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69 pages, 46804 KB  
Article
Colorless Polyimides Derived from Novel Role-Dividing Spiro-Type Monomers: Strategies to Overcome the Trade-Off Between Low Linear Coefficients of Thermal Expansion and Low Thickness-Direction Birefringence Without Fillers
by Masatoshi Hasegawa, Yoshihiko Terada, Ko Nagahaba, Soichi Tsukuda, Toya Ikuma, Hikaru Sugihara, Ryosuke Masaka, Shinya Takahashi, Junichi Ishii and Takao Miwa
Polymers 2026, 18(9), 1108; https://doi.org/10.3390/polym18091108 - 30 Apr 2026
Abstract
This study presents unique polymeric materials applicable to plastic substrates for use in flexible-display devices that overcome the trade-off between low linear coefficients of thermal expansion (CTE) and low thickness-direction birefringence (Δnth) while combining a very high Tg, [...] Read more.
This study presents unique polymeric materials applicable to plastic substrates for use in flexible-display devices that overcome the trade-off between low linear coefficients of thermal expansion (CTE) and low thickness-direction birefringence (Δnth) while combining a very high Tg, sufficiently high thermal stability, excellent optical transparency, good solubility, and minimum-required ductility. Polyimide (PI) films obtained from 1,2,3,4-cyclobutanetetracarboxylic dianhydride (CBDA) with 2,2′-bis(trifluoromethyl)benzidine (TFMB) under different conditions resulted in widely varying CTE values and provided a clear CTE–Δnth correlation, which can be regarded as a virtual lower boundary in the CTE–Δnth relationship for various PI systems. The pristine CBDA/TFMB and CpODA/TFMB (CpODA = norbornane-2-spiro-α-cyclopentanone-α′-spiro-2″-norbornane-5,5″,6,6″-tetracarboxylic dianhydride) systems were modified using numerous specifically designed monomers, i.e., a vertical-alignment-type liquid-crystalline diamine and cardo-type and spiro-type monomers. However, it was very challenging to overcome the trade-off between low CTE and low Δnth, that is, to significantly exceed this lower boundary by modifying the pristine systems, while ensuring other target properties. One of the keys to achieving the present goal was compatibility with chemical imidization or one-pot polymerization processes (i.e., high solubility of the PIs), because these processes were more advantageous in reducing CTE and enhancing film transparency than the conventional two-step process. The modifications using phenyl-substituted xanthene-pendant 2,7-diaminofluorene and fluorene-pendant 2,3,6,7-xanthenetetracarboxylic dianhydride exhibited a prominent effect on overcoming the trade-off without the help of any fillers, while combining other excellent target properties. Polarized FT-IR difference spectra measured at varying incidence angles suggested that these side groups, which are connected perpendicularly to the PI main chains, align in the Z-direction, rationalizing the observed prominent effect. Thus, unique high-temperature transparent materials applicable to plastic substrates were successfully obtained in this study. Full article
(This article belongs to the Section Polymer Chemistry)
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31 pages, 3239 KB  
Review
Ultrafast Fiber Lasers in the 2 μm Band: Mode-Locking Techniques, Performance Advances and Applications
by Silun Du, Tianshu Wang, Bo Zhang, Shimeng Tan and Tuo Chen
Photonics 2026, 13(5), 420; https://doi.org/10.3390/photonics13050420 - 24 Apr 2026
Viewed by 142
Abstract
Ultrafast fiber lasers operating near 2 μm have emerged as a critical platform for advancing mid-infrared photonics due to their narrow pulse durations, high peak powers, and broad tunability. These sources exploit the rich energy-level structures of Tm3+ and Ho3+ doped [...] Read more.
