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24 pages, 2121 KiB  
Article
Camellia japonica Flower Extract and the Active Constituent Hyperoside Repair DNA Damage Through FUNDC1-Mediated Mitophagy Pathway for Skin Anti-Aging
by Hongqi Gao, Jiahui Shi, Guangtao Li, Zhifang Lai, Yan Liu, Chanling Yuan and Wenjie Mei
Antioxidants 2025, 14(8), 968; https://doi.org/10.3390/antiox14080968 (registering DOI) - 6 Aug 2025
Abstract
Skin aging is closely related to mitochondrial dysfunction and cell cycle abnormalities, and developing intervention strategies targeting mitochondrial quality control is an important direction for anti-aging research. In this study, we investigated the anti-aging mechanism of Camellia japonica flower (CJF) extract and its [...] Read more.
Skin aging is closely related to mitochondrial dysfunction and cell cycle abnormalities, and developing intervention strategies targeting mitochondrial quality control is an important direction for anti-aging research. In this study, we investigated the anti-aging mechanism of Camellia japonica flower (CJF) extract and its active ingredient hyperoside based on a doxorubicin (DOX)-induced endogenous senescence model in human skin fibroblasts (HSFs). LC-MS proteomics analysis revealed that CJF extract and hyperoside specifically activated the FUNDC1-mediated mitochondrial autophagy pathway, significantly ameliorated the DOX-induced decrease in mitochondrial membrane potential and the accumulation of reactive oxygen species (ROS), and alleviated the cellular S-phase blockade and reversed the high expression of senescence-associated β-galactosidase (SA-β-gal). Further studies showed that the two cleared damaged mitochondria by enhancing mitochondrial autophagy and restoring cellular energy metabolism homeostasis while promoting type III collagen and elastin synthesis and repairing the expression of Claudin 1 related to skin barrier function. For the first time, the present study reveals the molecular mechanism of CJF extract in delaying skin aging by regulating the FUNDC1-dependent mitochondrial autophagy pathway, which provides a theoretical basis and a candidate strategy for developing novel anti-aging agents targeting mitochondrial quality control. Full article
(This article belongs to the Section Extraction and Industrial Applications of Antioxidants)
16 pages, 4197 KiB  
Review
Conformational Dynamics and Structural Transitions of Arginine Kinase: Implications for Catalysis and Allergen Control
by Sung-Min Kang
Life 2025, 15(8), 1248; https://doi.org/10.3390/life15081248 - 6 Aug 2025
Abstract
Arginine kinase is a key phosphagen kinase in invertebrates that facilitates rapid ATP regeneration by reversibly transferring phosphate groups between phosphoarginine and ADP. Structural studies have shown that the enzyme adopts distinct conformations in its ligand-free and ligand-bound states, known as the “open” [...] Read more.
Arginine kinase is a key phosphagen kinase in invertebrates that facilitates rapid ATP regeneration by reversibly transferring phosphate groups between phosphoarginine and ADP. Structural studies have shown that the enzyme adopts distinct conformations in its ligand-free and ligand-bound states, known as the “open” and “closed” forms, respectively. These conformational changes are crucial for catalytic activity, enabling precise positioning of active-site residues and loop closure during phosphoryl transfer. Transition-state analog complexes have provided additional insights by mimicking intermediate states of catalysis, supporting the functional relevance of the open/closed structural model. Furthermore, studies across multiple species reveal how monomeric and dimeric forms of arginine kinase contribute to its allosteric regulation and substrate specificity. Beyond its metabolic role, arginine kinase is also recognized as a major allergen in crustaceans. Its structural uniqueness and absence in vertebrates make it a promising candidate for selective drug targeting. By integrating crystallographic data with functional context, this review highlights conserved features and species-specific variations of arginine kinase that may inform the design of inhibitors. Such molecules have the potential to serve both as antiparasitic agents and as novel therapeutics to manage crustacean-related allergic responses in humans. Full article
(This article belongs to the Section Proteins and Proteomics)
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15 pages, 1820 KiB  
Article
Ozone Treatment Modulates Reactive Oxygen Species Metabolism Regulation and Enhances Storage Quality of Kiwifruit During Cold Storage
by Ziyu Jin, Jin Tan, Xinyu Zhang, Xin Li, Wenqiang Guan, Pu Liu and Aiqiang Chen
Horticulturae 2025, 11(8), 911; https://doi.org/10.3390/horticulturae11080911 (registering DOI) - 4 Aug 2025
Abstract
Fresh fruit are highly perishable commodities, facing significant postharvest losses primarily due to physiological deterioration and microbial spoilage. Conventional preservation methods often face limitations regarding safety, residue, and environmental impact. Because of its rapid decomposition and low-residue-impact characteristics, ozone has proven superior as [...] Read more.
