Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Identification of potential key genes and molecular mechanisms of oral squamous cell carcinoma based on integrated bioinformatics approach","authors":"Mohammad Khursheed Alam ,&nbsp;Md Rakibul Islam ,&nbsp;Tahsinul Haque ,&nbsp;Kiran Kumar Ganji ,&nbsp;Hamzah Ali Babkair ,&nbsp;Mohammed Enamur Rashid ,&nbsp;Kawsar Ahmed ,&nbsp;Francis M. Bui","doi":"10.1016/j.jgeb.2026.100668","DOIUrl":"10.1016/j.jgeb.2026.100668","url":null,"abstract":"<div><div>Oral Squamous Cell Carcinoma (OSCC) is one of the most occurred cancer types with yearly 377,713 cases and 177,000 deaths. Traditional risk factors of OSCC include smoking, alcohol consumption, excessive sun exposure, family history of cancer, and human papillomavirus (HPV). Last few years, the prevalence of OSCC is growing big in numbers particularly among younger people for their lifestyle. From the Gene Expression Omnibus, 2 gene-expression profiles (GSE23558 and GSE146483) were identified based on some conditions. The GEO2R tool was used to analyze those datasets to extract all the genes. Statistical cut-off criteria were applied to find out DEGs from both datasets, and after that common DEGs were identified by comparing both datasets. Common DEGs were used to perform bioinformatics analysis such as gene ontology and pathway analysis, protein–protein interaction (PPI) network construction, and generating Transcription factor − miRNA network. 265 common DEGs were identified from the datasets including 69 up-regulated and 196 down-regulated DEGs. Using the STRING database and a strong combine score &gt; 0.70, a PPI network is generated including 92 nodes and 226 interactions. Using 3 different hub DEGs seeking algorithm, we identified 9 top hub DEGs. The hub genes are Kinesin Family Member 23 (KIF23), Aurora Kinase A (AURKA), Centromere Protein F (CENPF), Cell Division Cycle 20 (CDC20), Discs Large Associated Protein 5 (DLGAP5), Centrosomal Protein 55 (CEP55), Anillin Actin Binding Protein (ANLN), Non-SMC Condensin I Complex Subunit G (NCAPG), and Kinesin Family Member 14 (KIF14). 3 significant clusters also identified from the PPI network. Previous study shows KIF23 takes part in raising Cell Proliferation in Hepatocellular carcinoma cells and AURKA shows notable overexpression in cancer tissues, which indicates that KIF23 and AURKA showed promising character to become possible biomarkers for OSCC. Further analysis needed to justify the statement.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100668"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147395710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimization of somatic embryogenesis protocol for Hevea brasiliensis clones RRIM 600 and REYAN 88-13","authors":"Florence Dessailly ,&nbsp;Li Zhe ,&nbsp;Florence Martin ,&nbsp;Julie Petit-Briand ,&nbsp;Pascal Montoro ,&nbsp;Julie Leclercq","doi":"10.1016/j.jgeb.2025.100640","DOIUrl":"10.1016/j.jgeb.2025.100640","url":null,"abstract":"<div><div>The challenges for the development of rubber cultivation are so agronomically significant in the face of climate change that it is crucial to introduce biotechnology into the clonal propagation of rubber trees. A protocol was developed on rubber clone PB 260. This protocol was used for two other clones, RRIM 600 and REYAN 88-13, which exhibited highly contrasting response to callus growth and embryogenic capacity. Optimization of somatic embryogenesis for these two clones led us to successful conduct genetic transformation trials. We discussed the <em>in vitro</em> behaviour of the calli considering the origin of the embryogenic callus and the endogenous redox status.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100640"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tissue culture and elicitor applications for sustainable secondary metabolite enhancement in Mentha longifolia (L.) Huds","authors":"Shaimaa N. Mizil","doi":"10.1016/j.jgeb.2025.100655","DOIUrl":"10.1016/j.jgeb.2025.100655","url":null,"abstract":"<div><div><em>Mentha longifolia</em> (L.) Huds., an aromatic herb from the <em>Lamiaceae</em> family, is well known for its bioactive compounds and high demand in the food, cosmetic, and pharmaceutical industries. To overcome several challenges due to overharvesting, disease, and climate change, a dependable, sustainable production method for the important secondary metabolites is necessary, and steady metabolite production under regulated circumstances may be achievable through plant tissue