Ultrafast fiber lasers operating near 2 μm have emerged as a critical platform for advancing mid-infrared photonics due to their narrow pulse durations, high peak powers, and broad tunability. These sources exploit the rich energy-level structures of Tm3+ and Ho3+ doped fibers and reside within an atmospheric transmission window, enabling applications spanning nonlinear microscopy, precision micromachining, optical frequency metrology, biophotonics, and free-space optical communication. Recent progress in low-loss fiber fabrication, dispersion-engineered cavity design, and mode-locking technologies has significantly expanded the performance boundaries of 2 μm ultrafast fiber lasers. This review systematically examines the underlying pulse-formation mechanisms and categorizes state-of-the-art mode-locking approaches. Representative laser architectures are compared with respect to pulse duration, energy scalability, repetition-rate enhancement, spectral characteristics, and environmental stability. Key application pathways in high-resolution spectroscopy, biomedical diagnostics, and mid-IR supercontinuum generation are highlighted. Finally, the remaining challenges and prospective research directions are discussed to inform the development of next-generation ultrafast photonic sources in the 2 μm band. Full article
(This article belongs to the Special Issue Advancements in Mode-Locked Lasers)
18 pages, 15071 KB  
Article
Structural, Thermal Behaviour and Tribological Performance in Cold Rolling of Mineral Lubricants with Graphene Nanoplatelets Functionalized with Oleic Acid
by Batuhan Özakın and Kürşat Gültekin
Nanomaterials 2026, 16(8), 495; https://doi.org/10.3390/nano16080495 - 21 Apr 2026
Viewed by 217
Abstract
In this study, nanolubricants based on SAE 5W-30 mineral oil were formulated using oleic acid-functionalized graphene nanoplatelets (GNPs), and their colloidal stability, rheological behaviour, thermal stability, and tribological performance under cold rolling conditions were systematically investigated. The nanolubricants were prepared at GNP concentrations [...] Read more.
In this study, nanolubricants based on SAE 5W-30 mineral oil were formulated using oleic acid-functionalized graphene nanoplatelets (GNPs), and their colloidal stability, rheological behaviour, thermal stability, and tribological performance under cold rolling conditions were systematically investigated. The nanolubricants were prepared at GNP concentrations of 0.05, 0.1, 0.2, 0.4, and 0.6 wt%. FT-IR analysis confirmed successful functionalization, evidenced by the characteristic C=O band at approximately 1710 cm−1 and changes in CH2 stretching vibrations in the 2850–3000 cm−1 range. UV–VIS results indicated initially homogeneous dispersions; however, after three days, relative concentrations decreased to 95%, 90%, and 75% for 0.05, 0.2, and 0.6 wt% GNPs, respectively. Viscosity measurements showed minimal variation at low concentrations, with only a 0.64% increase at 0.2 wt% compared to the base oil. TGA revealed enhanced oxidative stability at low GNP contents, with the oxidation onset temperature increasing from 205.3 °C to 207.2 °C at 0.05 wt%, while a marked decline was observed at higher concentrations (176.8 °C at 0.6 wt%). In cold rolling experiments at a 3% reduction ratio, the rolling force was measured at 1341 N/mm with the neat lubricant, decreasing to 1210 N/mm with a lubricant containing 0.1 wt% GNPs, corresponding to an approximate 10% reduction. Compared with dry conditions, this reduction was approximately 21%. Surface roughness and 3D topography analyses further showed that GNPs-containing lubricants reduced asperities and promoted the formation of a more uniform tribofilm. At low concentrations, the improved lubrication performance of oleic acid-functionalized graphene nanoplatelets is attributed to their homogeneous dispersion in mineral oil, where physically adsorbed oleic acid improves colloidal stability by reducing agglomeration and promotes the formation of a stable tribofilm, facilitating interlayer sliding under boundary lubrication conditions. Overall, the findings demonstrate that oleic acid-functionalized GNPs, when used at optimal concentrations, significantly enhance both lubricant stability and cold rolling performance. Full article
(This article belongs to the Section Physical Chemistry at Nanoscale)
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15 pages, 2880 KB  
Article
Electrical and Electronic Quality Improvement of Multicrystalline Silicon Solar Cells via Hydrogen Plasma Treatment
by Ameny El Haj, Achref Mannai, Hassen Nouri, Karim Choubani, Mohammed A. Almeshaal, Wissem Dimassi and Mohamed Ben Rabha
Inorganics 2026, 14(4), 105; https://doi.org/10.3390/inorganics14040105 - 7 Apr 2026
Viewed by 332
Abstract
In this work, the impact of hydrogen plasma treatment on the electrical and electronic quality of multicrystalline silicon (mc-Si) was systematically investigated using plasma-enhanced chemical vapor deposition (PE-CVD). Hydrogen radicals generated in the plasma effectively passivate dangling bonds, reducing electrically active defects and [...] Read more.