Fresh fruit are highly perishable commodities, facing significant postharvest losses primarily due to physiological deterioration and microbial spoilage. Conventional preservation methods often face limitations regarding safety, residue, and environmental impact. Because of its rapid decomposition and low-residue-impact characteristics, ozone has proven superior as an efficient and eco-friendly solution for preserving fruit quality after harvest. The maturation and aging processes of kiwifruit are closely linked to the involvement of reactive oxygen species (ROS) metabolism. This study aimed to investigate the effects of intermittent ozone treatment (21.4 mg/m3, applied for 0, 1, 3, or 5 h weekly) on ROS metabolism, the antioxidant defense system, and storage quality of kiwifruit during cold storage (0.0 ± 0.5 °C). The results showed ozone treatment slowed the decline in titratable acid (TA) content and fruit firmness, inhibited increases in total soluble solids (TSSs) and weight loss, and maintained the storage quality. Additionally, ozone treatment enhanced the activities of antioxidant-related enzymes. This includes superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX). Furthermore, it delayed the reduction in ascorbate (ASA), glutathione (GSH), total phenolic compounds, and flavonoid content, while also preventing the accumulation of ROS and the rise in malondialdehyde (MDA) levels. In summary, the results indicate that ozone treatment enhances the antioxidant capacity of kiwifruit by increasing the structural integrity of cell membranes, preserving the structural integrity of cell membranes, and effectively maintaining the storage quality of the fruit. Full article
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13 pages, 9267 KiB  
Article
Curcuma nivea (Zingiberaceae), a New Compact Species with Horticultural Potential from Eastern Thailand
by Piyaporn Saensouk, Surapon Saensouk, Charun Maknoi, Det Song and Thawatphong Boonma
Horticulturae 2025, 11(8), 908; https://doi.org/10.3390/horticulturae11080908 (registering DOI) - 4 Aug 2025
Viewed by 46
Abstract
The genus Curcuma (Zingiberaceae) is a diverse group of plants widely distributed across tropical Asia, with several new species recently described in Thailand. This study documents and clarifies the taxonomic status of a new species, Curcuma nivea Saensouk, P.Saensouk & Boonma sp. nov., [...] Read more.
