Abstract
To investigate the mitochondrial genome characteristics and evolutionary dynamics of Lagerstroemia suprareticulata, we performed complete assembly and annotation of its mitochondrial genome, followed by comparative genomic analyses with related species. This research presents the initial comprehensive mitogenome of L. suprareticulata, a 364,645 bp independent single cyclic structure with a whole average GC content of 46.20%, twice the size of the chloroplast genome and an approximately similar tetrad structure. It comprised 62 functional genes and 386 open reading frames. Besides two long repeats above 800 bp, simple sequence repeat analysis revealed a predominance of mono-nucleotide and tetra-nucleotide repeats, which is consistent with patterns observed in most Lythraceae species. A total of 480 C-to-U RNA editing sites were predicted in 36 protein-coding genes, with the highest number in nad4. AUG and UGG had a relative synonymous codon usage value of 1, while GCU had the highest RSCU (1.62). ccmB and rps4 may have undergone positive selection, whereas atp8 and cox1 experienced strong purifying selection. Phylogenetic analysis based on mitochondrial and chloroplast genomes confirmed a close relationship between L. suprareticulata and L. indica. Collinear segments decreased with increasing evolutionary distance, and gene rearrangement analysis revealed a lineage-specific gene arrangement pattern in Lagerstroemia. Homologous sequence analysis identified 34 mitochondrial-chloroplast homologous sequences (accounting for 4.63% of the mitochondrial genome) and 2182 mitochondrial-nuclear homologous sequences. These results provide a foundation for understanding the mitochondrial genome evolution of Lagerstroemia and Lythraceae, and may offer valuable genetic resources for horticultural and evolutionary studies.
Introduction
Lagerstroemia constitutes a genus of angiosperms that has garnered substantial scholarly and practical attention within horticultural and ecological research paradigms (Fang et al., 2019; Zhou et al., 2023b; Qiao et al., 2025). Characterized by their vibrant, prolonged floral displays, extensive cultivar diversity, and adaptability to heterogeneous climatic regimens, these taxa have emerged as foundational elements in landscape architecture, urban afforestation initiatives, and ornamental horticultural practices globally (Yue et al., 2024, 2025). Beyond their aesthetic utility, Lagerstroemia species fulfill critical ecological functionalities, contributing to biodiversity maintenance, edaphic stabilization, and the provisioning of niches and trophic resources for pollinators and faunal communities (Adhikari et al., 2019). Furthermore, select species within the genus have been subjected to phytochemical and stress physiology investigations, underscoring their potential as reservoirs for pharmaceutical compounds and stress-resistant genetic determinants, thereby holding significance for agricultural biotechnology and pharmacognosy research (Yu et al., 2022). L. suprareticulata, a deciduous tree or shrub in this family. It is endemic to the southwestern region of Guangxi, China, listed as endangered level in the Threatened Species List of China’s Higher Plants. This species flourishes in limestone regions, demonstrating potential for use in the greening of rocky mountains and ecological rehabilitation. Additionally, it bears fragrant blossoms, an uncommon feature within the Lagerstroemia genus (Zhou et al., 2023a).
Mitochondria, often designated as the “cellular powerhouses,” are indispensable organelles primarily responsible for adenosine triphosphate (ATP) synthesis via oxidative phosphorylation (Meyer et al., 2019; Carillo and Ferrante, 2025; Wang et al., 2025). However, their biological significance transcends energetic metabolism, as mitochondrial genomes (mitogenomes) exhibit extraordinary structural complexity and evolutionary plasticity (Wu et al., 2022). These genomic features—encompassing large molecular size, frequent intragenomic rearrangements, expansive intergenic regions, and recurrent horizontal gene transfer events-distinguish them from the relatively conserved nuclear and plastid genomes (Zhou et al., 2023c). Such unique attributes render mitogenomes invaluable substrates for investigating evolutionary processes, including species identification, speciation mechanisms, adaptive divergence, and phylogenetic reconstruction (Chen et al., 2017; Najer et al., 2024). Recent advancements in high-throughput sequencing technologies have catalyzed a paradigm shift in organelle genomics, facilitating the rapid and cost-efficient de novo assembly and annotation of mitogenomes across a broad spectrum of plant lineages (Zou et al., 2025). This technological progression has precipitated a proliferation of comparative mitogenomic analyses, which have elucidated evolutionary patterns and mechanistic processes governing genome diversification (Wang et al., 2024). Nevertheless, despite the accumulating body of knowledge, mitogenomic characterization remains conspicuously limited for numerous plant genera, including Lagerstroemia. To date, only fragmented sequence data and incomplete assemblies have been reported for a handful of Lagerstroemia species, impeding comprehensive elucidation of the genus’ mitogenomic architecture, genetic variability, and evolutionary trajectory.