In this work, the impact of hydrogen plasma treatment on the electrical and electronic quality of multicrystalline silicon (mc-Si) was systematically investigated using plasma-enhanced chemical vapor deposition (PE-CVD). Hydrogen radicals generated in the plasma effectively passivate dangling bonds, reducing electrically active defects and enhancing material quality. Optimized PE-CVD conditions were applied to promote efficient hydrogen incorporation and surface modification. Optical characterization, including reflectivity measurements and FT-IR spectroscopy, confirms the formation of Si–H bonds and a significant reduction in surface reflectivity of up to 66% at 600 nm. Electrical and optoelectronic analyses reveal pronounced improvements in carrier lifetime and diffusion length, increased by 200% and 79%, respectively. In addition, dark current–voltage (I–V) measurements show a 32% decrease in series resistance and a 51% increase in shunt resistance, indicating enhanced charge transport and suppressed leakage currents. These macroscopic electrical improvements are supported by light beam-induced current (LBIC) measurements, which demonstrate a 14% increase in grain boundary current, confirming effective hydrogen passivation and reduced recombination. Overall, hydrogen plasma PE-CVD treatment is shown to significantly improve the electronic quality and photovoltaic performance of mc-Si solar cells. Full article
(This article belongs to the Special Issue New Semiconductor Materials for Energy Conversion, 2nd Edition)
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18 pages, 2222 KB  
Article
Unsupervised Anomaly Detection of Internal Reconnection Events in the VEST Spherical Tokamak
by Dae-Won Ok, Dae-Yeol Pyo, Hong-Sik Yun, Yong-Seok Hwang and Yong-Su Na
Plasma 2026, 9(2), 9; https://doi.org/10.3390/plasma9020009 - 29 Mar 2026
Viewed by 342
Abstract
Internal reconnection events (IREs) are rapid magnetohydrodynamic phenomena that play an important role in the confinement and stability of spherical tokamak plasmas. Reliable identification of IREs in experimental data is challenging due to short discharge durations, ambiguous event boundaries, and the limited availability [...] Read more.
Internal reconnection events (IREs) are rapid magnetohydrodynamic phenomena that play an important role in the confinement and stability of spherical tokamak plasmas. Reliable identification of IREs in experimental data is challenging due to short discharge durations, ambiguous event boundaries, and the limited availability of labeled data. In this study, we propose an unsupervised, event-level IRE detection framework based on anomaly detection techniques and apply it to experimental data from the VEST spherical tokamak. The proposed framework combines a two-stage detection strategy using plasma current and Hα emission signals with sliding-window segmentation and event-level evaluation, enabling physically meaningful IRE identification without labeled training data. Three unsupervised models—K-Nearest Neighbors (KNN), One-Class Support Vector Machine (OCSVM), and an autoencoder (AE)—are evaluated within a unified framework. All models achieve stable detection performance, with precision exceeding 80% and recall above 70% under a precision-oriented operating point. To enhance detection robustness, a KNN-based cleaning procedure is introduced during training to remove noise-driven, locally isolated windows, significantly reducing spurious detections while preserving physically meaningful IRE signatures. Event-level analysis indicates that missed detections under this operating regime predominantly correspond to weak events with limited impact on global plasma behavior. The proposed framework is fully unsupervised, computationally efficient, and readily extensible to other spherical tokamak devices, providing a flexible foundation for incorporating additional diagnostics, such as Mirnov coil signals, toward precursor-aware detection and future predictive modeling of IRE activity. Full article
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16 pages, 3575 KB  
Article
Assembly of the Delphinium densiflorum Chloroplast Genome and Comparative Genomics Within Delphinium
by Siqi Chen, Min Wang, Xinhang Lu, Yuying Sun and Min Ma
Genes 2026, 17(2), 240; https://doi.org/10.3390/genes17020240 - 17 Feb 2026
Viewed by 440
Abstract
Background/Objectives: Chloroplast genomes are essential for understanding the systematics and adaptive evolution of alpine plants, yet genomic data for high-altitude Delphinium species remain scarce. Delphinium densiflorum, a medicinal plant endemic to the Qinghai-Tibet Plateau, exhibits notable high-altitude adaptations, but its plastome [...] Read more.