culture. <em>M. longifolia</em> callus cultures were used in this research to evaluate the effects of elicitors, methyl jasmonate (MeJA), salicylic acid (SA), and yeast extract (YE) on biomass accumulation and metabolite synthesis. Murashige and Skoog (MS) medium fortified with 1 mg/l 2,4-D was used to produce calli formed from leaves, which were then subjected to varying concentrations of elicitor. HPLC, quantitative analysis of phenolics, flavonoids, alkaloids, and essential oils were evaluated. The findings indicated that MeJA, at 100 µM supplementation, significantly increased biomass (dry weight increased by 65.12%) and metabolite accumulation, producing the significant levels of phenolics (95.3 ± 4.8 mg GAE/g DW), flavonoids (59.7 ± 3.5 mg QE/g DW), and essential oil content (3.28 ± 0.4% w/w). Both SA and YE increased the accumulation of metabolites, although SA (150 µM) was the most efficient at accumulating alkaloids (2.1 ± 0.1 mg/g DW). In response to the elicitors, the key secondary metabolites biosynthetic genes (PAL, CHS, TDC, and HMGR) were found to be upregulated, with MeJA eliciting (∼5 fold) the highest transcriptional response significantly. All the findings indicate that the use of elicitors, particularly MeJA, showed promise in augmenting the <em>in-vitro</em> production of important secondary metabolites from <em>M. longifolia</em>.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100655"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential role of Adansonia digitata nanoparticles on colorectal cancer induced by colorectal cancer cells (SW620) in nude mice","authors":"Lama R. Alagel ,&nbsp;Afrah F. Alkhuriji ,&nbsp;Manal A. Awad ,&nbsp;Doaa M. Elnagar ,&nbsp;Wejdan S. Al-Qahtani ,&nbsp;Zainab M. Almasawi ,&nbsp;Yasser A. Alshawakir ,&nbsp;Nada M. Merghani ,&nbsp;Nawal M. Al-Malahi","doi":"10.1016/j.jgeb.2026.100659","DOIUrl":"10.1016/j.jgeb.2026.100659","url":null,"abstract":"<div><h3>Background</h3><div>Colorectal cancer is among the most lethal malignancies worldwide and represents the second most commonly diagnosed cancer in both males and females globally. According to the Saudi Health Council (2020), colorectal cancer ranks first among Saudi males and third among Saudi females. The present study aimed to investigate the therapeutic potential of <em>Adansonia digitata</em> nanoparticles against colorectal cancer induced by SW620 human colorectal cancer cells in mice.</div></div><div><h3>Results</h3><div>The findings indicate that <em>Adansonia digitata</em> nanoparticles may represent a potential adjunctive therapeutic strategy for the treatment of colorectal cancer.</div></div><div><h3>Conclusions</h3><div><em>Adansonia digitata</em> nanoparticles (ADNPs), particularly the encapsulated formulation (ADNPs2), demonstrated promising therapeutic potential in colorectal cancer. Treatment with ADNPs improved colonic histoarchitecture and modulated key inflammatory and apoptotic signaling pathways. Although several molecular markers did not exhibit statistically significant changes, consistent pro-apoptotic trends, downregulation of transforming growth factor-β (TGF-β), and reduced tumor invasion were observed, indicating notable anticancer activity. These findings suggest that ADNPs2 may represent a potential adjunctive strategy for the management of colorectal cancer.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100659"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual targeting of IGF-1R and K-RAS with natural phytochemicals for lung cancer therapy: an in-silico study","authors":"SK.Faisal Ahmed ,&nbsp;Zubaer Hossen ,&nbsp;Indira Chakraborty ,&nbsp;Md. Masudur Rahman Munna ,&nbsp;Sanjarah Chowdhury ,&nbsp;Anika Zaheen ,&nbsp;Jhuma Tasmin ,&nbsp;A.B.M. Ashraful ,&nbsp;Md.Abrar Jahin ,&nbsp;Md.Hossain Ahmed","doi":"10.1016/j.jgeb.2026.100662","DOIUrl":"10.1016/j.jgeb.2026.100662","url":null,"abstract":"<div><div>Lung cancer remains one of the leading causes of cancer-related mortality worldwide, and the limitations and adverse effects of conventional chemotherapy necessitate the exploration of alternative therapeutic strategies. In this study, we used in-silico methods to identify bioactive compounds from medicinal plants with potential anti-lung cancer activity. We aimed to find potential inhibitors for the prevention of lung cancer, which can target two important proteins—insulin-like growth factor receptor (IGF-1R) and Kirsten rat sarcoma viral oncogene homologue (KRAS). A library of 1584 phytochemicals derived from 