the genus Abelmoschus experienced an increase in gene count owing to the incorporation of rps19, rpl22, and rps3 from the existing LSC region into the IR region, resulting in duplication. This led to a three-fold increase in the gene count. Although both synonymous and non-synonymous SNPs were observed within the infA gene of plants of the Hibiscus and Abelmoschus genera, they were well preserved within the cp genome. However, although a deletion of 7 bp within the infA gene in the Gossypium genus led to the appearance of a premature stop codon, an insertion of 11 bp resulted in a premature stop codon, confirming the loss of the infA gene in T. amurensis (Figure 3).

3.3. SSRs Analysis

The total number of SSRs in H. sinosyriacus was 686, comprising 192 mononucleotides, 408 dinucleotides, 76 trinucleotides, 6 tetranucleotides, and 4 pentanucleotides. A analysis of SSRs across 17 species, including H. sinosyriacus, revealed an average total SSR count of 692.35. The species with the highest number of SSRs was A. esculentus (748), whereas the one with the lowest was G. raimondii (633). Among these, Abelmoschus had the highest average SSR count (745.33), followed by T. amurensis (735), Hibiscus (689), and Gossypium (649.5). Notably, within the Hibiscus genus, H. rosa-sinensis had a particularly low SSR count (653). The distributions of total SSRs and monopenta-SSR motifs were not proportional across species. A. moschatus had the highest number of mononucleotide SSRs, whereas H. rosa-sinensis had the lowest. A. esculentus had the most dinucleotide SSRs, whereas G. raimondii had the least. A. manihot had the highest number of trinucleotide SSRs, whereas G. hirsutum had the lowest. With respect to the tetranucleotide SSRs, A. manihot had the highest count, whereas H. sinsyriacus, H. rosa-sinensis, and G. hirsutum had only six. T. amurensis had the highest count of pentanucleotides (11), whereas that in the other species ranged between 1 and 4. The distribution of SSRs was also analyzed according to region. SSRs in the LSC region accounted for ~63.3% of the total, whereas those in the SSC and IR regions accounted for 11.7% and ~25% of the total, respectively. The LSC region showed an SSR distribution pattern that was most similar to that of the overall genome of the 17 species, whereas the SSC region displayed a distinct pattern. In particular, H. sinosyriacus and H. syriacus had a notably higher number of SSRs than the other species, whereas pentanucleotide repeats were absent in all species. The IR regions had a distribution pattern that was more similar to the SSR distribution of the overall genome than that of the SSC region, but with a higher proportion of dinucleotides. Tetranucleotide repeats were absent in all the species, except T. amurensis (Figure 4). In the comparison of differences in the number of SSRs among the three closely related genera excluding T. amurensis, the quantity of SSRs in the Hibiscus genus was intermediate between the other two genera and showed no significant difference from them. However, there was a significant difference between Abelmoschus, which had the most SSRs, and Gossypium, which had fewer SSRs (

Table 3. Statistical analysis of variants and differences in the cp genomes of Hibiscus sinosyriacus and related species.

Variants Type	Kruskal–Wallis Test	Post hoc Analysis
	p-Value	H-G	G-A	A-H
SSRs	7.39 × 10−3 **	1.32 × 10−1	2.60 × 10−3 **	6.04 × 10−2
Identities	4.64 × 10−8 ***	9.95 × 10−7 ***	1.00	6.64 × 10−4 ***
Differences	8.52 × 10−3 **	3.56 × 10−2 *	4.42 × 10−3 **	3.24 × 10−1
Gaps	1.39 × 10−2 *	2.30 × 10−2 *	1.17 × 10−2 *	6.87 × 10−1
Gaps and differences	1.21 × 10−2 *	2.67 × 10−2 *	8.55 × 10−3 **	5.46 × 10−1

The non-parametric Kruskal–Wallis test was used to assess significance, followed by post hoc analyses using the Dunn’s test with Bonferroni correction for multiple comparisons. H, Hibiscus genus; G, Gossypium genus; A, Abelmoschus genus. *** p < 0.001, ** 0.001 ≤ p < 0.01, * 0.01 ≤ p < 0.05.

).