Background/Objectives: Chloroplast genomes are essential for understanding the systematics and adaptive evolution of alpine plants, yet genomic data for high-altitude Delphinium species remain scarce. Delphinium densiflorum, a medicinal plant endemic to the Qinghai-Tibet Plateau, exhibits notable high-altitude adaptations, but its plastome features and evolutionary position are still unclear. This study aims to assemble and characterize its complete chloroplast genome and clarify its phylogenetic placement within Delphinium. Methods: Using Illumina NovaSeq data, we de novo assembled the D. densiflorum plastome, annotated it with CPGAVAS2, and compared it with 12 published Ranunculaceae plastomes. We analyzed IR-boundary dynamics, genome-wide sequence variation, and codon-usage bias and constructed a maximum-likelihood phylogeny based on 69 shared protein-coding genes. Results: The plastome is 154,161 bp (GC 38.24%) with a canonical quadripartite structure, encoding 131 genes (87 CDS, 8 rRNA, 37 tRNA). An IR expansion into the SSC region yields the shortest SSC reported among the compared Delphinium species and produces unique structural variants. Photosynthetic genes are extremely conserved (nucleotide diversity Pi ≤ 0.01), whereas several loci (e.g., ycf1 and psaC) are highly divergent (Pi ≥ 0.05). Codon usage shows a strong bias toward AU-ending triplets. Phylogenetically, D. densiflorum forms a 100%-bootstrap clade with other high-altitude congeners, supporting the non-monophyly of Delphinium. Conclusions: This study delineates the plastome architecture and putative adaptive signatures of D. densiflorum, identifies robust candidate loci for DNA barcoding, and provides molecular evidence for taxonomic revision and conservation strategies in Delphinium. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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15 pages, 1948 KB  
Article
The Complete Chloroplast Genome Sequence of Pseudolysimachion pyrethrinum var. gasanensis
by Sang Heon Kim, Ji Hun Yi, Jin-Woo Kim, Wonwoo Cho and Ji Young Jung
Horticulturae 2026, 12(2), 196; https://doi.org/10.3390/horticulturae12020196 - 4 Feb 2026
Viewed by 478
Abstract
Pseudolysimachion pyrethrinum var. gasanensis (Gasan spike speedwell) is a valuable Korean endemic variety with significant horticultural potential. Despite its morphological distinctiveness, its taxonomic status and evolutionary position have remained a subject of debate. In this study, we assembled and characterized the first complete [...] Read more.
Pseudolysimachion pyrethrinum var. gasanensis (Gasan spike speedwell) is a valuable Korean endemic variety with significant horticultural potential. Despite its morphological distinctiveness, its taxonomic status and evolutionary position have remained a subject of debate. In this study, we assembled and characterized the first complete chloroplast (cp) genome of P. pyrethrinum var. gasanensis using high-throughput sequencing. The complete plastome is 152,251 bp in length, exhibiting a typical quadripartite structure with a large single-copy (LSC) region (83,191 bp), a small single-copy (SSC) region (17,690 bp), and two inverted repeats (IRs) (25,685 bp each). The genome contains 133 genes, including 88 protein-coding, 37 tRNA, and 8 rRNA genes. Genomic analysis identified 42 simple sequence repeat (SSR) units across 38 distinct loci, predominantly mononucleotide A/T motifs, which serve as potential molecular markers for variety-level identification. Selective pressure analysis revealed that the majority of protein-coding genes are under strong purifying selection (Ka/Ks < 1.0), emphasizing the evolutionary stability of the plastome. Comparative analysis of IR boundaries using IRscope revealed a high degree of structural conservation among Pseudolysimachion species, with minor variations at the junction sites. Phylogenetic analysis based on 18 complete plastomes strongly supported the monophyly of the genus Pseudolysimachion (Bootstrap = 100%) and placed P. pyrethrinum var. gasanensis as a sister to the European P. spicatum. These genomic resources provide a foundational tool for the molecular breeding, systematic conservation, and sustainable utilization of this endemic variety, while offering clarity to its taxonomic classification within the tribe Veroniceae. Full article
(This article belongs to the Special Issue Genetic Innovation and Breeding in Ornamental Plants)
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17 pages, 17966 KB  
Article
Sealing Performance of Phenyl-Silicone Rubber Based on Constitutive Model Under Thermo-Oxidative Aging
by Haiqiang Shi, Jian Wu, Zhihao Chen, Pengtao Cao, Tianxiao Zhou, Benlong Su and Youshan Wang
Polymers 2026, 18(3), 350; https://doi.org/10.3390/polym18030350 - 28 Jan 2026
Viewed by 529
Abstract
Phenyl-silicone rubber is the elastomer of choice for cryogenic and high-temperature static seals, yet quantitative links between thermo-oxidative aging and sealing reliability are still lacking. Here, sub-ambient (−70 °C to 25 °C) and room-temperature mechanical tests, compression set aging, SEM, FT-IR, and finite-element [...] Read more.