Given the confluence of ecological, horticultural, and scientific imperatives associated with Lagerstroemia, a comprehensive mitogenomic analysis represents a critical knowledge gap requiring redress. Such an investigation would not only augment the broader framework of plant mitogenomics but also yield mechanistic insights into evolutionary dynamics within the genus and its phylogenetic relationships with cognate taxa (Van de Paer et al., 2017). Specifically, de novo characterization of complete Lagerstroemia mitogenomes would enable the systematic identification of coding sequences, repetitive elements, and structural variants—fundamental components for deciphering mitochondrial functional biology, inheritance mechanisms, and evolutionary trajectories. Furthermore, comparative mitogenomic analyses between Lagerstroemia and related genera within the Lythraceae could reveal conserved and divergent patterns of genome evolution, including gene gain/loss events and rearrangement dynamics, thereby refining phylogenetic resolutions within the family (Wang et al., 2023). This, in turn, would contribute to the development of robust evolutionary frameworks for interpreting angiosperm diversification. Additionally, mitogenomic investigations may yield practical applications in horticultural science, such as the identification of molecular markers for marker-assisted selection programs targeting stress tolerance or ornamental trait enhancement. In the present study, we aim to generate, assemble, and annotate the complete mitogenome of Lagerstroemia suprareticulata. Through detailed analyses of genomic architecture, gene content, and sequence polymorphism, we seek to address the following research objectives: (1) What are the defining features of the Lagerstroemia mitogenome, including size, gene repertoire, and organizational structure? (2) What classes of repetitive sequences and structural variants are present, and how do they contribute to genomic complexity? (3) What phylogenetic insights can be derived from mitogenomic data regarding the placement of Lagerstroemia within the Lythraceae? By addressing these objectives, this research endeavors to advance our understanding of Lagerstroemia evolutionary biology and provide a foundational resource for future investigations in plant mitogenomics, phylogenetics, and horticultural biotechnology.
Results
L. suprareticulata mitochondrial complete genome assembly and annotation
The mitochondrial genome of L. suprareticulata is a single circular molecule 364,645 bp in length, with a base composition of A (26.72%), T (27.08%), C (22.93%), and G (23.28%). The GC content of the entire mitochondrial genome is 46.20% (Figure 1). Both genome size and GC content are similar to those of Punica granatum mitochondrial genome, which belongs to the same family. A total of 62 genes were located and annotated in this mitochondrial genome, with the vast majority of the sequence consisting of intergenic regions, and gene sequences accounting for only a small proportion. Among the 62 functional genes, there are 3 rRNA genes (4.84%), 21 tRNA genes (33.87%), and 38 protein-coding genes (61.29%). These 38 protein-coding genes can be further classified into 10 functional categories. With the exception of the sdh4 gene (two copies), all other genes in the L.suprareticulata mitochondrial genome were present in single copy. Furthermore, 386 open reading frames (ORFs) were identified, comprising 191 on the forward strand and 195 on the reverse strand. Among these, 50 ORFs are longer than 300 bp. Repeat event analysis of the L.suprareticulata mitochondrial genome identified 60 repeat sequences longer than 100 bp, with the two long repeat over 500 bp, being 888 bp and 889 bp, two middle repeat, being 463 bp, respectively (Figure 2).
Figure 1
Figure 2
Comparison of simple sequence repeats in L. suprareticulata and its related species
The simple sequence repeats (mtSSRs) in the mitochondrial genomes of five species within Lythraceae were identified and compared (Figure 3). The results showed that the mtSSRs were dominated by mono-nucleotide and tetra-nucleotide repeats. This characteristic was also observed in most of the analyzed mitochondrial genomes. Specifically, the number of mono-nucleotide repeats was 42, which was only lower than that of P. granatum but much higher than those of species in the genus Trapa and the congeneric Lagerstroemia indica. The number of tetra-nucleotide repeats was 36, which was comparable to that of P. granatum and significantly higher than those of Trapa species and L. indica. Its dinucleotide repeats were comparable to those of most species, while the abundances of penta-nucleotide and hexa-nucleotide repeats were extremely low, this result consisted with that in other species.
Figure 3
Codon preference and RNA editing sites of L. suprareticulata
Using the default settings of Deepred-Mt software, a total of 480 potential RNA editing sites were identified in the mitochondrial genome of L. suprareticulata(Figure 4). All edits were of the C-to-U type and were distributed in 36 mitochondrial protein-coding genes. Among them, the nad4 gene contained the largest number of RNA editing sites (41), followed by the ccmB gene with 30 sites. Notably, no predicted RNA editing sites were detected in the mitochondrial rpl2 gene. Analysis of the codon usage bias of mitochondrial protein-coding genes revealed that only the relative synonymous codon usage (RSCU) values of AUG (methionine) and UGG (tryptophan) were 1, while the RSCU values of all other codons were greater than 1. Among these, GCU had the highest RSCU value (1.62), followed by CAU (1.53). In contrast, the RSCU values of GCG and CAG were both less than 0.5, indicating their relatively low codon usage frequencies.
Figure 4
Analysis of genetic variations in L. suprareticulata
The Ka/Ks values were calculated based on 15 PCGs shared by all selected plants. As shown (Figure 5), the Ka/Ks ratios of the ccmB and rps4 genes in four species of the Lythraceae family (Punica granatum, Trapa incisa, Trapa bicornis, and Lagerstroemia indica) exceeded 1. The Ka/Ks ratios of most other genes were relatively low (approximately 0.2 to 1.0), they might have undergone a purifying selection that the ccmB and rps4 genes may exhibit unique stress resistance when facing selective pressure. On the contrary, the average Ka/Ks values of atp8 and cox1 were the lowest among all genes (about 0.2), indicating a most obvious purifying selection for these genes. They have shown extremely high conservation during the evolution of PCGs in the plant mitochondrial genome.