The genus Curcuma (Zingiberaceae) is a diverse group of plants widely distributed across tropical Asia, with several new species recently described in Thailand. This study documents and clarifies the taxonomic status of a new species, Curcuma nivea Saensouk, P.Saensouk & Boonma sp. nov., discovered in eastern Thailand, and evaluates its horticultural potential. Morphological comparisons were conducted with closely related species in the Curcuma subgenus Hitcheniopsis (Baker) K. Schum., focusing on diagnostic vegetative and floral traits. Curcuma nivea is characterized by its compact habit and white flowers marked with two reddish lines at the base of the labellum, lacking the yellow blotch typical of related species. Additionally, it shows the absence of both epigynous glands and anther spurs, consistent with subgeneric features. Its distinctive morphology and attractive floral display have led to its cultivation as an ornamental pot plant. The discovery of C. nivea contributes to the growing documentation of Curcuma diversity in Thailand and underscores the significance of ongoing botanical exploration and conservation. Furthermore, its compact form and unique floral traits highlight its promise for use in ornamental horticulture and breeding programs. Full article
(This article belongs to the Section Medicinals, Herbs, and Specialty Crops)
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21 pages, 3086 KiB  
Article
Integrative Population Genomics Reveals Niche Differentiation and Gene Flow in Chinese Sclerophyllous Oaks (Quercus Sect. Ilex)
by Miao-Miao Ju, Ming Yue and Gui-Fang Zhao
Plants 2025, 14(15), 2403; https://doi.org/10.3390/plants14152403 - 3 Aug 2025
Viewed by 198
Abstract
Elucidating the coexistence mechanisms of rapidly diverging species has long been a challenge in evolutionary biology. Genome-wide polymorphic loci are expected to provide insights into the speciation processes of these closely related species. This study focused on seven Chinese sclerophyllous oaks, represented by [...] Read more.
Elucidating the coexistence mechanisms of rapidly diverging species has long been a challenge in evolutionary biology. Genome-wide polymorphic loci are expected to provide insights into the speciation processes of these closely related species. This study focused on seven Chinese sclerophyllous oaks, represented by Quercus spinosa, Quercus aquifolioides, Quercus rehderiana, Quercus guyavifolia, Quercus monimotricha, Quercus semecarpifolia, and Quercus senescens, employing 27,592 single-nucleotide polymorphisms to examine their phylogenetic relationships at the genomic level. Combined with genetic structure analysis, phylogenetic trees revealed that the genetic clustering of individuals was influenced by both geographic distance and ancestral genetic components. Furthermore, this study confirmed the existence of reticulate evolutionary relationships among the species. Frequent gene flow and introgression within the seven species were primarily responsible for the ambiguous interspecies boundaries, with hybridization serving as a major driver of reticulate evolution. Additionally, the seven species exhibited distinct differences in niche occupancy. By reconstructing the climatic adaptability of ancestral taxonomic units, we found that the climatic tolerance of each species displayed differential responses to 19 climatic factors. Consequently, ecological niche differentiation and variations in habitat adaptation contributed to the preservation of species boundaries. This study provides a comprehensive understanding of the speciation processes in rapidly diverging genera and underscores the significance of both genetic and ecological factors in the formation and maintenance of species boundaries. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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17 pages, 3038 KiB  
Article
Neighbor Relatedness Contributes to Improvement in Grain Yields in Rice Cultivar Mixtures
by You Xu, Qin-Hang Han, Shuai-Shuai Xie and Chui-Hua Kong
Plants 2025, 14(15), 2385; https://doi.org/10.3390/plants14152385 - 2 Aug 2025
Viewed by 248
Abstract
The improvement in yield in cultivar mixtures has been well established. Despite increasing knowledge of the improvement involving within-species diversification and resource use efficiency, little is known about the benefits arising from relatedness-mediated intraspecific interactions in cultivar mixtures. This study used a relatedness [...] Read more.