Phenyl-silicone rubber is the elastomer of choice for cryogenic and high-temperature static seals, yet quantitative links between thermo-oxidative aging and sealing reliability are still lacking. Here, sub-ambient (−70 °C to 25 °C) and room-temperature mechanical tests, compression set aging, SEM, FT-IR, and finite-element simulations are integrated to trace how aging translates into contact-pressure decay of an Omega-profile gasket. Compression set rises monotonically with time and temperature; an Arrhenius model derived from 80 to 140 °C data predicts 34 d (10% set) and 286 d (45% set) of storage life at 25 °C. SEM reveals a progressive shift from ductile dimple fracture to brittle, honeycomb porosity, while FT-IR confirms limited surface oxidation without bulk chain scission. Finite element analyses show that contact pressure always peaks at the two lateral necks; short-term aging increases in the shear modulus C10 from 1.87 to 2.27 MPa, raising CPRESS by 8~21%, yet this benefit is ultimately offset by displacement loss from compression set (8.0 mm to 6.1 mm), yielding a net pressure reduction of 0.006 MPa. Critically, even under the most severe coupled condition (56 days aging with compression set), the predicted CPRESS remains above the 0.1 MPa leak-tightness criterion across the entire cryogenic service envelope. This framework provides deterministic boundaries for temperature, aging duration, and allowable preload relaxation, enabling risk-informed maintenance and replacement scheduling for safety-critical phenyl-silicone seals. Full article
(This article belongs to the Special Issue Constitutive Modeling of Polymer Matrix Composites)
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16 pages, 4926 KB  
Article
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Tibetan Medicinal Plant Soroseris hookeriana
by Tian Tian, Xiuying Lin, Yiming Wang and Jiuli Wang
Genes 2026, 17(1), 24; https://doi.org/10.3390/genes17010024 - 27 Dec 2025
Cited by 1 | Viewed by 566
Abstract
Background/Objectives: Soroseris hookeriana, a Tibetan medicinal plant endemic to the high-altitude Qinghai–Tibet Plateau, possesses significant pharmacological value but lacks fundamental genomic characterization. This study aims to generate and comparatively analyse its complete chloroplast genome. Methods: Total DNA was sequenced, assembled [...] Read more.
Background/Objectives: Soroseris hookeriana, a Tibetan medicinal plant endemic to the high-altitude Qinghai–Tibet Plateau, possesses significant pharmacological value but lacks fundamental genomic characterization. This study aims to generate and comparatively analyse its complete chloroplast genome. Methods: Total DNA was sequenced, assembled with GetOrganelle, annotated with CPGAVAS2, and compared with eight Asteraceae species; phylogenetic placement was inferred with IQ-TREE from 21 complete plastomes. Results: The circular chloroplast genome is 152,514 bp with a typical quadripartite structure (LSC 84,168 bp, SSC 18,528 bp, two IRs 24,909 bp each). It contains 132 unique genes (87 protein-coding, 37 tRNA, 8 rRNA; 18 duplicated in IRs yield 150 total copies). Twenty-three genes harbour introns; clpP and ycf3 have two. Overall GC content is 37.73%, elevated in IRs (43.12%). Codon usage shows strong A/U bias at the third position; 172 SSRs and 39 long repeats are detected. IR-SC boundaries exhibit the greatest inter-specific variation, notably in ycf1 and ndhF. Conclusions: The complete plastome robustly supports S. hookeriana and Stebbinsia umbrella as sister species (100% bootstrap) and provides essential genomic resources for species identification, population genetics, and studies of high-altitude adaptation. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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18 pages, 5504 KB  
Article
The Complete Chloroplast Genome and the Phylogenetic Analysis of Panicum bisulcatum (Thumb.) (Poaceae)
by Yuan Gao, Yutong Cai, Huifeng Wang, Zhihui Tian and Zhaofeng Huang
Int. J. Mol. Sci. 2026, 27(1), 135; https://doi.org/10.3390/ijms27010135 - 22 Dec 2025
Viewed by 625
Abstract
The chloroplast (cp) genome of Panicum bisulcatum (Thumb.), a significant agricultural weed, was sequenced and characterized to elucidate its genomic architecture, evolutionary dynamics, and phylogenetic relationships. The complete cp genome was assembled as a circular DNA molecule of 138,489 bp, exhibiting a typical [...] Read more.