12 medicinal plants was retrieved from the IMPPAT 2.0 database and virtually screened using PyRx 0.8 software. According to the results, 17Beta-Hydroxywithanolide K and Ginkgolide A demonstrated strong binding affinity to IGF-1R (−9.4 Kcal/mol) and KRAS (−6.9 Kcal/mol), respectively, compared to the synthetic inhibitors Picropodophyllin (−7.7 Kcal/mol) and Sotorasib (−5.9 Kcal/mol). Pharmacokinetic (ADME) and toxicity analysis indicated favorable characteristics, including high gastrointestinal absorption and non-toxicity. Molecular dynamics (MD) simulations of 100 ns duration confirmed the stability of the protein–ligand complex. Overall, 17Beta-Hydroxywithanolide K and Ginkgolide A have potential as natural therapeutic agents for the treatment of lung cancer. However, additional in vitro and in vivo experiments are needed to validate these computational results.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100662"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146188327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Astragalus membranaceus polysaccharide (APs) and Eugenol: Multi-target Anti-inflammatory, Antioxidant, Antimicrobial, and anticancer effects validated by in Silico studies","authors":"Mohamed Khedr ,&nbsp;Ahmed E.M. Abdelaziz ,&nbsp;Fatima Albadwi ,&nbsp;Fady Sayed Youssef ,&nbsp;Eman M. Abd El-maksoud ,&nbsp;Alsayed E. Mekky ,&nbsp;Ebrahim Saied ,&nbsp;Mohamed A.M. El-Tabakh ,&nbsp;Eslam S Abdelmouty ,&nbsp;Jayda G. Eldiasty ,&nbsp;Mohammad Y. Alfaifih ,&nbsp;Ali A. Shatii ,&nbsp;Serag Eldin I. Elbehairii ,&nbsp;Mohammed Aufy","doi":"10.1016/j.jgeb.2025.100646","DOIUrl":"10.1016/j.jgeb.2025.100646","url":null,"abstract":"<div><div><em>Astragalus membranaceus</em> is a traditional medicinal plant with diverse therapeutic properties largely attributed to its polysaccharides (APs). This study evaluated the antimicrobial, anti-inflammatory, antioxidant, and anticancer activities of APs and eugenol, both individually and in combination, against multidrug-resistant (MDR) pathogens and HepG2 liver cancer cells. Thirty bacterial and ten <em>Candida</em> isolates were recovered from skin abscesses, with five identified as MDR strains (<em>Staphylococcus haemolyticus, S. aureus, E. coli, Acinetobacter baumannii</em>, and <em>Candida auris</em>), confirmed by 16S rDNA and ITS sequencing. Both APs and eugenol exhibited marked antimicrobial activity, while their combination achieved the strongest inhibition (up to 27.3 ± 0.4 mm). <em>C. auris</em> was highly sensitive to APs alone (MIC: 2 ± 0.2 µg/mL). The combination also significantly downregulated IL-6, IL-17, and TNF-α levels, and showed potent COX-2 inhibition (0.10 ± 0.01 µg/mL), surpassing celecoxib (0.9 ± 0.05 µg/mL). Antioxidant analysis (DPPH assay) revealed superior radical scavenging by the combination (57.5 ± 1.3 % %). Molecular docking confirmed the activity of eugenol, showing favorable binding to DNA gyrase B, sterol demethylase, COX-2, xanthine oxidase, and caspase-3, with the strongest affinity for xanthine oxidase (−5.25 kcal/mol). In anticancer assays, eugenol induced dose-dependent inhibition of HepG2 cell proliferation, while APs displayed limited cytotoxicity. Notably, the combination reduced cell viability to 3.77 ± 0.4 % % at 400 µg/mL, consistent with apoptotic changes. Collectively, these findings highlight the synergistic potential of APs and eugenol as a multi-target therapeutic approach against MDR infections, inflammation, oxidative stress, and liver cancer.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100646"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of low-dose gamma irradiation on seed-borne transmission of tomato brown rugose fruit virus in tomato","authors":"Kimia Tokhmechi ,&nbsp;Abozar Ghorbani ,&nbsp;Davoud Koolivand ,&nbsp;Mahsa Rostami ,&nbsp;Nahid Hajiloo","doi":"10.1016/j.jgeb.2025.100644","DOIUrl":"10.1016/j.jgeb.2025.100644","url":null,"abstract":"<div><div>Tomato brown rugose fruit virus (ToBRFV), a highly virulent tobamovirus, poses a major threat to global tomato production by overcoming host resistance and traditional control measures. This study evaluates the efficacy of low-dose gamma irradiation (10, 15, and 20 Gy) in reducing ToBRFV contamination in tomato seeds. Contaminated seeds were irradiated and assessed for germination rate, chlorophyll content, stem diameter, and viral accumulation with RT-qPCR. The potential synergistic effect of combining 15 Gy gamma irradiation with 2.5 % sodium hypochlorite (NaOCl) was also investigated. Results revealed that 15 Gy significantly improved germination, enhanced chlorophyll levels, and increased stem thickness, while substantially reducing viral replication. In contrast, 20 Gy had detrimental effects on both plant growth and viral suppression. The combination of 15 Gy and NaOCl further decreased viral accumulation, though at the cost of reduced germination rates. Applying 15 Gy confers dual benefits, including effective seed disinfection and improved host resistance. It shows strong potential for use in integrated tomato disease management in greenhouse and field conditions.