The complete chloroplast genome of Dianthus helenae, an endemic species with medicinal potential from the Nuratau Range, Uzbekistan

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In this study, we sequenced, assembled, and characterized the complete chloroplast genome of D. helenae and evaluated its phylogenetic position within Dianthus. The plastome exhibited a typical circular quadripartite structure with a total length of 149,567 bp, comprising a large single-copy (LSC) region of 82,856 bp, a small single-copy (SSC) region of 17,105 bp, and a pair of inverted repeats (IRs) of 24,804 bp each. The genome contained the typical set of chloroplast genes, including protein-coding genes, transfer RNAs, and ribosomal RNAs, with duplicated genes located in the IR regions. Phylogenetic analysis based on complete chloroplast genome sequences strongly supported the placement of D. helenae within Dianthus and recovered it as a distinct lineage relative to other sampled species. Sliding window analysis of nucleotide diversity revealed uneven sequence variation across the plastome, with higher variability in the SSC and LSC regions than in the IRs. Several highly variable loci, including trnK-UUU , rps16–trnQ-UUG , rpl32, ycf1, and ndh-associated regions, were identified as potential molecular markers. These results provide an important genomic resource for Dianthus and establish a foundation for future phylogenetic, taxonomic, conservation, and molecular identification studies of this endemic Central Asian species." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/15-727", "name": "The complete chloroplast genome of Dianthus helenae, an endemic species..." } } ] } Home Browse The complete chloroplast genome of Dianthus helenae, an endemic species... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Ergashov I, Mingboev F, Rasulov F et al. The complete chloroplast genome of Dianthus helenae , an endemic species with medicinal potential from the Nuratau Range, Uzbekistan [version 1; peer review: awaiting peer review] . F1000Research 2026, 15 :727 ( https://doi.org/10.12688/f1000research.180038.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Genome Note The complete chloroplast genome of Dianthus helenae , an endemic species with medicinal potential from the Nuratau Range, Uzbekistan [version 1; peer review: awaiting peer review] Previosuly titled: " The complete chloroplast genome of Dianthus helenae , an endemic medicinal plant from the Nuratau Range, Uzbekistan" Ibrokhimjon Ergashov https://orcid.org/0000-0002-0991-1076 1 , Farkhodjon Mingboev 1 , Farruhbek Rasulov 2 , [...] Diyorjon Hamrayev 1 , Davronjon Sultonov 3 , Risolat Achilova 4 , Saidkamol Xaydarov 3 , Bakhrom Khujamkulov 5 , Feruza Utayeva 6 , Oysha Jabborova 7 , Ziyoviddin Yusupov 1 Ibrokhimjon Ergashov https://orcid.org/0000-0002-0991-1076 1 , Farkhodjon Mingboev 1 , [...] Farruhbek Rasulov 2 , Diyorjon Hamrayev 1 , Davronjon Sultonov 3 , Risolat Achilova 4 , Saidkamol Xaydarov 3 , Bakhrom Khujamkulov 5 , Feruza Utayeva 6 , Oysha Jabborova 7 , Ziyoviddin Yusupov 1 PUBLISHED 13 May 2026 Author details Author details 1 Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan 2 Andijan State Medical Institute, Andijan State Medical Institute, Andijan, Uzbekistan 3 Department of Botany and Biotechnology, Fergana State University, Fergana, Uzbekistan 4 Department of Foreign Language Teaching Methodology, Bukhara State Pedagogical Institute, Bukhara, Uzbekistan 5 Karshi State University, Kashkadarya, Uzbekistan 6 Bukhara State University, Bukhara, Uzbekistan 7 Bukhara State Medical Institute named after Abu Ali ibn Sino, Bukhara, Uzbekistan Ibrokhimjon Ergashov Roles: Writing – Original Draft Preparation Farkhodjon Mingboev Roles: Formal Analysis, Software, Writing – Review & Editing Farruhbek Rasulov Roles: Investigation, Resources, Writing – Review & Editing Diyorjon Hamrayev Roles: Formal Analysis, Resources Davronjon Sultonov Roles: Investigation, Methodology Risolat Achilova Roles: Investigation, Software Saidkamol Xaydarov Roles: Investigation, Writing – Review & Editing Bakhrom Khujamkulov Roles: Methodology, Resources, Writing – Review & Editing Feruza Utayeva Roles: Formal Analysis, Writing – Review & Editing Oysha Jabborova Roles: Formal Analysis, Writing – Original Draft Preparation Ziyoviddin Yusupov Roles: Conceptualization, Supervision OPEN PEER REVIEW REVIEWER STATUS AWAITING PEER REVIEW This article is included in the Genomics and Genetics gateway. Abstract Dianthus helenae Vved. is an endemic medicinal species of the Nuratau Mountains, Uzbekistan, and its genomic resources have remained largely unavailable. In this study, we sequenced, assembled, and characterized the complete chloroplast genome of D. helenae and evaluated its phylogenetic position within Dianthus. The plastome exhibited a typical circular quadripartite structure with a total length of 149,567 bp, comprising a large single-copy (LSC) region of 82,856 bp, a small single-copy (SSC) region of 17,105 bp, and a pair of inverted repeats (IRs) of 24,804 bp each. The genome contained the typical set of chloroplast genes, including protein-coding genes, transfer RNAs, and ribosomal RNAs, with duplicated genes located in the IR regions. Phylogenetic analysis based on complete chloroplast genome sequences strongly supported the placement of D. helenae within Dianthus and recovered it as a distinct lineage relative to other sampled species. Sliding window analysis of nucleotide diversity revealed uneven sequence variation across the plastome, with higher variability in the SSC and LSC regions than in the IRs. Several highly variable loci, including trnK-UUU , rps16–trnQ-UUG , rpl32 , ycf1 , and ndh-associated regions, were identified as potential molecular markers. These results provide an important genomic resource for Dianthus and establish a foundation for future phylogenetic, taxonomic, conservation, and molecular identification studies of this endemic Central Asian species. READ ALL READ LESS Keywords Caryophyllaceae, chloroplast genome, endemic species, Dianthus Corresponding Author(s) Ibrokhimjon Ergashov ( [email protected] ) Close Corresponding author: Ibrokhimjon Ergashov Competing interests: No competing interests were disclosed. Grant information: The author(s) declared that no grants were involved in supporting this work. Copyright: © 2026 Ergashov I et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The author(s) is/are employees of the US Government and therefore domestic copyright protection in USA does not apply to this work. The work may be protected under the copyright laws of other jurisdictions when used in those jurisdictions. How to cite: Ergashov I, Mingboev F, Rasulov F et al. The complete chloroplast genome of Dianthus helenae , an endemic species with medicinal potential from the Nuratau Range, Uzbekistan [version 1; peer review: awaiting peer review] . F1000Research 2026, 15 :727 ( https://doi.org/10.12688/f1000research.180038.1 ) First published: 13 May 2026, 15 :727 ( https://doi.org/10.12688/f1000research.180038.1 ) Latest published: 13 May 2026, 15 :727 ( https://doi.org/10.12688/f1000research.180038.1 ) Introduction Dianthus L. is one of the major genera of Caryophyllaceae and represents a taxonomically complex and evolutionarily important lineage within Caryophyllales. Recent taxonomic work has provided the first broad phylogenetic framework for the genus using plastid markers together with nuclear ITS data and has recognized 384 accepted species, confirming that Dianthus is far more diverse than traditionally assumed ( Fassou et al., 2022 ). At the same time, phylogenetic reconstruction in the genus remains challenging. Previous studies have shown that genetic distances among many Dianthus taxa are very low, species-level relationships are often weakly resolved, and plastid haplotypes may be deeply shared among related species, suggesting rapid radiation and a complex evolutionary history ( Fassou et al., 2022 ). More recent molecular analyses have nevertheless begun to recover major lineages within the genus. Combined plastid and nuclear datasets support the monophyly of Dianthus and indicate clear geographic and sectional structuring, while plastome-based analyses have resolved two strongly supported major