The chloroplast (cp) genome of Panicum bisulcatum (Thumb.), a significant agricultural weed, was sequenced and characterized to elucidate its genomic architecture, evolutionary dynamics, and phylogenetic relationships. The complete cp genome was assembled as a circular DNA molecule of 138,489 bp, exhibiting a typical quadripartite structure comprising a large single-copy (LSC, 82,260 bp), a small single-copy (SSC, 12,569 bp), and a pair of inverted repeats (IR, 21,830 bp each) regions. It encodes 135 genes, including 89 protein-coding genes, 49 tRNAs, and 8 rRNAs. Functional annotation revealed that most genes are involved in photosynthesis and genetic system. A total of 51 simple sequence repeats (SSRs) and 62 long repeats (LRs) were identified, providing potential molecular markers. Comparative analysis of IR boundaries highlighted both conserved features and species-specific expansion/contraction events among Panicum species. Phylogenomic analysis robustly placed P. bisulcatum within the genus Panicum, showing a closest relationship with P. incomtum and confirming the monophyly of the genus. Furthermore, single nucleotide polymorphism (SNP) analysis with its closest relative, P. incomtum, revealed 4659 SNPs, with a dominance of synonymous substitutions, indicating the action of purifying selection. This study provides the first comprehensive cp genomic resource for P. bisulcatum, which will facilitate future studies in species identification, phylogenetic reconstruction, population genetics, and the development of sustainable management strategies for this weed. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing, 2nd Edition)
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16 pages, 5227 KB  
Article
Chloroplast Genome Analysis of Six Camellia sinensis Accessions: Genetic Divergence, Adaptive Evolution, and Molecular Marker Development
by Yanli Fu, Lei Pan, Xiaoxi Du and Zhigang Hao
Biology 2026, 15(1), 7; https://doi.org/10.3390/biology15010007 - 19 Dec 2025
Viewed by 684
Abstract
Camellia sinensis ‘hainanensis’ (Hainan Sheng tea) is an endemic tea germplasm resource native to Hainan Island, China. Using complete chloroplast genome sequencing combined with comprehensive comparative analyses, we elucidated the genetic architecture of six C. sinensis accessions. The chloroplast genomes exhibited a typical [...] Read more.
Camellia sinensis ‘hainanensis’ (Hainan Sheng tea) is an endemic tea germplasm resource native to Hainan Island, China. Using complete chloroplast genome sequencing combined with comprehensive comparative analyses, we elucidated the genetic architecture of six C. sinensis accessions. The chloroplast genomes exhibited a typical quadripartite circular structure (~157 Kb) comprising 80 unique protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Expansion and contraction of the inverted repeat (IR) regions led to boundary shifts affecting genes, while nucleotide diversity within the large single-copy (LSC) and small single-copy (SSC) regions (Pi > 0.0035) markedly exceeded that of the conserved IR regions. Phylogenetic reconstruction revealed that C. sinensis ‘hainanensis’ shared the closest evolutionary relationship with Yunnan large-leaf tea (Camellia grandibracteata), supporting its independent lineage within the genus. A polymorphic molecular marker derived from the hypervariable non-coding region (trnT–psbD) may serve as a useful preliminary marker for distinguishing C. sinensis ‘hainanensis’ from related taxa and hybrids. This study provides the first comprehensive comparison of complete chloroplast genomes of six C. sinensis ‘hainanensis’, identifies three distinct plastome types, and develops a molecular marker that can reliably distinguish these types, offering valuable genomic resources for future studies on tea evolution and germplasm identification. Full article
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22 pages, 4709 KB  
Article
Sequencing, Assembly, and Comparative Evolutionary Analysis of the Chloroplast Genome of Kenaf (Hibiscus cannabinus L.)
by Ziyi Zhu, Juan Liu, Shenyue Tang, Qingqing Ji, Xingcai An, Junyuan Dong, Xiahong Luo, Changli Chen, Tingting Liu, Lina Zou, Shaocui Li, Mingbao Luan and Xia An
Genes 2025, 16(12), 1519; https://doi.org/10.3390/genes16121519 - 18 Dec 2025
Viewed by 603
Abstract
Background: Kenaf (Hibiscus cannabinus L.) is an important fiber crop belonging to the genus Hibiscus in the Malvaceae family. Research on its chloroplast genome holds significant importance for deciphering the evolutionary relationships of the Hibiscus species, developing genetic markers, and promoting kenaf [...] Read more.