Figure 5
Phylogenetic evolution and sequence collinearity
Phylogenetic trees were constructed for the mitochondrial and chloroplast genomes of 38 species representing diverse taxonomic positions, with Aglaia odorata set as the outgroup (Figure 6). The resulting tree indicated a close evolutionary relationship between L. suprareticulata and L. indica, both belonging to the same genus. The phylogenies inferred from chloroplast and mitochondrial genomes were largely congruent and aligned with the established evolutionary relationships among angiosperm species. Nevertheless, subtle discrepancies in the internal relationships of Brassicaceae species were found between the trees inferred from mitochondrial and chloroplast data. These inconsistencies may stem from incomplete lineage sorting, where differences in evolutionary rate and sequence conservation across genomic regions lead to inferred phylogenies that do not fully reflect the actual evolutionary relationships.
Figure 6
To explore collinearity across species from different phylogenetic positions, we also performed a comparative analysis of mitochondrial genomes from nine species, including L. suprareticulata (Figure 7). The dataset included Trapa incisa, L. indica, Trapa bicornis, Punica granatum, and L. suprareticulata from Lythraceae; Rhodomyrtus tomentosa from Myrtaceae; Gossypium arboreum from Malvaceae; Vatica mangachapoi from Dipterocarpaceae; and Sapindus mukorossi from Sapindaceae. The analysis revealed that L. suprareticulata exhibited collinear segments with all the selected species, but these blocks were mostly short. Among these species, L. suprareticulata displayed the strongest collinearity with L. indica, a species from the same genus, with the most collinear blocks identified. Fewer collinear fragments were detected between L. suprareticulata and the more distantly related species. The decreasing number of collinear segments with increasing evolutionary distance indicates a high level of mitochondrial genome variation across species.
Figure 7
Gene rearrangement in L. suprareticulata and Lythraceae species
Mitochondrial genome structures exhibit substantial divergence across species, resulting in widespread gene rearrangement phenomena. We compared the gene arrangement pattern of the L. suprareticulata mitochondrial genome with four species from the Lythraceae family (P. granatum, T. incisa, T. bicornis, L. indica) and four other Magnoliopsida plants (S. mukorossi, V. mangachapoi, G. arboreum, and R. tomentosa) (Figure 8). The results reveal significant interspecific variation in the arrangement of the COX3-ATP8 segment. This region is relatively conserved in S. mukorossi, V. mangachapoi, P. granatum, and T. bicornis, whereas in the genus Lagerstroemia, a distinct NAD4-ATP8-COX3-NAD4L arrangement pattern is observed, accompanied by an inversion in two species. The CYTB-NAD3-ATP6 arrangement pattern remains relatively consistent among the closely related species T. incisa, T. bicornis, L. suprareticulata, and L. indica, although inversion or translocation events have occurred during evolution. These differences indicate that species-specific gene rearrangements have occurred in the mitochondrial genomes of Lythraceae plants during evolution. Furthermore, the detailed variations in gene arrangement patterns among different species within the family (such as between L. suprareticulata and L. indica) further reflect the dynamic and diverse nature of mitochondrial genome evolution.
Figure 8
Homologous sequence analysis between the mitochondrial and chloroplast genomes of L. suprareticulata
When comparing the mitochondrial and chloroplast genomes of L. suprareticulata, we identified 34 homologous sequences (Figure 9A), with a total length of 16,866 bp, accounting for 4.63% of the mitochondrial genome. Among these, homologous sequences of lower than 100 bp were the most abundant, totaling 14, followed by sequences of 1001–2000 bp, which amounted to eight (Figure 9B). The longest sequence was 1,485 bp, while the shortest was 33 bp. In addition, a total of seven homologous sequences were detected in the mitochondrial genome. Through comparison between the mitochondrial and nuclear genomes, we identified 2,182 homologous sequences, with a total length of 230,716 bp (Figure 9C). Among these, sequences of 51–100 bp were the most numerous, totaling 943, followed by sequences of 30–50 bp, which amounted to 829 (Figure 9D).
Figure 9
Discussion
The structure and function of plant mitochondrial genomes have always been the core difficulties in current research. The structural organization of the Lagerstroemia mitogenome exhibits both conserved and lineage, its specific characteristics are relative to known angiosperm mitogenomes (Hu et al., 2023). Its size, which falls within the range observed for most dicotyledonous plants, is primarily driven by expansive intergenic regions and the presence of repetitive sequences, these features align with the general trend of plant mitogenome gigantism and complexity (Wu et al., 2022). Notably, the identification of multiple large inverted repeats and tandem repeat clusters within the Lagerstroemia mitogenome suggests that recombination-mediated rearrangements may play a pivotal role in genome plasticity, as has been documented in other plant groups (Ma et al., 2022; Sanchez-Puerta et al., 2023; Huang et al., 2025). Such structural variations could contribute to phenotypic diversity and adaptive responses to environmental stress, a hypothesis warranting further functional validation. Sloan et al. in their work on plant mitochondrial genome diversity emphasized the significance of repeat-mediated recombination in driving genomic changes (Sloan et al., 2012). These rearrangements have been associated with various aspects of plant evolution, and in the case of Lagerstroemia, could potentially be linked to its adaptation to different ecological niches.