The improvement in yield in cultivar mixtures has been well established. Despite increasing knowledge of the improvement involving within-species diversification and resource use efficiency, little is known about the benefits arising from relatedness-mediated intraspecific interactions in cultivar mixtures. This study used a relatedness gradient of rice cultivars to test whether neighbor relatedness contributes to improvements in grain yields in cultivar mixtures. We experimentally demonstrated the grain yield of rice cultivar mixtures with varying genetic relatedness under both field and controlled conditions. As a result, a closely related cultivar mixture had increased grain yield compared to monoculture and distantly related mixtures by optimizing the root-to-shoot ratio and accelerating flowering. The benefits over monoculture were most pronounced when compared to the significant yield reductions observed in distantly related mixtures. The relatedness-mediated improvement in yields depended on soil volume and nitrogen use level, with effects attenuating under larger soil volumes or nitrogen deficiency. Furthermore, neighbor relatedness enhanced the richness and diversity of both bacterial and fungal communities in the rhizosphere soil, leading to a significant restructuring of the microbial community composition. These findings suggest that neighbor relatedness may improve the grain yield of rice cultivar mixtures. Beneficial plant–plant interactions may be generated by manipulating cultivar kinship within a crop species. A thorough understanding of kinship strategies in cultivar mixtures offers promising prospects for increasing crop production. Full article
(This article belongs to the Special Issue Plant Chemical Ecology—2nd Edition)
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15 pages, 1194 KiB  
Article
DNA Methylation-Associated Epigenetic Changes in Thermotolerance of Bemisia tabaci During Biological Invasions
by Tianmei Dai, Yusheng Wang, Xiaona Shen, Zhichuang Lü, Fanghao Wan and Wanxue Liu
Int. J. Mol. Sci. 2025, 26(15), 7466; https://doi.org/10.3390/ijms26157466 - 1 Aug 2025
Viewed by 129
Abstract
Global warming and anthropogenic climate change are projected to expand the geographic distribution and population abundance of ectothermic species and exacerbate the biological invasion of exotic species. DNA methylation, as a reversible epigenetic modification, could provide a putative link between the phenotypic plasticity [...] Read more.
Global warming and anthropogenic climate change are projected to expand the geographic distribution and population abundance of ectothermic species and exacerbate the biological invasion of exotic species. DNA methylation, as a reversible epigenetic modification, could provide a putative link between the phenotypic plasticity of invasive species and environmental temperature variations. We assessed and interpreted the epigenetic mechanisms of invasive and indigenous species’ differential tolerance to thermal stress through the invasive species Bemisia tabaci Mediterranean (MED) and the indigenous species Bemisia tabaci AsiaII3. We examine their thermal tolerance following exposure to heat and cold stress. We found that MED exhibits higher thermal resistance than AsiaII3 under heat stress. The fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) results proved that the increased thermal tolerance in MED is closely related to DNA methylation changes, other than genetic variation. Furthermore, the quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting analysis of DNA methyltransferases (Dnmts) suggested that increased expression of Dnmt3 regulates the higher thermal tolerance of female MED adults. A mechanism is revealed whereby DNA methylation enhances thermal tolerance in invasive species. Our results show that the Dnmt-mediated regulation mechanism is particularly significant for understanding invasive species’ successful invasion and rapid adaptation under global warming, providing new potential targets for controlling invasive species worldwide. Full article
(This article belongs to the Section Molecular Biology)
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17 pages, 877 KiB  
Review
Mitochondrial Metabolism in T-Cell Exhaustion
by Fei Li, Yu Feng, Zesheng Yin and Yahong Wang
Int. J. Mol. Sci. 2025, 26(15), 7400; https://doi.org/10.3390/ijms26157400 - 31 Jul 2025
Viewed by 440
Abstract
T cells play a vital role in resisting pathogen invasion and maintaining immune homeostasis. However, T cells gradually become exhausted under chronic antigenic stimulation, and this exhaustion is closely related to mitochondrial dysfunction in T cells. Mitochondria play a crucial role in the [...] Read more.