3.4. Comparative Sequence Identification Analysis via Visualization

The mVISTA program, which visualizes the similarity of comparative sequences, was used to understand these differences intuitively [36]. We explored the sequence variations in 17 species using H. sinosyriacus as a reference (Figure 5). Generally, sequence differences are observed more frequently in non-coding regions than in coding regions. In the non-coding regions, significant differences were observed within the intron regions of matK-atpA, atpF-atpI, rpoB-psbD, psbC-psaB, rps4-ndhJ, ndhC-atpE, atpB-rbcL, pafII-cemA, petA-psbJ, and clpP1-rpl16. These differences were predominantly distributed in the LSC region. In the coding regions, differences were frequently found within genes such as rpoC2, rpoB, pafI, ycf2, ycf1, and ndhF. In the SSC region, differences were observed between the ndhF and ccsA genes and within the intron region of ndhA. In the IR region, differences were observed between rps12 and trnV-GAC. The location of the ycf1 gene exhibited two distinct patterns across species. The first pattern showed a portion of the ycf1 gene initiated at the start of the SSC region in the forward direction, with the entire sequence of the ycf1 gene located in the reverse direction at the end of the SSC. This pattern was observed in eight species of the Hibiscus genus, excluding H. rosa-sinensis, and in three species of the Abelmoschus genus. Conversely, the second pattern, distinct from the first, lacked the partial ycf1 gene at the beginning of the SSC but contained the complete sequence in the reverse direction at the end. The latter pattern was characteristic of four species from the Gossypium genus and T. amurensis. Notably, H. rosa-sinensis deviated from the first pattern, where the species typically had an ycf1 partial sequence spanning 500–600 bp. Instead, H. rosa-sinensis replicated only a short 113 bp partial sequence at the beginning. Additionally, upon examining the sequence identity patterns, it was evident that the patterns were either grouped by genus or varied distinctly. Species-specific patterns were also observed. For instance, a unique pattern was identified between the atpF and atpH introns in H. syriacus and within the IR region between rps12 and trnV-GAC intron in H. trionum. Excluding H. syriacus, the remaining species showed similar patterns of variation; however, unique patterns were often observed, depending on the species. Notably, H. syriacus showed much less difference from H. sinosyriacus than the other species. Unlike other species, these two species can be crossbred and have flower shapes similar to those of shrubs. Noticeable differences between the two species were observed in the non-coding regions of atpF and atpH, psbZ and rps14, accD and psaI, petA and psbJ, rps18 and rpl20, rps12 and trnV-GAC, rpl32 and trnL-UAG, and so on. H. mutabilis had a different pattern of sequence similarity between atpF and atpH and trnR-ACG and trnN-GUU, as compared with the other species. H. rosa-sinensis showed large differences in the rpoC2, ycf2, and ycf1 partial genes. In terms of sequence similarity, H. sinosyriacus, H. syriacus, H. mutabilis, H. coccineus, H. sabdariffa, and H. cannabinus exhibited similar patterns.

3.5. Comparison Analysis of Pairwise Heatmap

From the pairwise analysis results of 17 species in the Malvaceae family, we confirmed that they are well grouped by genus. First, the heatmaps of whole genome, within the Hibiscus genus, the combinations of H. sinosyriacus and H. syriacus (99.72% and 2.43 × 10⁻⁴), and H. taiwanensis and H. mutabilis (99.81% and 3.23 × 10⁻⁴) showed similar values for similarity and distance, respectively. H. coccineus showed close values with H. mutabilis (97.59% and 5.01 × 10⁻³), H. trionum (96.99% and 5.47 × 10⁻³), and H. taiwanensis (97.56% and 5.20 × 10⁻³). In the Gossypium genus, G. gossypioides and G. reimondii had the closest distance of 2.79 × 10⁻³, whereas G. herbaceum and G. reimondii were the most similar (99.23%). In the Abelmoschus genus, A. manihot and A. moschatus were the closest, at 99.95% similarity. The distances between A. esculentus and A. manihot and between A. esculentus and A. moschatus were both 6.95 × 10⁻⁴. The pairwise heatmap for “Gaps and differences” on the right appeared to be proportional to the sequence similarity on the left. Following this, upon examining the heatmaps for CDS, the identity and distance in relation to CDS displayed a pattern similar to that of the whole genome. The interspecies sequence similarity did not show significant differences when compared with those of the whole genome. As CDS sequences are better conserved than non-coding sequences, the sequence similarity for most species increased. However, the similarity between the combination of H. sinosyriacus and H. syriacus was observed to decrease to 99.59%, compared with 99.72% in the whole genome (Figure 6). Upon analyzing the sequence similarity differences among the three genera, contrary to the results from the SSR analysis, there was no significant difference between the Gossypium and Abelmoschus genera. However, there was a substantial difference between these two genera and Hibiscus, with values of 9.95 × 10⁻⁷ and 6.64 × 10⁻⁴, respectively. Furthermore, in the indices for gaps and differences, there was no significant difference between Abelmoschus and Hibiscus. However, significant differences were observed in the other two combinations, Hibiscus and Gossypium (2.67 × 10⁻²) and Gossypium and Abelmoschus (8.55 × 10⁻³) (Table 3).