Gene content analysis revealed a core set of mitochondrial genes conserved across angiosperms, including those encoding subunits of the respiratory chain complexes and ribosomal RNAs (Fučíková et al., 2014). However, the presence of several lineage-specific gene losses and pseudogenization events distinguishes the Lagerstroemia mitogenome from its relatives in the Lythraceae. For instance, the loss of rpl3 and truncation of sdh3 observed in our assembly mirror patterns reported in certain genera of the Myrtales, suggesting convergent evolutionary pressures on mitochondrial gene repertoires (Wang et al., 2021; Yu et al., 2024). These gene losses may reflect functional redundancy or compensation by nuclear-encoded homologs, highlighting the dynamic interplay between mitochondrial and nuclear genomes in maintaining cellular homeostasis (Adams et al., 2002). The evolution of mitochondrial gene content in plants and gene losses can occur independently in different lineages due to various evolutionary forces. In the context of Lagerstroemia, these losses might have been influenced by its unique evolutionary history and the functional requirements of its mitochondria (Wang et al., 2023).
Comparative mitogenomic analyses with related taxa within the Lythraceae and outgroups provide compelling evidence for distinct evolutionary trajectories. The high degree of sequence divergence in non-coding regions, coupled with conserved synteny of core genes, supports the notion that plant mitogenomes evolve through a combination of stabilizing selection on essential loci and rapid drift in intergenic regions (Cao et al., 2023; Xu et al., 2023). Phylogenetic reconstructions based on concatenated mitochondrial gene sequences robustly place Lagerstroemia within the Lythraceae, resolving ambiguities in previous nuclear and plastid-based phylogenies. The mitogenomic tree topology aligns with morphological classifications but reveals a closer relationship with Punica granatum than previously inferred (Feng et al., 2023), suggesting that mitochondrial markers may provide complementary phylogenetic signals for resolving deep divergences in this clade (Liu et al., 2012; Grosser et al., 2023). Wolfe et al. reported the concept of differential evolution in mitochondrial genomes, with essential genes being under strong selection and non-coding regions evolving more freely (Wolfe et al., 1987). This concept has been widely accepted and applied in understanding the evolutionary patterns of various plant groups, including Lagerstroemia.
Mitochondrial SSR (Simple Sequence Repeat) markers, leveraging their maternal inheritance and moderate polymorphism, hold unique value in plant genetic research (de Freitas et al., 2021). They facilitate the elucidation of maternal population dispersal routes (e.g., tracking southward dispersal along the Alps in Norway spruce), precise identification of crop cytoplasmic male sterility (CMS) lines, and discrimination of closely related species/varieties (e.g., differentiating L. suprareticulata from L. indica in the Lagerstroemia genus(Figure 3)). Moreover, the abundance of mtSSRs varies among plant groups (higher in monocots like rice than in dicots like Lagerstroemia), repeat type preferences (mononucleotide repeats dominate in angiosperms, while dinucleotide repeats are prevalent in bryophytes), and polymorphism levels (higher in woody plants like pine than in herbaceous plants like wheat). Therefore, their functional positioning and group-specific characteristics must be clearly defined in accordance with research objectives when applied.
Repetitive sequences, including tandem repeats and transposable element-like fragments constitute a significant portion of the Lagerstroemia mitogenome, consistent with their role as drivers of genome expansion and rearrangement (Goremykin et al., 2012). The identification of conserved repeat motifs shared with other Lythraceae species suggests ancestral origins, while lineage-specific repeats may have emerged through de novo evolution or horizontal transfer (Wu et al., 2015). Horizontal gene transfer (HGT) events (Stegemann et al., 2003, 2012), remain a plausible mechanism for introducing foreign DNA into the Lagerstroemia mitogenome, as observed in numerous plant lineages. Future investigations utilizing long-read sequencing and comparative genomics across Lagerstroemia species may uncover evidence of HGT and its impact on genome evolution.