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100644"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arbuscular mycorrhizal fungi as integrative modulators of plant tolerance to drought, salinity, and heavy metal stress: mechanistic insights and future directions","authors":"Mutaz Mohammed Abdallah ,&nbsp;Chenmei Suo ,&nbsp;Youxin Cui ,&nbsp;Rana Hissan Ullah ,&nbsp;Hoang Hong Nhung ,&nbsp;Lixin Li ,&nbsp;Changli Liu","doi":"10.1016/j.jgeb.2025.100636","DOIUrl":"10.1016/j.jgeb.2025.100636","url":null,"abstract":"<div><div>Climate change and anthropogenic pressures have intensified abiotic stresses such as drought, salinity, and heavy metal (HM) contamination, severely impairing plant growth and productivity. Arbuscular mycorrhizal fungi (AMF), through their symbiotic association with plant roots, offer a promising biological strategy to enhance plant resilience under these stresses. This review synthesizes recent advances in understanding the physiological, biochemical, and molecular mechanisms by which AMF confer stress tolerance. Key mechanisms include modulation of aquaporin expression for water homeostasis, regulation of abscisic acid (ABA) and mitogen-activated protein kinase (MAPK) signaling pathways, enhancement of antioxidant defenses, and fine-tuning of osmolyte metabolism such as proline. Under salinity, AMF improves ion homeostasis by regulating SOS1 and NHX transporters and enhancing K⁺/Na⁺ discrimination. In HM-contaminated environments, AMF facilitate metal immobilization, chelation via phytochelatins and metallothioneins, and vacuolar sequestration, thereby reducing oxidative damage. The review also highlights AMF-mediated transcriptional reprogramming involving 14-3-3 proteins and stress-responsive transcription factors (e.g., WRKY, MYB, bHLH). By integrating rhizospheric interactions with intracellular signaling, AMF emerge as multifaceted modulators of plant stress physiology.</div><div>This review delineates key gaps in current understanding and outlines strategic directions for harnessing AMF in sustainable agriculture under complex abiotic stress scenarios. By integrating mechanistic insights across drought, salinity, and heavy metal stress, it emphasizes the convergence of AMF-mediated signaling pathways and cross-tolerance mechanisms that underpin plant resilience.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100636"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145840891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing clinical insights in glioma grading using Bayesian Optimization and Explainable AI","authors":"Alaa M. Elsayad ,&nbsp;Omar A. Elsayad","doi":"10.1016/j.jgeb.2026.100669","DOIUrl":"10.1016/j.jgeb.2026.100669","url":null,"abstract":"<div><div>Accurate glioma grading is paramount for guiding treatment strategies and predicting patient prognosis. This study introduces a novel and clinically relevant framework for glioma grade classification, specifically distinguishing between low-grade gliomas (LGG) and glioblastomas (GBM), by leveraging the unique strengths of Generalized Additive Models (GAMs). GAMs, chosen for their ability to model complex, non-linear relationships while maintaining inherent interpretability, were optimized using <em>Bayesian Optimization for efficient hyperparameter tuning</em> and augmented by Explainable Artificial Intelligence (XAI) methodologies. The ’Glioma Grading Clinical and Mutation Features’ dataset from Kaggle underwent meticulous preprocessing. A feature ranking algorithm identified the most informative features, reducing noise and enhancing model accuracy. The Bayesian-optimized GAM achieved an accuracy of 0.9012 and F1-score of 0.8975 on a held-out test set, demonstrating superior or competitive performance compared to other established models, including Random Forest, LogitBoost, Support Vector Machines, and Artificial Neural Networks. Notably, among these