3.6. Exploration of Variants in the CDS of Hibiscus spp.

In this comprehensive study of the cp genome of H. sinosyriacus, we successfully assembled it for the first time and explored its evolutionary relationship with eight closely related species, by examining variations within the CDS. Using H. sinosyriacus as the reference, 130 genes were examined. Notably, 36 genes showed no variations. These genes included 28 tRNA genes (such as trnH-GUG, trnK-UUU, trnQ-UUU, trnS-GCU, trnG-UCC, trnC-GCA, trnY-GUA, trnG-UCC, trnM-CAU, trnS-GGA, trnF-GAA, trnM-CAU, trnW-CCA, trnM-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-ACG, trnN-GUU, trnL-UAG, trnN-GUU, trnR-ACG, trnA-UGC, trnL-GAU, trnV-GAC, trnL-CAA, and trnI-CAU), 2 rRNA genes (rrn5), and 6 other genes. In an analysis of variants across different species, several distinct patterns emerged. In H. sinosyriacus, species-specific SNPs were identified in the CDS regions of the matK, psbC, ndhK, and ycf2 genes, with one SNP detected for each gene, totaling four SNPs. H. syriacus had only 4 species-specific SNPs, 6 common SNPs, and 3 species-specific inserts, resulting in a total variant count of 13. H. coccineus displayed 136 species-specific SNPs, 608 common SNPs, and a combined total of 198 indels, resulting in 942 variants. Both H. mutabilis and H. taiwanensis showed 4 species-specific SNPs, 655 common SNPs, and 815 and 821 total variants, respectively. H. sabdariffa had 76 species-specific SNPs, 708 common SNPs, and 1083 variants. H. rosa-sinensis contained 326 species-specific SNPs, 311 common SNPs, and 877 variants. H. trionum had 89 species-specific SNPs, 624 common SNPs, and 927 variants. Finally, H. cannabinus had 101 species-specific SNPs, 705 common SNPs, and 1067 variants. Indel regions were identified in the following 13 genes: matK, rpoB, atpB, rbcL, rpl20, rpl23, ccsA, rpoC2, rps14, accD, ycf2, ndh5, and ycf1. Species-specific indels were observed in several genes. The gene rpoC2 exhibited a species-specific insert exclusive to H. rosa-sinensis. Similarly, rps14 exhibited a species-specific insertion in H. rosa-sinensis. The accD gene revealed species-specific indels in H. trionum and a unique insert in H. rosa-sinensis. The ycf2 gene displayed general indels with species-specific inserts in H. trionum and H. rosa-sinensis. The ndh5 gene had species-specific indels in H. sabdariffa, H. trionum, and H. rosa-sinensis. Finally, the ycf1 gene presented general indels and species-specific indels in H. syriacus, H. rosa-sinensis, and H. coccineus. The ycf1 gene is particularly notable for its extensive variation. It harbored a diverse range of indels, especially between positions 5688 and 5742 bp, and was densely populated with species-specific SNPs and indels. Intriguingly, although H. sinosyriacus and H. syriacus exhibited significant similarities, a unique indel specific to H. syriacus was identified in this region. Among the 13 genes analyzed, matK, rpoB, atpB, rbcL, rpl20, rpoC2, and rps14 were located in the LSC region, whereas accD, ccsA, ndh5, and ycf1 were located in the SSC region, and rpl23 and ycf2 were duplicated and present in the IR regions (

Table 4. Summary of variation among CDS of nine Hibiscus spp.

Name	SNP				Indels				Variants Total
	Species-Specific SNP	Common	Total SNP	Species-Specific Insert	Species-Specific Deletion	Common Insert	Common Deletion	Total Indel
H. sinosyriacus	4	–	4	–	–	–	–	–	4
H. syriacus	4	6	10	3	–	–	–	3	13
H. coccineus	136	608	744	6	18	99	75	198	942
H. mutabilis	4	655	659	–	–	87	69	156	815
H. sabdariffa	76	708	784	19	15	156	109	299	1083
H. rosa-sinensis	326	311	637	102	15	51	72	240	877
H. trionum	89	624	713	26	8	105	75	214	927
H. cannabinus	101	705	806	6	2	144	109	261	1067
H. taiwanensis	4	655	659	–	–	87	75	162	821

).