Materials and methods
Plant materials and assembly sequence collection
L. suprareticulata were collected and planted in Nanning City, Guangxi, China (Lat. 22.921932° N, Lon.108.353726° E), the process of plant collection and propagation strictly complies with local government regulations, and no destructive collection has been made on the plants themselves. All the voucher specimens were kept by the local laboratory, and can be obtained with the accession number (Holotype: 2025LS0001, isotype: 2025LS0002). Fresh L. suprareticulata samples including leaves stems and flowers were collected from a propagate three-year-old seedlings by cuttings. (May 2022 to October 2023). All the sequenced materials, tender leaves, were surface-cleaned by 70% alcohol to remove dirt and debris. Then they were rapidly frozen in liquid nitrogen for next experiments. High-molecular-weight genomic DNA was isolated from target samples using a modified CTAB method, with residual RNA removed by RNase A digestion. The quantity and integrity of purified DNA were assessed using both of the Qubit fluorometer and agarose gel electrophoresis. Only DNA samples around 10kb were used for subsequent library preparation. SMRTbell template libraries were constructed following the manufacturer’s standard protocol for PacBio HiFi sequencing. After damage repair, end-prep and adapter ligation, the libraries were subjected to primer annealing and polymerase binding. Sequencing was conducted on a PacBio Sequel II/IIe system, and circular consensus sequencing (CCS) was applied to generate highly accurate HiFi reads. Raw sequencing data were processed using official PacBio bioinformatics pipelines to remove low-quality reads and adapters, yielding clean HiFi reads for further bioinformatic analysis.
The direct mitochondrial genome assembly and gene annotation
The mitogenome was assembled by two approaches to guarantee accuracy. Initially, the PMAT was used for first mitogenome assembly, with the settings as ‘-st HiFi -g 300M’ (Bi et al., 2024). The second assembly was performed using Canu with default parameters (Koren et al., 2017). The two data were compared by minimap2, the final assembly was confirmed through comparison. For the convenience of description, we processed mitogenome into a linear molecule by utilizing bandage v 0.8.1 (Wick et al., 2015) to expand the common snippets. The mitogenomes were annotated using the web-based tool PMGA (www.lkmpg.cn/mgavas). Subsequently, the tRNA and rRNA genes were further examined using BLASTn, respectively. We also assembled the chloroplast genome of L. suprareticulata and annotated it with CPGAVAS2 (http://47.96.249.172:16019/analyzer/home) to obtain gbf files (Shi et al., 2019). The final graphs were manually checked.
SSR site and repeat fragment detection
Simple sequence repeats (SSRs) were fast calculated by the MISA online platform (https://webblast.ipk-gatersleben.de/misa/) (Beier et al., 2017). The specified parameters were same as the previous research (Zhou et al., 2023c), encompassing mono-, di-, tri-, tetra-, penta- and hexa-nucleotides with a minimum occurrence of 10, 5, 4, 3, 3 and 3, respectively. Dispersed repeat was calculated based on a local BLAST (Altschul et al., 1990), and a cutoff of e-value 1-e-5 was applied. Links for repeat sequences were visualized in TBtools functions (Chen et al., 2023).
RSCU in codons, RNA editing sites and Ka/Ks analysis
The synonymous codons (RSCU) were calculated by Phylosuite function (Zhang et al., 2020) by default parameters. PREPACT3.0 was used to predict the RNA editing sites of PCGs in the mitochondrial genomes. The threshold was established at 0.8 to minimize the similarity score in the plagiarism detector. Using TBtools Ka/Ks calculator function, we calculated the synonymous mutation rates, non-synonymous mutation rates, and their ratios (Ka/Ks).
Phylogenetic tree construction for species with L. suprareticulata and comparative analysis
The other mitochondrial genomes except L. suprareticulata were retrieved and downloaded from NCBI for further comparison, data were obtained by April 2024 (37 species including 11 in Myrtales: Trapa incisa NC_086691, Lagerstroemia indica NC_035616, Trapa bicornis NC_086690, Punica granatum NC_071229, Rhodomyrtus tomentosa NC_071968, Melaleuca alternifolia PP533606, Eucalyptus camaldulensis NC_085240, Eucalyptus grandis NC_040010, Syzygium samarangense OQ701348, Psidium guajava PP934632, Eucalyptus rudis PP920092; 6 in Malvales: Tilia amurensis PQ072837, Gossypium arboreum KR736342, Vatica mangachapoi PP861159, Microcos paniculata NC_086687, Gossypium trilobum NC_035076, Hibiscus cannabinus NC_035549; 8 in Sapindales: Sapindus mukorossi NC_050850, Xanthoceras sorbifolium MK333231, Aglaia odorata NC_084341, Melicope pteleifolia PQ221923, Citrus medica PQ636878, Toona fargesii PQ287271, Nephelium lappaceum PP916047, Litchi chinensis PP932631, Limonia acidissima NC_086955; 8 in Brassicales: Brassica rapa NC_049892, Lepidium apetalum NC_088489, Crucihimalaya lasiocarpa NC_085700, Malcolmia africana OQ784930, Arabidopsis lyrata OQ852786, Brassica nigra NC_029182, Camelina sativa PQ165104, Rorippa indica, PP780168; 4 in Fagales: Castanopsis carlesii PP853255, Fagus sylvatica MW771358, Morella rubra PP533608, Lithocarpus litseifolius NC_065018). To ascertain the phylogenetic location and conflict of the PCGs of selected species were extracted and conserved mitochondrial and chloroplast PCGs were screened for tree building, respectively. After alignment and trimming, a maximum likelihood (ML) method was chosen in IQ-TREE to make the basic tree structure (Minh et al., 2020), based on a default nucleotide replacement model with 1000 self-developing values. The final visualization of the phylogenetic tree was achieved through iTOL software (Letunic and Bork, 2024).