clades among sampled species, demonstrating that chloroplast data are informative for understanding evolutionary relationships in the genus ( Lin et al., 2022 ; Mnxati & Mankga, 2025 ). Beyond its phylogenetic importance, Dianthus is also notable for its ornamental, economic, and medicinal value. Several species are widely cultivated, and a number of taxa have long been used in traditional medicine, making the genus relevant not only to systematics but also to applied plant science ( Lin et al., 2022 ; Raman & Park, 2015 ; Meng et al., 2023 ). However, morphological similarity among species, frequent hybridization, and the limited availability of genomic resources have complicated species delimitation and the interpretation of evolutionary relationships in Dianthus ( Lin et al., 2022 ; Meng et al., 2023 ). In this context, complete chloroplast genomes provide a particularly useful source of evidence because they are generally conserved in structure and gene content, maternally inherited in most angiosperms, and widely used in comparative genomics, DNA marker development, and phylogenetic reconstruction ( Nikitina et al., 2025 ; Alieva et al., 2025 ; Tojiboeva et al., 2025 ; Dekhkonov et al., 2025 ; Ergashov et al., 2026a , b , c ). Previous plastome studies in Dianthus have shown that chloroplast genomes are structurally conserved and phylogenetically informative, but taxon sampling remains limited and is still insufficient to fully clarify relationships across the genus ( Lin et al., 2022 ; Yang et al., 2021 ). Dianthus helenae Vved., an accepted species originally described in 1941, remains poorly studied at the genomic level ( Fassou et al., 2022 ). Therefore, characterization of its complete chloroplast genome will not only provide a new genomic resource for the genus, but will also help clarify its phylogenetic placement within Dianthus , contribute to comparative plastome studies, and support future taxonomic and conservation research on this endemic medicinal species from the Nuratau Mountains of Uzbekistan. Methods Fresh leaves of Dianthus helenae Vved. were collected from a wild population in the Nuratau Range, Uzbekistan ( Figure 1 ). Species identification was carried out by N. Beshko, and the voucher specimen is deposited in the National Herbarium of Uzbekistan (TASH) under accession number TASH139868. Figure 1. Habit of Dianthus helenae in the natural habitat. Various individuals of D. helenae in a shrub–grassland-steppe community on rocky and fine-soiled slopes in the Ustuksay area, Nuratau Range, Uzbekistan (approximately 1450 m a.s.l.; 4 July 2024; photograph by N. Beshko). Total genomic DNA was extracted from approximately 100 mg of fresh leaf tissue using a Tiangen Plant Genomic DNA Kit (Tiangen Biotech Co., Beijing, China; Cat. No. DP305) following the manufacturer’s protocol. Sequencing libraries were prepared using ~1 μg of purified DNA with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, USA; Cat. No. E7645S), including fragmentation to ~350 bp, end repair, adapter ligation, and PCR amplification. Library quality and fragment size distribution were assessed using an Agilent 5400 system. Qualified libraries were sequenced on an Illumina platform at Novogene Bioinformatics Technology Co. Clean reads were assembled using NOVOPlasty ( Dierckxsens et al., 2017 ). Gene annotation was performed in Geneious Prime using Dianthus chinensis (GenBank accession OP136025) as the reference genome and manually verified for start and stop codons as well as exon–intron boundaries ( Kearse et al., 2012 ). A circular chloroplast genome map was generated using OGDRAW ( Greiner et al., 2019 ). The assembled chloroplast genome was deposited in GenBank under accession number PZ251004. Nucleotide diversity (Pi) was calculated using DnaSP v6.12.03 ( Rozas et al., 2017 ). A sliding-window analysis was performed with a window length of 1000 bp and a step size of 500 bp. For phylogenetic reconstruction, 22 plastome sequences representing nine Dianthus species and one outgroup taxon ( Petrorhagia saxifraga ) were retrieved from NCBI GenBank ( Table 1 ). Complete chloroplast genomes were aligned