Genes

19 pages, 1128 KB

Open AccessArticle

Barriers, Limitations, and Experiences with Clinical Trials—Treatment in Rare Diseases with Prader–Willi Syndrome as an Example

by Merlin G. Butler, Spencer Silvey and Harold J. P. van Bosse

Genes 2025, 16(12), 1436; https://doi.org/10.3390/genes16121436 - 1 Dec 2025

Abstract

Background/Objectives: Developing and implementing clinical trials for rare diseases is complicated by the incomplete understanding of the varied genotype and subsequent phenotypic differences of a condition, particularly when low numbers of subjects are enrolled in a study. Moreover, a small-scale clinical study [...] Read more.

Background/Objectives: Developing and implementing clinical trials for rare diseases is complicated by the incomplete understanding of the varied genotype and subsequent phenotypic differences of a condition, particularly when low numbers of subjects are enrolled in a study. Moreover, a small-scale clinical study may indicate a positive outcome but have too small of a sampling population to adequately evaluate unwanted outcomes. Prader–Willi syndrome (PWS) is one such genetic disorder with varied subtypes and heterogeneity, where little progress has been made in treatment discoveries. Recently, the FDA approved diazoxide choline for treating key features of hyperphagia and obesity associated with PWS based on clinical trial experience. Diazoxide choline activates the ATP-sensitive potassium channel (KATP) of pancreatic beta cells, inhibiting the release of insulin. One of the subunits of KATP is the protein Kir6.2, the gene product of KCNJ11. Methods: Web-based programs and datasets were used to study the gene and protein functional enrichments of Kir6.2 and KCNJ11, including shared gene and/or protein–protein interactions, and biological processes and functions. Results: Four essential domains of related functions were identified: (1) apoptosis, protein degradation, and inflammation; (2) the coupling of G proteins needed for KATP channel activation; (3) glucose metabolism and control; and (4) the maintenance of intracellular ionic homeostasis. Conclusions: Cellular metabolism in the pancreas is linked to membrane excitability by KATP, which regulates insulin production, energy production and storage, appetite regulation, and fatty acid synthesis. As such, diazoxide choline may influence several biological systems beyond pancreatic and metabolic functions. Full article

(This article belongs to the Special Issue Molecular Basis in Rare Genetic Disorders)

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12 pages, 2887 KB

Open AccessArticle

Gene Regulation in Comorbid Migraine and Myogenic Temporomandibular Disorder Pain

by Ran Tao, Sufang Liu, Hui Maltezos and Feng Tao

Genes 2025, 16(12), 1435; https://doi.org/10.3390/genes16121435 - 1 Dec 2025

Abstract

Background/Objectives: Previous studies have demonstrated an association between migraine headache and temporomandibular joint disorders (TMDs), with a higher prevalence of TMD symptoms in patients with migraine. Methods: In this study, we conducted RNA sequencing to identify differentially expressed genes (DEGs) in the spinal [...] Read more.

Background/Objectives: Previous studies have demonstrated an association between migraine headache and temporomandibular joint disorders (TMDs), with a higher prevalence of TMD symptoms in patients with migraine. Methods: In this study, we conducted RNA sequencing to identify differentially expressed genes (DEGs) in the spinal trigeminal nucleus caudalis of mice with migraine-like pain and/or myogenic TMD. Results: We observed 204 upregulated and 274 downregulated genes in the comorbid migraine and TMD group compared to the control group. We identified 15 ferroptosis-related DEGs enriched in the pathways of neurodegeneration, cellular homeostasis, interleukin signaling, and pain response. Gene Ontology analysis highlighted the involvement of neuroinflammatory response and monoamine transmembrane transporter activity, while Gene Set Enrichment analysis showed enrichment in chemokine signaling, cell cycle, and calcium signaling pathways. Immune infiltration analysis identified M0 macrophages, immature dendritic cells, neutrophils, and eosinophils as key responders. Hub genes in the protein–protein interaction network included Gm7536, Rpl17, Rpl22l1, Rpl14, Rps8, Rps29, Rpl35, Gm4889, Gm11808, Rps27rt, Rps12-ps3, Rpl10-ps3, Gm9843, Oas1c, Il1b, and Serpine1, indicating their synergistic roles in such orofacial pain comorbidity. Conclusions: Our results suggest that the comorbid migraine and TMD can regulate gene expressions involving ferroptosis and immune cell responses and the identified DEGs could be targeted to develop novel therapies for this painful comorbidity. Full article