T cells play a vital role in resisting pathogen invasion and maintaining immune homeostasis. However, T cells gradually become exhausted under chronic antigenic stimulation, and this exhaustion is closely related to mitochondrial dysfunction in T cells. Mitochondria play a crucial role in the metabolic reprogramming of T cells to achieve the desired immune response. Here, we compiled the latest research on how mitochondrial metabolism determines T cell function and differentiation, with the mechanisms mainly including mitochondrial biogenesis, fission, fusion, mitophagy, and mitochondrial transfer. In addition, the alterations in mitochondrial metabolism in T-cell exhaustion were also reviewed. Furthermore, we discussed intervention strategies targeting mitochondrial metabolism to reverse T cell exhaustion in detail, including inducing PGC-1α expression, alleviating reactive oxygen species (ROS) production or hypoxia, enhancing ATP production, and utilizing mitochondrial transfer. Targeting mitochondrial metabolism in exhausted T cells may achieve the goal of reversing and preventing T cell exhaustion. Full article
(This article belongs to the Special Issue Mitochondria: Transport of Metabolites Across Biological Membranes)
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18 pages, 2943 KiB  
Article
Cadmium Inhibits Proliferation of Human Bronchial Epithelial BEAS-2B Cells Through Inducing Ferroptosis via Targeted Regulation of the Nrf2/SLC7A11/GPX4 Pathway
by Huan Li, Zixin Qiu, Long Chen, Tianbao Zhang, Diandian Wei, Xue Chen and Yun Wang
Int. J. Mol. Sci. 2025, 26(15), 7204; https://doi.org/10.3390/ijms26157204 - 25 Jul 2025
Viewed by 245
Abstract
Cadmium (Cd)-induced pulmonary toxicity is closely associated with ferroptosis, a regulated form of cell death characterized by iron-dependent lipid peroxidation (LPO). Luteolin (Lut) is a natural flavonoid compound that exists in many plants. In this study, we used human bronchial epithelial BEAS-2B cells [...] Read more.
Cadmium (Cd)-induced pulmonary toxicity is closely associated with ferroptosis, a regulated form of cell death characterized by iron-dependent lipid peroxidation (LPO). Luteolin (Lut) is a natural flavonoid compound that exists in many plants. In this study, we used human bronchial epithelial BEAS-2B cells to explore the impact of ferroptosis in the inhibition of Cd-induced BEAS-2B cells proliferation. BEAS-2B cells were exposed to Cd (5 μM) with/without Lut (10 μM), ferroptosis modulators (Ferrostatin-1 (Fer-1)/Erastin), or nuclear factor erythroid 2-related factor 2 (Nrf2) regulators (tert-butylhydroquinone (TBHQ)/ML385). Viability, iron content, reactive oxygen species (ROS), LPO, mitochondrial membrane potential (MMP), and glutathione peroxidase (GSH-PX) activity were assessed. Exposure to Cd significantly decreased cell viability, increased intracellular iron levels, ROS production, and LPO activity, while simultaneously reducing MMP and GSH-PX activity. Fer-1 mitigated Cd-induced cytotoxicity, but Erastin intensified these effects. Mechanistically, Cd exposure suppressed the Nrf2/Solute Carrier Family 7 Member 11 (SLC7A11)/glutathione peroxidase 4 (GPX4) signaling pathway, which plays a crucial role in maintaining redox homeostasis. Activation of Nrf2 using TBHQ mitigated oxidative stress and upregulated the expression of key proteins within this pathway, while inhibition of Nrf2 with ML385 exacerbated cellular damage. Notably, Lut treatment could significantly alleviate Cd-induced cytotoxicity, oxidative stress, and downregulation of Nrf2/SLC7A11/GPX4 proteins. These findings demonstrate that ferroptosis is a critical mechanism underlying Cd-mediated lung epithelial injury and identify Lut as a promising therapeutic candidate via its activation of Nrf2-driven antioxidant defense mechanisms. This study provides novel insights into molecular targets for the prevention and treatment of Cd-associated pulmonary disorders. Full article
(This article belongs to the Section Biochemistry)
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28 pages, 16355 KiB  
Article
Renicola spp. (Digenea, Renicolidae) of the ‘Duck Clade’ with Description of the Renicola mollissima Kulachkova, 1957 Life Cycle
by Kirill V. Galaktionov, Anna I. Solovyeva, Aleksei A. Miroliubov, Kira V. Regel and Anna E. Romanovich
Diversity 2025, 17(8), 512; https://doi.org/10.3390/d17080512 - 25 Jul 2025
Viewed by 272
Abstract
Renicolid digeneans parasitise aquatic birds. In molecular trees, they are divided into three clades, one of which, the ‘duck clade’, parasitises anatids. Renicola mollissima, a member of this clade, parasitises sea ducks, mainly eiders. Its life cycle remains unknown. We verified the [...] Read more.