In the analysis of stop codon usage across various species, we examined the termination codons in 85 genes (Table S1). The distribution of stop codons was as follows: TAA, 55.95%; TGA, 20.78%; TAG, 23.27%. Among the nine Hibiscus spp. analyzed, variations in stop codons were observed for five genes: atpB, accD, petA, rpl16, and ccsA (

Table 5. Variation of stop codons among genes of nine Hibiscus spp.

Gene Name	H. sinosyriacus	H. syriacus	H. coccineus	H. mutabilis	H. sabdariffa	H. rosa-sinensis	H. trionum	H. cannabinus	H. taiwanensis
atpB	TGA	TGA	TGA	TGA	TAG	TGA	TGA	TAG	TGA
accD	TAG	TAG	TAG	TAG	TAG	TAG	TAA	TAG	TAG
petA	TAA	TAA	TAG	TAG	TAG	TAG	TAG	TAG	TAG
rpl16	TAG	TAG	TAA	TAG	TAG	TAG	TAG	TAG	TAG
ccsA	TGA	TGA	TGA	TGA	TGA	TAA	TGA	TGA	TGA

). Specifically, for the atpB gene, H. sabdariffa and H. cannabinus both utilized TAG, whereas the remaining seven species used TGA. In the case of the accD gene, only H. trionum had TAA, whereas the other eight species used TAG. In the case of the petA gene, both H. sinosyriacus and H. syriacus used TAA, whereas the other seven species used TAG. In the case of the rpl16 gene, H. coccineus was the only species with TAA, with TAG being prevalent in the other eight species. Finally, in the case of the ccsA gene, only H. rosa-sinensis had TAA, whereas TGA was observed in the remaining eight species. The distribution of the variations was as follows: TAG to TGA in one instance, TAA to TAG in three instances, and TAA to TGA in one instance.

3.7. Compararive Phylogenetic Analyses

We performed a comparative analysis of phylogenetic trees derived from both the whole cp genome and CDS regions (Figure 7). The results from the pairwise heatmap analysis displayed minor differences between the whole genome and CDS. However, the comparative outcomes utilizing both phylogenetic trees were almost identical. Using 17 species from four genera of the Malvaceae family, we investigated the evolutionary process of H. sinosyriacus. Among the four genera, T. amurensis, which was anticipated to have the greatest genetic distance, appropriately diverged early as an outgroup. Subsequently, the Gossypium genus differentiated earlier than the other two genera. H. sinosyriacus, H. syriacus, and H. rosa-sinensis diverged earlier from other species, with H. sinosyriacus and H. syriacus displaying a monophyletic relationship. This was followed by the divergence of H. cannabinus and H. sabdariffa, both showing a monophyletic structure. H. coccineus and H. trionum sequentially differentiated in a paraphyletic manner. The remaining species of the Hibiscus genus, H. mutabilis and H. taiwanensis, diverged with the species of the Abelmoschus genus in a monophyletic pattern.

4. Discussion

This study successfully executed the assembly of the cp genome of H. sinosyriacus, and the data obtained from this study offer profound insights into the structure and content of the cp genome of this species. Notably, the lengths and compositions of the four distinct regions of the genome—LSC, IRs (IRa and IRb), and SSC—were consistent with those of many other angiosperm cp genomes. Additionally, the number of intrinsic genes and tRNAs found in the H. sinosyriacus cp genome underscores its complexity and diversity. The number of genes containing introns and their locations can indicate the structural characteristics and evolutionary significance of the genome.

An analysis of the cp genome structure of H. sinosyriacus and other related species provides crucial information for elucidating the structural differences and features of each genome. Gene positions at the boundaries between the four distinct regions of each genome play a pivotal role in observing large-frame insertions, deletions, and structural alterations within the genome. Specifically, the genome of the genus Abelmoschus showed an increase in the number of genes owing to the expansion of the IR region and the inclusion of rps19, rpl22, and rps3. Such changes may be associated with the movement or replication of specific genes during genome evolution. Moreover, the infA gene is the most mobile cp gene known in plants, and species of the genera Gossypium and Tilia have probably repeatedly transferred the infA gene from the cp to the nucleus for functional or evolutionary reasons [37]. Additionally, as plants evolve into higher plants, the infA gene tends to disappear from the cp. Although the gene is reported to be almost absent in the Malvales order, it has been confirmed that it remains intact in the cp of many higher plants, including those in the Hibiscus and Abelmoschus genera [17].