(This article belongs to the Section Neurogenomics)

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17 pages, 8806 KB

Open AccessArticle

Identification and Characterization of the Efbzip Gene Family in Erianthus fulvus and Exploration of Functional Genes Involved in Sucrose Metabolism

by Changzu Zhao, Weiyou Nong, Zhenfeng Qian, Qian Ding, Yujie Wang, Lilian He and Fusheng Li

Genes 2025, 16(12), 1434; https://doi.org/10.3390/genes16121434 - 1 Dec 2025

Abstract

Background/Objectives: Sugarcane (Saccharum spp.) is a major global sugar crop, and improving sucrose accumulation is critical for industry and bioenergy. Due to its high Brix content, Erianthus fulvus (E. fulvus) is valuable for genetic improvement of sugarcane. The bZIP [...] Read more.

Background/Objectives: Sugarcane (Saccharum spp.) is a major global sugar crop, and improving sucrose accumulation is critical for industry and bioenergy. Due to its high Brix content, Erianthus fulvus (E. fulvus) is valuable for genetic improvement of sugarcane. The bZIP transcription factor family critically regulates plant sucrose metabolism, but its roles in sugarcane remain largely unexplored. Methods: Through bioinformatics methods, Efbzip gene family members were systematically identified within the genome of E. fulvus. Gene expression patterns in distinct plant tissues were examined by RNA-seq and quantitative real-time PCR (qRT-PCR). Furthermore, genes potentially involved in sucrose metabolism were screened using transient expression assays and subcellular localization studies conducted in tobacco. Results: Seventy-nine Efbzip genes were identified and classified into nine subgroups, showing uneven distribution across ten chromosomes. Among ten conserved motifs, Motif1 was most conserved. Subcellular localization and physicochemical analyses showed most Efbzip proteins were hydrophilic and nuclear-localized. Cis-regulatory element analysis suggested Efbzip proteins regulate sucrose metabolism through hormone and light-responsive pathways. Segmental duplication primarily drove Efbzip gene family expansion. qRT-PCR showed predominant expression in stems and leaves, with subgroup-specific patterns. Nuclear localization of Efbzip52 was confirmed. Transient overexpression of Efbzip52, Efbzip61, and Efbzip64 significantly increased sucrose content in tobacco leaves, with highly statistically significant (p < 0.0001). Conclusions: In this study, the Efbzip gene family of E. fulvus was systematically characterized for the first time. Key candidate genes potentially involved in sucrose metabolism were identified, providing potential targets for the genetic improvement of sugarcane. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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20 pages, 4060 KB

Open AccessArticle

Secondary Ophthalmic Features Represent Diagnostic Clues and Potential Points of Intervention for Inherited Retinal Diseases (Target 5000 Report 3)

by Kirk A. J. Stephenson, Julia Zhu, Marcus Conway, Bridget Moran, Adrian Dockery, Laura Whelan, Jacqueline Turner, James J. O’Byrne, D. Ian Flitcroft, G. Jane Farrar and David J. Keegan

Genes 2025, 16(12), 1433; https://doi.org/10.3390/genes16121433 - 1 Dec 2025

Abstract

Background/Objective: Inherited retinal degenerations (IRDs) are the leading cause of blind registration in children and adults, yet 30–40% of cases remain genetically unresolved. Deep ophthalmic phenotyping may help to address this shortfall by identifying characteristic phenotypes. We describe the ophthalmic features of patients [...] Read more.