traditional methods, the Random Forest performed strongly on the training set (accuracy 0.8899); however, GAM outperformed in the test set. To elucidate model decision-making and promote clinical translation, XAI techniques, including Permutation Feature Importance (PFI), SHapley Additive exPlanations (SHAP), and Partial Dependence Plots (PDPs), were employed. PFI identified IDH1 as the most critical predictor, while SHAP values revealed that, in addition to <em>IDH1</em>, features like <em>Age</em>, <em>PTEN</em>, <em>ATRX</em>, and <em>CIC</em> have considerable influence on model predictions. Furthermore, PDPs demonstrated the non-linear functional relationships of these features with the predicted outcome. These techniques provided interpretable insights into both global and local feature effects, highlighted the non-linearities in the data, and fostered trust in the model’s predictions. This study demonstrates that integrating GAMs, Bayesian Optimization, and XAI techniques provides a robust, accurate, and clinically interpretable framework for glioma grade classification, showcasing their potential to enhance diagnostic accuracy, improve clinicians’ understanding of glioma biology, and ultimately inform more personalized treatment strategies.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100669"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147395711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural analysis of clingstone and freestone peach (Prunus persica L.) plastome genome: provides insight into phylogeny and time diversification","authors":"Mokhtar Said Rizk ,&nbsp;Alsamman M. Alsamman ,&nbsp;Heba A.M. AbdAlla ,&nbsp;Mohamed Abd. S. El Zayat ,&nbsp;Ahmed H. Hassan ,&nbsp;El-Shaimaa Saad El-Demerdash ,&nbsp;Mohamed Z.S. Ahmed ,&nbsp;Yuepeng Han ,&nbsp;Mohamed Hamdy Amar ,&nbsp;Achraf El Allali","doi":"10.1016/j.jgeb.2026.100660","DOIUrl":"10.1016/j.jgeb.2026.100660","url":null,"abstract":"<div><h3>Background</h3><div>The complete plastome genome of peach represents a valuable genomic resource for elucidating the evolutionary history and phylogenetic relationships within Prunus species.</div></div><div><h3>Methods</h3><div>This study performed plastome sequencing of two peach cultivars Clingstone (CLS) and Freestone (FRS) along with the wild relative <em>Prunus mira,</em> using the Illumina HiSeq 2500 platform. In this study, the plastomes of two peach cultivars—Clingstone (CLS) and Freestone (FRS)—and the wild relative <em>Prunus mira</em> were sequenced using the Illumina HiSeq 2500 platform. A broad comparative assessment was enabled by comparing these sequences with 22 previously sequenced Prunus plastomes.</div></div><div><h3>Results</h3><div>All 25 plastomes exhibited a conserved quadripartite structure, with genome sizes ranging from 157,685 to 158,955 bp and an average GC content of 37.72 %. Structural variations were observed, including gene rearrangements and boundary shifts between the IR, LSC,and Small Single-Copy (SSC) regions. These boundary shifts, together with the identified sequence rearrangements, highlighted potential mutational hotspot regions. Considerable diversity was detected in Simple Sequence Repeats (SSRs), including polymorphic loci with total counts ranging from 559 to 1064 per plastome, comprising mono-, di-, penta-, and hexa-nucleotide motifs.Variable Simple Sequence Repeats (SSRs) and codon usage patterns were identified as evolutionary hotspots. Out of 40 genes, 28 single-copy and 12 multi-copy were consistently found across all plastomes. Such variation patterns underscore regions with high phylogenetic informativeness. Phylogenomic analysis revealed well-supported monophyletic clades, clarifying evolutionary relationships among peach, cherry, and almond groups. Divergence time estimates place the split between cultivated peach (<em>Prunus persica</em>, including CLS and FRS) and P. mira in the Eocene.</div></div><div><h3>Conclusion</h3><div>This comprehensive plastome-based study enriches our understanding of the evolutionary dynamics of peach cultivars, particularly Clingstone and Freestone, in relation to wild Prunus relatives. The identified SSR loci, codon usage features, and structural variations offer potential molecular markers for peach genetic evolution and precise taxonomic resolution at the subspecies level.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100660"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147395715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}