Renicolid digeneans parasitise aquatic birds. In molecular trees, they are divided into three clades, one of which, the ‘duck clade’, parasitises anatids. Renicola mollissima, a member of this clade, parasitises sea ducks, mainly eiders. Its life cycle remains unknown. We verified the diagnosis of R. mollissima using integrated morphological and molecular data and provided the first information on its life cycle in northern Palaearctic. We proved that intramolluscan stages of R. mollissima, previously known as Cercaria pacifica 2, develop in intertidal snails Littorina squalida and L. saxatilis. We provided a detailed morphological description of cercariae and adults of R. mollissima and a discriminative analysis with closely related species. Molecular data demonstrated an amphiboreal distribution of R. mollissima and the existence of a single population in Europe and the North Pacific. Using molecular methods, we also found metacercariae of an unknown renicolid species from the ‘duck clade’, designated as Cercaria cf. nordica I, in subtidal mussels of the Barents Sea. All individuals of C. cf. nordica I examined in our study were represented by the same haplotype. We discuss possible ways of formation of this phylogeographic structure, the composition of the ‘duck clade’ and the evolutionary pathways of the family Renicolidae. Full article
(This article belongs to the Section Marine Diversity)
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17 pages, 5736 KiB  
Article
Unveiling Adulteration in Herbal Markets: MassARRAY iPLEX Assay for Accurate Identification of Plumbago indica L.
by Kannika Thongkhao, Aekkhaluck Intharuksa and Ampai Phrutivorapongkul
Int. J. Mol. Sci. 2025, 26(15), 7168; https://doi.org/10.3390/ijms26157168 - 24 Jul 2025
Viewed by 216
Abstract
The root of Plumbago indica L. is commercially available in herbal markets in both crude and powdered forms. P. indica root is a key ingredient in numerous polyherbal formulations. However, P. indica has two closely related species, P. zeylanica L. and P. auriculata [...] Read more.
The root of Plumbago indica L. is commercially available in herbal markets in both crude and powdered forms. P. indica root is a key ingredient in numerous polyherbal formulations. However, P. indica has two closely related species, P. zeylanica L. and P. auriculata Lam. Since only P. indica is traditionally used in Thai polyherbal products, adulteration with other species could potentially compromise the therapeutic efficacy and overall effectiveness of these formulations. To address this issue, a MassARRAY iPLEX assay was developed to accurately identify and differentiate P. indica from its closely related species. Five single nucleotide polymorphism (SNP) sites—positions 18, 112, 577, 623, and 652—within the internal transcribed spacer (ITS) region were selected as genetic markers for species identification. The assay demonstrated high accuracy in identifying P. indica and was capable of detecting the species at DNA concentrations as low as 0.01 ng/µL. Additionally, the assay successfully identified P. zeylanica in commercial crude drug samples, highlighting potential instances of adulteration. Furthermore, it was able to distinguish P. indica in mixed samples containing P. indica, along with either P. zeylanica or P. auriculata. The developed MassARRAY iPLEX assay proves to be a reliable and effective molecular tool for authenticating P. indica raw materials. Its application holds significant potential for ensuring the integrity of herbal products by preventing misidentification and adulteration. Full article
(This article belongs to the Section Molecular Pharmacology)
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27 pages, 1254 KiB  
Article
Evaluating Inflorescence Morphology in Two Species and Subspecies of the Genus Hierochloë R. Brown
by Károly Penksza, Tünde Szabó-Szöllösi, András Neményi, László Sipos, Szilárd Szentes, Zsombor Wagenhoffer, Balázs Palla, Dániel Ákos Balogh and Eszter Saláta-Falusi
Plants 2025, 14(15), 2270; https://doi.org/10.3390/plants14152270 - 23 Jul 2025
Viewed by 166
Abstract
(1) The primary objective was to determine whether, within this taxonomically challenging group, the closely related European species and their subspecies exhibit distinct inflorescence characters that allow for unambiguous differentiation. This study focuses on two closely related species within the genus Hierochloë: [...] Read more.