Background/Objective: Inherited retinal degenerations (IRDs) are the leading cause of blind registration in children and adults, yet 30–40% of cases remain genetically unresolved. Deep ophthalmic phenotyping may help to address this shortfall by identifying characteristic phenotypes. We describe the ophthalmic features of patients with stationary or progressive inherited retinal diseases other than outer retinal degeneration (i.e., secondary ophthalmic features, SOFs). Methods: This is a retrospective review of all patients attending an ophthalmic genetics clinic with a genetically confirmed IRD focusing on SOFs including refractive error, cataract, retinal detachment (RRD), cystoid macular lesions (CML) and epiretinal membrane (ERM). These features were assessed in the context of phenotype and genotype. Results: In a cohort of 429 genotyped patients, ≥1 SOFs were seen in 70.2% of patients, with 36.6% being affected by multiple SOFs. Refractive error (63.3%) and cataract (43.4%) were the most common secondary features, with a subset affected by CML (14.7%), ERM (10%) and RRD (4.7%). Conclusions: SOFs are common in patients with IRDs and most are amenable to therapeutic intervention even when no primary treatment (e.g., gene therapy) is available. We highlight patterns associated with genotypes and disease groups which may aid harmonisation of clinical and genetic diagnoses. Full article

(This article belongs to the Special Issue Genetic Diagnosis and Therapeutics of Eye Diseases)

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13 pages, 789 KB

Open AccessArticle

Endometrial Microbial Profile in Infertile Women with Chronic Endometritis: Intensified Culturomics and 16S rDNA Gene Sequencing

by Bárbara Lara-del-Río, Rocío Sánchez-Ruiz, Mónica Bernal-Sánchez, Francisco Ruiz-Cabello-Osuna, José María Navarro-Marí and José Gutiérrez-Fernández

Genes 2025, 16(12), 1432; https://doi.org/10.3390/genes16121432 - 1 Dec 2025

Abstract

Background/Objectives: Chronic endometritis (CE) has been linked to implantation failure, recurrent pregnancy loss, and endometrial dysbiosis with low Lactobacillus abundance. We assessed the endometrial microbiota in infertile women with CE and the added value of combining intensified culturomics with 16S rDNA NGS. Methods: [...] Read more.

Background/Objectives: Chronic endometritis (CE) has been linked to implantation failure, recurrent pregnancy loss, and endometrial dysbiosis with low Lactobacillus abundance. We assessed the endometrial microbiota in infertile women with CE and the added value of combining intensified culturomics with 16S rDNA NGS. Methods: Cross-sectional study with descriptive results of 15 endometrial biopsies analyzed in parallel by intensified culture and 16S rDNA (V3–V6) sequencing (RA threshold ≥ 5%). Results: Culture yielded growth in 13/15 samples (86.7%), whereas NGS reported findings in 15/15 (100%). NGS provided additional taxa beyond culture in 14/15 (93.3%), while culture identified taxa missed by NGS in 10/15 (66.7%). In both culture-negative cases, NGS detected ≥1 taxon. Lactobacillus spp. appeared exclusively by NGS in 26.7% of samples; Fannyhessea vaginae showed the highest mean RA by NGS and did not grow in culture, underscoring complementarity. Conclusions: 16S NGS complements intensified culturomics for characterizing the endometrial microbiota in CE, enhancing detection—especially when culture is negative—and supports a combined, clinically contextualized interpretation. Larger, controlled cohorts are warranted to validate diagnostic and prognostic utility. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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19 pages, 5799 KB

Open AccessArticle

Unveiling Novel Traits Associated with Ulcerative Colitis via Phenome-Wide Associations Enhanced by Polygenic Risk Statistics

by Yiming Wu, Ling Liu, Meltem Ece Kars, Rui Li, Menglong Li and Yuval Itan

Genes 2025, 16(12), 1431; https://doi.org/10.3390/genes16121431 - 30 Nov 2025

Abstract

Background: Ulcerative colitis (UC) is a major form of inflammatory bowel disease affecting the gastrointestinal tract. Increasing evidence suggests UC is predisposed to co-occurring with other autoimmune diseases, yet its pathogenesis remains insufficiently understood. Large-scale biobank-based cross-trait genetic analyses may provide insights [...] Read more.