Background: Kenaf (Hibiscus cannabinus L.) is an important fiber crop belonging to the genus Hibiscus in the Malvaceae family. Research on its chloroplast genome holds significant importance for deciphering the evolutionary relationships of the Hibiscus species, developing genetic markers, and promoting kenaf (H. cannabinus) genetic breeding. Methods: Based on high-throughput sequencing technology, this study completed the sequencing and assembly of the kenaf (H. cannabinus) chloroplast genome. Results: (1) The kenaf (H. cannabinus) chloroplast genome exhibits a typical circular quadripartite structure with a total length of 163,019 bp, including a large single-copy region (LSC) of 90,467 bp, a small single-copy region (SSC) of 19,486 bp, and a pair of inverted repeat regions (IRa/IRb) of 26,533 bp each. The total GC content is 36.62%, among which, the IR region has the highest GC content (42.61%) and the SSC region the lowest (30.87%). (2) A total of 131 genes were annotated, including 85 mRNAs, 37 tRNAs, 8 rRNAs, and 1 pseudogene. Their functions cover photosynthesis (e.g., pet and atp family genes), self-replication (e.g., rpl, rps, and rpo family genes), and genes with unknown functions (e.g., ycf1 and ycf2). A codon usage bias analysis revealed that the relative synonymous codon usage (RSCU) value of the stop codon UAA is the highest (1.6329), and codons ending with A/U are preferentially used (e.g., GCU for alanine with RSCU = 1.778). (3) A repeat sequence analysis identified various interspersed repeat sequences (predominantly 30~31 bp in length, with a relatively high proportion in the 30~40 bp range, including forward and palindromic types) and simple sequence repeats (cpSSRs). Among them, single-base repeat SSRs account for the highest proportion (e.g., (A)8 and (T)9), and specific SSR primers were designed. (4) A comparative evolutionary analysis indicated that the Ka/Ks ratios (nonsynonymous substitution rate/synonymous substitution rate) of core chloroplast genes (e.g., rps2 and rpoC2) in kenaf (H. cannabinus) are all less than 1 (0.145~0.415), suggesting that they are under purifying selection. The collinearity similarity of chloroplast genomes between kenaf (H. cannabinus) and its closely related species reaches over 99.97%, and the IR region boundaries are relatively conserved. The phylogenetic tree shows that kenaf (H. cannabinus) clusters with closely related Hibiscus species with a 100% bootstrap value, indicating a close genetic relationship. Conclusions: This study provides basic data for the functional analysis of the kenaf (H. cannabinus) chloroplast genome, the phylogeny of Hibiscus, and the utilization of genetic resources. Full article
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14 pages, 5353 KB  
Article
Comparative Analysis of Chloroplast Genomes in Sansevieria Reveals Phylogenetic Relationships and High Variability Molecular Markers
by Zhigang Hao, Hua Kong, Xiaojun Lv, Xiaoxi Du, Hui Zhao and Jinghua Lu
Agriculture 2025, 15(24), 2606; https://doi.org/10.3390/agriculture15242606 - 17 Dec 2025
Viewed by 612
Abstract
Sansevieria, a perennial herb known for its ornamental and medicinal value, has many varieties due to its leaf size and stripe color. However, it is very difficult to distinguish them during the seedling stage. In this study, we conducted chloroplast genome sequencing [...] Read more.