(1) The primary objective was to determine whether, within this taxonomically challenging group, the closely related European species and their subspecies exhibit distinct inflorescence characters that allow for unambiguous differentiation. This study focuses on two closely related species within the genus Hierochloë: Hierochloë hirta (Schrank) Borbás and Hierochloë odorata (L.) Beauv. (2) For four subspecies, data were collected from 15 inflorescences each, while for one subspecies, 10 inflorescences were examined. From each inflorescence, six spikelets were selected. The statistical analyses were non-parametric methods, the Kruskal–Wallis test, and principal component analysis. (3) Morphological traits showed consistent patterns within each subspecies, indicating their suitability for taxonomic differentiation. The most reliable diagnostic traits were the length of the outer glume of the first flower and the lengths of the awns. (4) The study concludes that while some subspecies can be clearly distinguished based on inflorescence morphology, no single trait is sufficient to completely separate all taxa. The authors recommend recognizing Hierochloë odorata subsp. praetermissa as a subspecies rather than a distinct species and affirm the validity of the species names Hierochloë hirta and Hierochloë odorata. Full article
(This article belongs to the Section Plant Systematics, Taxonomy, Nomenclature and Classification)
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12 pages, 5254 KiB  
Article
The Complete Mitochondrial Genome of a Natural Triploid Crucian Carp Mutant, Carassius auratus var. suogu, and Its Phylogenetic Analysis
by Yicheng Zhou, Binhua Deng, Shengyue Lin, Shuzheng Ye, Peng Zheng, Guojun Cai, Weiqian Liang, Chong Han and Qiang Li
Life 2025, 15(8), 1156; https://doi.org/10.3390/life15081156 - 22 Jul 2025
Viewed by 280
Abstract
Carassius auratus var. suogu, an endemic fish in southern China, is a natural triploid crucian carp mutant. In this study, the characteristics of mitochondrial DNA sequences were analyzed to understand their taxonomic status and genetic background at the gene level. The complete [...] Read more.
Carassius auratus var. suogu, an endemic fish in southern China, is a natural triploid crucian carp mutant. In this study, the characteristics of mitochondrial DNA sequences were analyzed to understand their taxonomic status and genetic background at the gene level. The complete mitochondrial genome of C. auratus var. suogu (length, 16,580 bp) comprises 37 genes (13 protein-coding genes, 22 transfer RNA (tRNAs) genes, and 2 ribosomal RNA (rRNAs) genes) and a non-coding control region. The RSCU of the mtDNA of Carassius was similar. Ka/Ks analyses showed the ND4 gene had the highest evolutionary rate. Moreover, the whole mitogenome sequences and D-loop region were employed to examine phylogenetic relationships among C. auratus var. suogu and other closely related species. The result indicated that Carassius auratus suogu var clustered with Carassius auratus auratus and divided Carassius into four clades, providing new insights and data support for the taxonomic status of Carassius. Full article
(This article belongs to the Section Genetics and Genomics)
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19 pages, 12441 KiB  
Article
Mitogenome Characteristics and Intracellular Gene Transfer Analysis of Four Adansonia Species
by Tingting Hu, Fengjuan Zhou, Lisha Wang, Xinwei Hu, Zhongxiang Li, Xinzeng Li, Daoyuan Zhou and Hui Wang
Genes 2025, 16(7), 846; https://doi.org/10.3390/genes16070846 - 21 Jul 2025
Viewed by 287
Abstract
Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the ‘tree of life.’ Although its nuclear genome has been reported, the mitogenome [...] Read more.
Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the ‘tree of life.’ Although its nuclear genome has been reported, the mitogenome has not yet been studied. Mitogenome research is crucial for understanding the evolution of the entire genome. In this study, we assembled and analyzed the mitogenomes of four Adansonia species by integrating short-read and long-read data. The results showed that the mitogenomes of all four Adansonia species were resolved as single circular sequences. Their total genome lengths ranged from 507,138 to 607,344 bp and contained a large number of repetitive sequences. Despite extensive and complex rearrangements between the mitogenomes of Adansonia and other Malvaceae species, a phylogenetic tree constructed based on protein-coding genes clearly indicated that Adansonia is more closely related to the Bombax. Selection pressure analysis suggests that the rps4 gene in Adansonia may have undergone positive selection compared to other Malvaceae species, indicating that this gene may play a significant role in the evolution of Adansonia. Additionally, by analyzing intracellular gene transfer between the chloroplast, mitochondria, and nuclear genomes, we found that genes from the chloroplast and mitochondria can successfully transfer to each chromosome of the nuclear genome, and the psbJ gene from the chloroplast remains intact in both the mitochondrial and nuclear genomes. This study enriches the genetic information of Adansonia and provides important evidence for evolutionary research in the family Malvaceae. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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16 pages, 10516 KiB  
Article
Morphological and Phylogenetic Characterization of Alternaria Section Undifilum Fungal Endophytes from Astragalus and Swainsona spp.
by Marwa Neyaz, Olabisi Adebisi, Daniel Cook and Rebecca Creamer
J. Fungi 2025, 11(7), 541; https://doi.org/10.3390/jof11070541 - 19 Jul 2025
Viewed by 472
Abstract
The locoweeds Astragalus and Oxytropis in the Americas and China, as well as Swainsona in Australia, harbor swainsonine-producing endophytes responsible for “locoism” or “pea struck” syndromes in grazing animals. Demonstration of Alternaria section Undifilum spp. requires demonstration of morphological characters such as a [...] Read more.
The locoweeds Astragalus and Oxytropis in the Americas and China, as well as Swainsona in Australia, harbor swainsonine-producing endophytes responsible for “locoism” or “pea struck” syndromes in grazing animals. Demonstration of Alternaria section Undifilum spp. requires demonstration of morphological characters such as a wavy germ tube and slow growth. While Astragalus wetherilli, A. pubentissimus, Swainsona canescens, and S. galegifolia plants have been shown to contain swainsonine, and fungi isolated from the plants have been partially characterized genetically, the fungi have not been characterized morphologically. This work sought to complete morphological characterization and determine species for those fungi and from fungi associated with Swainsona luteola and S. brachycarpa. The fungi were isolated from their hosts onto media and exhibited slow growth, resulting in a colony diameter of approximately 10 mm after 30 days. Morphological identification revealed production of conidia that produced a wavy germ tube for the endophytes from Astragalus pubentissimus species, Swainsona canescens, and S. galegifolia. Sequence analyses of the ITS region and the swnK-KS and swnK-TR genes of these fungi suggest that the fungi isolated from Astragalus are closely related and distinct from the fungi isolated from Swainsona. Presence of the swnK gene demonstrates that all the fungi have a necessary component to produce swainsonine. Fungi isolated from Astragalus spp. differed in color, growth, and conidium size, and/or their sequences. While the fungi isolated from Swainsona canescens and S. galegifolia endophytes differed in color, growth, and conidium size, those isolated from Swainsona luteola and S. brachycarpa did not produce conidia. Sequences from all Swainsona endophytes were almost identical and were concluded to be the same species. The new species described here are Alternaria wetherii, A. pubentissima, A. pubentissimoides, and A. swainsonii. Full article
(This article belongs to the Special Issue Fungal Endophytes of Plants: Friend or Foe?)
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