Conclusions
The complete assembly and annotation of the L. suprareticulata mitogenome presented herein represent a significant advancement in the understanding of mitochondrial genome evolution within the Lythraceae and broader angiosperm lineages. For the first time, our study provides a comprehensive characterization of L. suprareticulata mitogenome. From a practical perspective, the mitogenomic resources generated in this study offer valuable tools for horticultural research and breeding. The identification of polymorphic regions and repetitive elements provides potential molecular markers for germplasm characterization, hybrid authentication, and marker assisted selection. Additionally, insights into mitochondrial - nuclear interactions may inform strategies for enhancing stress tolerance. In conclusion, the L. suprareticulata mitogenome revealed novel insights into structure, evolution, and phylogenetic significance. The findings underscore the dynamic nature of plant mitochondrial genomes and their utility in addressing fundamental questions in evolutionary biology and horticulture. By establishing a foundation for future research, this work contributes to our broader understanding of angiosperm mitogenomics and enhances the practical toolkit for Lagerstroemia conservation and improvement.
Statements
Data availability statement
The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author.
Author contributions
BQ: Conceptualization, Supervision, Writing – review & editing, Methodology, Validation, Writing – original draft, Data curation. XH: Writing – review & editing, Writing – original draft, Data curation, Validation. RJ: Writing – original draft, Writing – review & editing, Data curation. YH: Data curation, Writing – original draft, Resources. KS: Data curation, Writing – original draft, Resources. JL: Writing – original draft, Validation. GZ: Writing – review & editing, Supervision, Data curation, Methodology, Conceptualization, Writing – original draft.
Funding
The author(s) declared that financial support was received for this work and/or its publication. The authors are grateful for financial support from the Fundamental Research Funds for Guangxi Forestry Research Institute under Grant No. 202303 and the Guangxi Key Research and Development Program under Grant No. GuikeAB25069136.
Conflict of interest
The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
The reviewer HP declared a shared affiliation with the author(s) GZ to the handling editor at the time of review.
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The author(s) declared that generative AI was not used in the creation of this manuscript.
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Supplementary material
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fpls.2026.1746941/full#supplementary-material
References
1
AdamsK. L.QiuY. L.StoutemyerM.PalmerJ. D. (2002). Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc. Natl. Acad. Sci. United. States America99, 9905–9912. doi: 10.1073/pnas.042694899
2
AdhikariD.TiwaryR.SinghP. P.UpadhayaK.SinghB.HaridasanK. E.et al. (2019). Ecological niche modeling as a cumulative environmental impact assessment tool for biodiversity assessment and conservation planning: A case study of critically endangered plant Lagerstroemia minuticarpa in the Indian Eastern Himalaya. J. Environ. Manage.243, 299–307. doi: 10.1016/j.jenvman.2019.05.036
3
AltschulS. F.GishW.MillerW.MyersE. W.LipmanD. J. (1990). Basic local alignment search tool. J. Mol. Biol.215, 403–410. doi: 10.1006/jmbi.1990.9999
4
BeierS.ThielT.MünchT.ScholzU.MascherM. (2017). MISA-web: a web server for microsatellite prediction. Bioinformatics33, 2583–2585. doi: 10.1093/bioinformatics/btx198
5
BiC. W.ShenF.HanF. C.QuY. S.HouJ.XuK. W.et al. (2024). PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data. Horticult. Res.11. doi: 10.1093/hr/uhae023
6
CaoY.YinD. P.PangB.LiH. B.LiuQ.ZhaiY. F.et al. (2023). Assembly and phylogenetic analysis of the mitochondrial genome of endangered medicinal plant Huperzia crispata. Funct. Integr. Genomics23. doi: 10.1007/s10142-023-01223-9
7
CarilloP.FerranteA. (2025). Decoding the intricate metabolic and biochemical changes in plant senescence: a focus on chloroplasts and mitochondria. Ann. Botany, 113. doi: 10.1093/aob/mcaf003
8
ChenC.WuY.LiJ.WangX.ZengZ.XuJ.et al. (2023). TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining. Mol. Plant16, 1733–1742. doi: 10.1016/j.molp.2023.09.010
9