using MAFFT ( Katoh & Standley, 2013 ). Maximum likelihood analysis was performed in RAxML with 1,000 bootstrap replicates ( Stamatakis, 2014 ). The GTR + G model was selected using jModelTest v2.1.4 under the Akaike Information Criterion ( Darriba et al., 2012 ). Table 1. Dianthus chloroplast genome sequences used in this study. Bold accession means sequenced sample for this study. No. Organism Accession 1 Dianthus nudiflorus OP_353926 2 Dianthus nudiflorus NC_087621 3 Dianthus helenae PZ251004 4 Dianthus longicalyx MT_001881 5 Dianthus longicalyx NC_050834 6 Dianthus longicalyx KM_668208 7 Dianthus chinensis OP_136025 8 Dianthus chinensis OP_136018 9 Dianthus chinensis OP_136016 10 Dianthus superbus OP_136023 11 Dianthus superbus NC_082201 12 Dianthus barbatus NC_082202 13 Dianthus barbatus OP_136024 14 Dianthus barbatus OP_136026 15 Dianthus cincinnatus OP_136020 16 Dianthus gratianopolitanus LN_877389 17 Dianthus gratianopolitanus LN_877395 18 Dianthus gratianopolitanus LN_877393 19 Dianthus caryophyllus MG_989277 20 Dianthus caryophyllus NC_039650 21 Dianthus caryophyllus OP_136027 22 Dianthus caryophyllus KU_904222 23 Petrorhagia saxifraga OP_353913 Results The chloroplast genome map of Dianthus helenae revealed a typical circular quadripartite structure, consisting of a large single-copy (LSC) region of 82,836 bp, a small single-copy (SSC) region of 17,105 bp, and a pair of inverted repeats (IRa and IRb) of 24,884 bp each, giving a total genome length of 149,709 bp ( Figure 2 ). The genome contained the usual set of plastid genes involved in photosynthesis, ATP synthesis, transcription, and translation, including protein-coding genes, transfer RNAs, and ribosomal RNAs. As shown in the map, genes were distributed on both strands, while several genes located in the IR regions were duplicated, including rRNA and some tRNA/protein-coding genes. This agrees well with comparative studies showing that Dianthus chloroplast genomes are highly uniform in overall architecture, generally falling within a narrow size range and containing largely conserved gene sets, with only limited variation at IR/SC boundaries ( Lin et al., 2022 ; Meng et al., 2023 ; Wicke et al., 2011 ; Daniell et al., 2016 ; Yang et al., 2021 ). Figure 2. Circular map of the chloroplast genome of Dianthus helenae. Genes located on the outer and inner circles are transcribed in opposite directions, respectively. The inner histogram represents the GC content across the genome. IRa and IRb indicate the inverted repeat regions, while LSC and SSC denote the large single-copy and small single-copy regions, respectively. Phylogenetic analysis based on complete chloroplast genome sequences strongly supports the placement of D. helenae within the genus Dianthus ( Figure 3 ). The maximum likelihood tree reveals that D. helenae forms a well-supported clade closely related to D. chinensis and D. caryophyllus , with high bootstrap values (≥100), indicating robust phylogenetic inference. Figure 3. Maximum-likelihood tree of Dianthus plastomes. Phylogenetic relationships inferred from complete chloroplast genome sequences. Bootstrap values are shown at the nodes. Petrorhagia saxifraga was used as the outgroup. The clustering pattern is consistent with previous plastome-based phylogenies, confirming the reliability of whole chloroplast genome data fogeir resolving relationships within Caryophyllaceae. The distinct positioning of D. helenae suggests its independent evolutionary trajectory within the genus. This is broadly compatible with previous whole-plastome analyses, which also resolved two major, well-supported chloroplast groups within Dianthus , one centered on D. caryophyllus , D. barbatus , and D. gratianopolitanus , and the other on D. superbus , D. chinensis , and D. longicalyx ( Lin et al., 2022 ). Sliding window analysis of nucleotide diversity (Pi) revealed heterogeneous variation across the plastome ( Figure 4 ). The SSC region exhibited higher variability compared to LSC and IR regions, consistent with patterns observed in other angiosperms. Several highly variable regions were identified, including coding regions such as