Sansevieria, a perennial herb known for its ornamental and medicinal value, has many varieties due to its leaf size and stripe color. However, it is very difficult to distinguish them during the seedling stage. In this study, we conducted chloroplast genome sequencing analysis on 10 cultivars of Sansevieria trifasciata. The chloroplast genomes exhibited a typical quadripartite circular structure (154.2–158.7 kb), encoding 113 functional genes with highly conserved gene order. Phylogenetic analysis supported the evolutionary linkage between Sansevieria and Dracaena. Dynamic inverted repeats (IR) boundary expansions/contractions, particularly species-specific patterns in ndhF and rps19 gene distributions across IR junctions, indicating its adaptive divergence. We also discovered the trnT-psbD marker, which is a deletion marker developed from hypervariable regions and can effectively distinguish closely related species. This work provides critical molecular tools and theoretical foundations for germplasm identification, phylogenetic reconstruction, and chloroplast genome evolution in Sansevieria, and also promotes taxonomic revisions in Asparagaceae. Full article
(This article belongs to the Section Crop Genetics, Genomics and Breeding)
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15 pages, 2091 KB  
Article
Complete Chloroplast Genome Characterization, and Phylogenetic Analyses of the Rare and Endangered Plant Platycrater arguta
by Xiaohua Ma, Youju Ye, Ren’an Lin, Qingdi Hu, Xule Zhang, Yaping Hu, Lei Feng, Renjuan Qian and Jian Zheng
Biology 2025, 14(12), 1726; https://doi.org/10.3390/biology14121726 - 1 Dec 2025
Cited by 1 | Viewed by 696
Abstract
As an important rare and endangered plant, Platycrater arguta urgently requires protective measures. In this study, we assembled and annotated a more complete chloroplast genome of P. arguta, which has a size of 157,812 bp. The chloroplast genome comprises a large single-copy [...] Read more.
As an important rare and endangered plant, Platycrater arguta urgently requires protective measures. In this study, we assembled and annotated a more complete chloroplast genome of P. arguta, which has a size of 157,812 bp. The chloroplast genome comprises a large single-copy (LSC) region of 86,825 bp, a small single-copy (SSC) region of 18,735 bp, and a pair of inverted repeats (IRa and IRb) of 26,126 bp each. SSR detection revealed that the chloroplast genome contains 199 simple repeat loci, with mononucleotide repeats of A and T being the most frequent, accounting for 59.8%. Comparative analysis of the chloroplast genome structure showed that the IR region boundaries are relatively conserved. The results of the phylogenetic tree indicate that P. arguta shares high homology with Hydrangea davidii. This work provides a scientific basis for future research on the genetics, biology, and conservation of P. arguta. Full article
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18 pages, 6094 KB  
Article
Evolutionary Dynamics of Chloroplast Genome and Codon Usage in the Genus Diospyros (Ebenaceae)
by Jisi Zhang and Zhuo Li
Biology 2025, 14(11), 1568; https://doi.org/10.3390/biology14111568 - 9 Nov 2025
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Abstract
Diospyros, the most species-rich woody plant genus in Ebenaceae, has attracted significant academic interest due to its ecological and economic importance. This study presented the first complete assembly and annotation of the chloroplast genome of Diospyros tsangii. The chloroplast genome measured [...] Read more.
Diospyros, the most species-rich woody plant genus in Ebenaceae, has attracted significant academic interest due to its ecological and economic importance. This study presented the first complete assembly and annotation of the chloroplast genome of Diospyros tsangii. The chloroplast genome measured 157,445 bp, with a typical quadripartite circular structure and 132 annotated coding genes. A comprehensive analysis of evolutionary traits and codon usage preferences across chloroplast genomes of 15 Diospyros species were conducted. The main objective was to provide a theoretical basis for understanding phylogenetic relationships and assessing genetic diversity within Diospyros. Our findings showed that genetic diversity in the IR regions of the chloroplast genomes is notably lower than that in the LSC and SSC regions. The boundary regions exhibited high conservation with minimal variation. Selected pressure analysis indicated that most coding genes are under purifying selection. Phylogenetic analysis showed that D. tangii was sister to Diospyros oleifera, and Diospyros kaki was closely related to Diospyros vaccinioides with high supporting values. The examination of codon usage patterns showed that the GC content at the first, second, and third codon positions of 52 protein-coding sequences followed the order GC1 > GC2 > GC3, with a preference for A or U bases at the third position. The effective number of codons ranged from 45.13 to 45.43, which indicated the weak codon bias. The neutral-plot, ENC-plot, and PR2-plot analysis suggested that natural selection predominantly influences the codon usage patterns in Diospyros plants. These results would be vital to understand the evolutionary dynamics of the genus Diospyros. Full article
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