ChenZ.ZhaoN.LiS.GroverC. E.NieH.WendelJ. F.et al. (2017). Plant mitochondrial genome evolution and cytoplasmic male sterility. Crit. Rev. Plant Sci.36, 55–69. doi: 10.1080/07352689.2017.1327762
10
de FreitasK. E. J.BusanelloC.VianaV. E.PegoraroC.de Carvalho VictoriaF.da MaiaL. C.et al. (2021). An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants? Funct. Integr. Genomics22, 35–53. doi: 10.1007/s10142-021-00815-7
11
FangM.MeilanL.HuaxinW.MaoL.QingT.JinhuaL.et al. (2019). Analysis on factors affecting rooting of lagerstroemia speciosa. Guangxi. Forestry. Sci.48, 4. doi: 10.19692/j.cnki.gfs.2019.04.018
12
FengL. J.WangZ. H.WangC. Z.YangX. M.AnM. M.YinY. L. (2023). Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes. BMC Plant Biol.23. doi: 10.1186/s12870-023-04538-8
13
FučíkováK.LewisP. O.González-HalphenD.LewisL. A. (2014). Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of sphaeropleales (Chlorophyta). Genome Biol. Evol.6, 2170–2180. doi: 10.1093/gbe/evu172
14
GoremykinV. V.LockhartP. J.ViolaR.VelascoR. (2012). The mitochondrial genome of Malus domestica and the import-driven hypothesis of mitochondrial genome expansion in seed plants. Plant J.71, 615–626. doi: 10.1111/j.1365-313X.2012.05014.x
15
GrosserM. R.SitesS. K.MurataM. M.LopezY.ChamuscoK. C.HarriageK. L.et al. (2023). Plant mitochondrial introns as genetic markers-conservation and variation. Front. Plant Sci.14. doi: 10.3389/fpls.2023.1116851
16
HuH. Y.SunP. C.YangY. Z.MaJ. X.LiuJ. Q. (2023). Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets. J. Integr. Plant Biol.65, 1479–1489. doi: 10.1111/jipb.13455
17
HuangK.XuW.HuH.JiangX.SunL.ZhaoW.et al. (2025). Super-large record-breaking mitochondrial genome of Cathaya argyrophylla in Pinaceae. Front. Plant Sci.16. doi: 10.3389/fpls.2025.1556332
18
KorenS.WalenzB. P.BerlinK.MillerJ. R.BergmanN. H.PhillippyA. M. (2017). Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res.27, 722–736. doi: 10.1101/gr.215087.116
19
LetunicI.BorkP. (2024). Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res.52, W78–W82. doi: 10.1093/nar/gkae268
20
LiuY.MoskwaN. L.GoffinetB. (2012). Development of eight mitochondrial markers for funariaceae (Musci) and their amplification success in other mosses. Am. J. Bot.99, E62–E65. doi: 10.3732/ajb.1100402
21
MaQ.WangY.LiS. (2022). Assembly and comparative analysis of the first complete mitochondrial genome of Acer truncatum Bunge: a woody oil-tree species producing nervonic acid. BMC Plant Biol.22. doi: 10.1186/s12870-021-03416-5
22
MeyerE. H.WelchenE.CarrieC. (2019). Assembly of the complexes of the oxidative phosphorylation system in land plant mitochondria. Annu. Rev. Plant Biol. Vol70 70, 23–50. doi: 10.1146/annurev-arplant-050718-100412
23
MinhB. Q.SchmidtH. A.ChernomorO.SchrempfD.WoodhamsM. D.von HaeselerA.et al. (2020). IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol.37, 1530–1534. doi: 10.1093/molbev/msaa015
24
NajerT.DoñaJ.BucekA.SweetA. D.SychraO.JohnsonK. P. (2024). Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution. PloS Genet.20. doi: 10.1371/journal.pgen.1011266
25
QiaoZ. Q.ChenY.WangX. M.LiY. X.LiuS. S.DengF. Y.et al. (2025). Genome assembly and multiomic analyses reveal insights into flower and bark colors of Lagerstroemia excelsa. Plant Physiol. Biochem.220. doi: 10.1016/j.plaphy.2025.109482
26
Sanchez-PuertaM. V.CeriottiL. F.Gatica-SoriaL. M.RouletM. E.GarciaL. E.SatoH. A. (2023). Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites. Ann. Bot.132, 909–928. doi: 10.1093/aob/mcad108
27
ShiL. C.ChenH. M.JiangM.WangL. Q.WuX.HuangL. F.et al. (2019). CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res.47, W65–W73. doi: 10.1093/nar/gkz345
28
SloanD. B.MüllerK.McCauleyD. E.TaylorD. R.StorchováH. (2012). Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility. New Phytol.196, 1228–1239. doi: 10.1111/j.1469-8137.2012.04340.x
29
StegemannS.HartmannS.RufS.BockR. (2003). High-frequency gene transfer from the chloroplast genome to the nucleus. Proc. Natl. Acad. Sci. United. States America100, 8828–8833. doi: 10.1073/pnas.1430924100
30
StegemannS.KeutheM.GreinerS.BockR. (2012). Horizontal transfer of chloroplast genomes between plant species. Proc. Natl. Acad. Sci. United. States America109, 2434–2438. doi: 10.1073/pnas.1114076109
31
Van de PaerC.BouchezO.BesnardG. (2017). Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae). Mol. Ecol. Resour.18, 407–423. doi: 10.1111/1755-0998.12742
32
WangJ.HeW. C.LiaoX. Z.MaJ.GaoW.WangH. Q.et al. (2023). Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences. Hortic. Plant J.9, 345–355. doi: 10.1016/j.hpj.2022.06.005