ycf1, rpl32 and intergenic spacers ndh-ndhE, rps16-trnQ-UUG. These hotspots represent potential candidate regions for molecular marker development and phylogeographic studies. In contrast, IR regions showed significantly lower nucleotide diversity, reflecting their conserved nature and the stabilizing effect of gene duplication. Figure 4. Sliding window analysis of nucleotide diversity across Dianthus chloroplast genomes. Nucleotide variability (Pi) is plotted along the genome sequence. The window length was set to 800 bp with a step size of 200 bp. Overall, the present results show that D. helenae combines strong plastome structural conservatism with enough sequence divergence in a small number of highly informative loci to support phylogenetic placement and future species-level identification. Because D. helenae is an accepted Central Asian species of medicinal interest and several phytoecdysteroids have already been reported from it, the plastome resource generated here should be valuable for molecular authentication, population-level marker development, and future conservation-oriented studies of the genus in the region ( Yusupova et al., 2022 ). Software availability No custom code was used in this study. Software used in the analysis included NOVOPlasty, Geneious Prime, OGDRAW, DnaSP v6.12.03, MAFFT, RAxML, and jModelTest v2.1.4, as cited in the Methods section. Ethics and consent This study did not involve human participants or animals. Ethical approval and informed consent were therefore not required. Data and software availability Underlying data NCBI GenBank: Dianthus helenae chloroplast genome. Accession number PZ251004. The accession numbers of comparative chloroplast genomes used in this study are provided in Table 1 . Acknowledgments This research was supported by the State Program “Digital Nature: Development of a digital platform for the flora of Central Uzbekistan”, implemented by the Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan for the period 2025-2029. 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PubMed Abstract | Publisher Full Text Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 13 May 2026 ADD YOUR COMMENT Comment Author details Author details 1 Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan 2 Andijan State Medical Institute, Andijan State Medical Institute, Andijan, Uzbekistan 3 Department of Botany and Biotechnology, Fergana State University, Fergana, Uzbekistan 4 Department of Foreign Language Teaching Methodology, Bukhara State Pedagogical Institute, Bukhara, Uzbekistan 5 Karshi State University, Kashkadarya, Uzbekistan 6 Bukhara State University, Bukhara, Uzbekistan 7 Bukhara State Medical Institute named after Abu Ali ibn Sino, Bukhara, Uzbekistan Ibrokhimjon Ergashov Roles: Writing – Original Draft Preparation Farkhodjon Mingboev Roles: Formal Analysis, Software, Writing – Review & Editing Farruhbek Rasulov Roles: Investigation, Resources, Writing – Review & Editing Diyorjon Hamrayev Roles: Formal Analysis, Resources Davronjon Sultonov Roles: Investigation, Methodology Risolat Achilova Roles: Investigation, Software Saidkamol Xaydarov Roles: Investigation, Writing – Review & Editing Bakhrom Khujamkulov Roles: Methodology, Resources, Writing – Review & Editing Feruza Utayeva Roles: Formal Analysis, Writing – Review & Editing Oysha Jabborova Roles: Formal Analysis, Writing – Original Draft Preparation Ziyoviddin Yusupov Roles: Conceptualization, Supervision Competing interests No competing interests were disclosed. Grant information The author(s) declared that no grants were involved in supporting this work. Article Versions (1) version 1 Published: 13 May 2026, 15:727 https://doi.org/10.12688/f1000research.180038.1 Copyright © 2026 Ergashov I et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The author(s) is/are employees of the US Government and therefore domestic copyright protection in USA does not apply to this work. The work may be protected under the copyright laws of other jurisdictions when used in those jurisdictions. Download Export To Sciwheel Bibtex EndNote ProCite Ref. 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