An analysis of SSRs in the cp genomes of 17 species, including H. sinosyriacus, provides vital information for understanding the structural characteristics and evolutionary patterns of the genome. The total number and distribution of SSRs varied between species and genera. In particular, Abelmoschus had the highest average number of SSRs. Such differences may stem from the evolutionary background and structural changes in the genomes of each genus. Statistical analysis revealed significant differences in SSR distribution among the three genera, interpreted as reflecting the evolutionary characteristics and genomic structural variability of each genus. In particular, the differences between Abelmoschus and Gossypium may be related to the evolutionary distance between the two genera. These findings offer valuable insights into plant evolution and diversity through SSR analyses of the cp genome.

Visualization analysis using the mVISTA program clearly delineated the cp genome sequence differences among 17 species, including H. sinosyriacus. Generally, sequence differences are observed more frequently in non-coding regions than in coding regions. In particular, the differences in the LSC region were noteworthy. In the coding regions, differences were frequently observed within specific genes, potentially reflecting evolutionary differences between species. Additionally, the position of the ycf1 gene exhibited two distinct patterns depending on the species. These differences in pattern may be related to the evolutionary background [22]. The similarities between H. sinosyriacus and H. syriacus align with the fact that the two species can be interbred and have similar flower morphologies. Furthermore, the unique sequence similarity patterns observed only in specific species may indicate a unique evolutionary background of this species.

Through a pairwise heatmap analysis of the overall identity and distance of the cp genome, clear genetic differences among the three genera, Hibiscus, Gossypium, and Abelmoschus, were identified. Color-coded clustering facilitates an intuitive understanding of sequence similarities and differences between species. Specifically, the Hibiscus genus showed significant genetic differences in most regions, compared with the other two genera. However, no significant differences were observed between Abelmoschus and Gossypium. These findings suggest that the Hibiscus genus may have unique evolutionary characteristics compared to the other two genera.

By studying the cp genome of H. sinosyriacus, evolutionary relationships with eight species were successfully explored, focusing on variations within the CDS. In this study, 130 genes were reviewed, with no variations found in 36 genes. These results suggested that certain genes maintained stable characteristics throughout the evolutionary process. Several unique patterns emerged in the analysis of variation among various species. Notably, a high similarity was observed between H. syriacus and H. sinosyriacus, but species-specific indels were found in H. syriacus. These results indicated that despite the close relationship between the two species, each has unique evolutionary characteristics. Additionally, species-specific indels were observed in each species, especially in the ycf1 gene, where various indels, as well as species-specific SNPs and indels, were densely distributed. These results indicated that the ycf1 gene underwent various mutations during the evolutionary process. An extensive analysis of stop codon usage confirmed the distributions of TAA, TGA, and TAG. For specific genes, there were species-specific differences in stop codon usage, which might be related to the genetic characteristics [38].

In this study, the comparative analysis of the phylogenetic tree based on the whole cp genome and the CDS region provides a crucial key to deeply understanding the evolutionary relationships among species within the Malvaceae family. The subtle differences in the pairwise heatmap analysis between the whole genome and the CDS region offer significant insights into how information is extracted from various parts of the genome. The early branching and interspecific relationships within the genera Gossypium and Hibiscus clarify the evolutionary characteristics and timeline of these genera. In particular, the close relationship between H. sinosyriacus and H. syriacus suggests that these two species share a common recent ancestor and are evolutionarily proximate. Additionally, the classification of T. amurensis emphasizes how this species is evolutionarily unique compared with other species.

5. Conclusions

This study offers foundational insights into the structure and function of the H. sinosyriacus cp genome and establishes a basis for more in-depth research on its evolutionary position. We provide a comprehensive understanding of the cp genome structure of H. sinosyriacus and related species, whereas emphasizing the significance of gene positions within their respective boundaries. These structural variations and gene placements reflect the evolutionary traits and adaptations of each species. Such data are pivotal for phylogenetic and evolutionary studies of these taxa. Our findings shed light on the genetic relationships and evolutionary nuances of species within the Hibiscus genus. The numerous species-specific variations and characteristics identified through interspecific variation analysis will be useful for distinguishing species and developing various markers in the future. This study underscores the significance of the cp genome in understanding plant evolution and offers a foundation for future research in the Malvaceae family.