33
WangJ.KanS. L.LiaoX. Z.ZhouJ. W.TembrockL. R.DaniellH.et al. (2024). Plant organellar genomes: much done, much more to do. Trends Plant Sci.29, 754–769. doi: 10.1016/j.tplants.2023.12.014
34
WangW.MahboubiA.ZhuS. C.HansonJ.MateusA.NiittyläT. (2025). Ribosome biogenesis in plants requires the nuclear envelope and mitochondria localized OPENER complex. Nat. Commun.16. doi: 10.1038/s41467-025-62652-7
35
WangX.ZhangR. G.YunQ. Z.XuY. Y.ZhaoG. C.LiuJ. M.et al. (2021). Comprehensive analysis of complete mitochondrial genome of Sapindus mukorossi Gaertn.: an important industrial oil tree species in China. Ind. Crops Products.174. doi: 10.1016/j.indcrop.2021.114210
36
WickR. R.SchultzM. B.JustinZ.HoltK. E. J. B. (2015). Bandage: interactive visualization of de novo genome assemblies. Bioinformatics20), 3350–3352. doi: 10.1093/bioinformatics/btv383
37
WolfeK. H.LiW. H.SharpP. M. (1987). Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear dnas. Proc. Natl. Acad. Sci. United. States America84, 9054–9058. doi: 10.1073/pnas.84.24.9054
38
WuB. J.BuljicA.HaoW. L. (2015). Extensive horizontal transfer and homologous recombination generate highly chimeric mitochondrial genomes in yeast. Mol. Biol. Evol.32, 2559–2570. doi: 10.1093/molbev/msv127
39
WuZ.-Q.LiaoX.-Z.ZhangX.-N.TembrockL. R.BrozA. (2022). Genomic architectural variation of plant mitochondria - A review of multichromosomal structuring. J. Syst. Evol.60, 160–168. doi: 10.1111/jse.12655
40
XuS. J.TengK.ZhangH.WuJ. Y.DuanL. S.ZhangH. Y.et al. (2023). The first complete mitochondrial genome of Carex (C. breviculmis): a significantly expanded genome with highly structural variations. Planta258. doi: 10.1007/s00425-023-04169-1
41
YuC. M.KeY. C.QinJ.HuangY. P.ZhaoY. C.LiuY.et al. (2022). Genome-wide identification of calcineurin B-like protein-interacting protein kinase gene family reveals members participating in abiotic stress in the ornamental woody plant. Front. Plant Sci.13. doi: 10.3389/fpls.2022.942217
42
YuX. L.MaZ. B.LiuS.DuanZ. G. (2024). Analysis of the Rhodomyrtus tomentosa mitochondrial genome: Insights into repeat-mediated recombination and intra-cellular DNA transfer. Gene909. doi: 10.1016/j.gene.2024.148288
43
YueY. J.ChenZ. M.ZhangD. L. (2025). Three new crape myrtle (Lagerstroemia) cultivars for southern landscape. Hortscience60, 254–257. doi: 10.21273/Hortsci18163-24
44
YueZ. W.XuY.CaiM.FanX. H.PanH. T.ZhangD. L.et al. (2024). Floral elegance meets medicinal marvels: traditional uses, phytochemistry, and pharmacology of the genus lagerstroemia L. Plants-Basel13. doi: 10.3390/plants13213016
45
ZhangD.GaoF.JakovlićI.ZouH.ZhangJ.LiW. X.et al. (2020). PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol. Ecol. Resour.20, 348–355. doi: 10.1111/1755-0998.13096
46
ZhouT.NingK.HanW.ZhouY.LiY.WangC.et al. (2023a). Floral scent components of the hybrids between Lagerstroemia fauriei and Lagerstroemia ‘Tuscarora’. Sci. Hortic.309. doi: 10.1016/j.scienta.2022.111670
47
ZhouY.ZhengT. C.CaiM.FengL.ChiX. F.ShenP.et al. (2023b). Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle. Horticult. Res.10. doi: 10.1093/hr/uhad146
48
ZhouY. Z.ZhengR. Y.PengY. K.ChenJ. M.ZhuX. Y.XieK.et al. (2023c). The first mitochondrial genome of Melastoma dodecandrum resolved structure evolution in Melastomataceae and micro inversions from inner horizontal gene transfer. Ind. Crops Products.205. doi: 10.1016/j.indcrop.2023.117390
49
ZouY.ZhuW. D.HouY. K.SloanD. B.WuZ. Q. (2025). The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana. Genome Biol.26. doi: 10.1186/s13059-025-03717-0
Summary
Keywords
evolution, horizontal gene transfer, Lagerstroemia, mitochondrial genome, structure evolution
Citation
Qin B, Huang X, Jiang R, Huang Y, Sun K, Li J and Zhang G (2026) The mitochondrial and chloroplast genomes of Lagerstroemia suprareticulata revealed a convergent genome morphology in genetic material evolution. Front. Plant Sci. 17:1746941. doi: 10.3389/fpls.2026.1746941
Received
15 November 2025
Revised
04 February 2026
Accepted
11 February 2026
Published
25 February 2026
Volume
17 - 2026
Edited by
Bozena Kolano, University of Silesia in Katowice, Poland
Reviewed by
Jacob Olagbenro Popoola, Bowen University, Nigeria
Kai Zhao, Fujian Normal University, China
Huitang Pan, Beijing Forestry University, China
Updates
Copyright
© 2026 Qin, Huang, Jiang, Huang, Sun, Li and Zhang.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Gangmin Zhang, gary1967@bjfu.edu.cn
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