Background: Ulcerative colitis (UC) is a major form of inflammatory bowel disease affecting the gastrointestinal tract. Increasing evidence suggests UC is predisposed to co-occurring with other autoimmune diseases, yet its pathogenesis remains insufficiently understood. Large-scale biobank-based cross-trait genetic analyses may provide insights into the origins of UC and its comorbidities. Methods: Using the UK Biobank and Mount Sinai BioMe Biobank, we conducted genome-wide association studies (GWASs) in individuals of European ancestry. High-impact rare variants were aggregated for collapsing analysis. Genome-wide significant variants were tested in a phenome-wide association study (PheWAS) to explore UC comorbidities. Polygenic risk scores (PRSs) were derived from large-scale GWASs under different thresholds and functionalities, and the best-performing PRS was further applied in a PRS-based PheWAS. Genetic correlation between UC and highly associated traits was evaluated. Results: GWASs identified four genome-wide significant loci, including two novel variants (rs2314757, p = 4.82 × 10⁻¹¹, OR = 0.81; rs6869382, p = 2.48 × 10⁻⁸, OR = 0.83) and two previously reported UC-associated sites (rs4654925, p = 1.85 × 10⁻⁸, OR = 0.84; rs2836882, p = 1.23 × 10⁻¹¹, OR = 0.78) outside the HLA region. The optimal PRS, constructed with SNPs at p < 0.05, conferred an odds ratio of 5.86 (95% CI: 5.05–6.86) for UC in individuals with the highest versus lowest quintile. Both variant- and PRS-based PheWASs consistently highlighted type 1 diabetes (T1D) as the most significant comorbidity, confirmed by genetic correlation analysis. Conclusions: This study reveals novel loci contributing to UC and highlights comorbidities with shared genetic bases. UC PRSs demonstrated strong utility beyond risk prediction, effectively identifying UC-associated traits. A robust genetic correlation was established between UC and T1D. Full article

(This article belongs to the Section Technologies and Resources for Genetics)

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24 pages, 1095 KB

Open AccessArticle

Generation of a Compendium of Transcription Factor Cascades and Identification of Potential Therapeutic Targets Using Graph Machine Learning

by Sonish Sivarajkumar, Romy Roy, Pratyush Tandale, Ankit Bhardwaj, Kipp W. Johnson, Anoop Titus, Benjamin S. Glicksberg, Shameer Khader, Kamlesh K. Yadav and Lakshminarayanan Subramanian

Genes 2025, 16(12), 1430; https://doi.org/10.3390/genes16121430 - 30 Nov 2025

Abstract

Background: Transcription factors (TFs) are critical regulators of gene expression, and their dysregulation is implicated in diseases like cancer. This study aims to create a comprehensive resource of TF cascades to identify potential therapeutic targets. Methods: We extracted TF interactions from the STRING [...] Read more.

Background: Transcription factors (TFs) are critical regulators of gene expression, and their dysregulation is implicated in diseases like cancer. This study aims to create a comprehensive resource of TF cascades to identify potential therapeutic targets. Methods: We extracted TF interactions from the STRING database, constructed a knowledge graph using graph machine learning, and performed pathway enrichment analysis with Enrichr. Network analysis and PageRank identified influential TFs. Results: We generated 81,488 unique TF cascades, with the longest containing 62 TFs. Key TFs (e.g., MYC, TP53, STAT3) were identified, and enriched pathways included cancer-related processes. A knowledge graph and dataset were made publicly available. Conclusions: This compendium of TF cascades provides a valuable resource for understanding TF interactions and identifying novel drug targets for precision therapeutics. Full article

(This article belongs to the Section Bioinformatics)

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21 pages, 1456 KB

Open AccessArticle

Surviving the Heat: Genetic Diversity and Adaptation in Sudanese Butana Cattle

by Guilherme B. Neumann, Paula Korkuć, Siham A. Rahmatalla, Monika Reißmann, Elhady A. M. Omer, Salma Elzaki and Gudrun A. Brockmann

Genes 2025, 16(12), 1429; https://doi.org/10.3390/genes16121429 - 30 Nov 2025

Abstract

Background: Butana are native Sudanese Bos indicus cattle that are well adapted to arid environments and valued for their relatively high milk performance and resilience under harsh conditions. Despite their adaptive advantages, Butana cattle face the risk of genetic erosion due to low [...] Read more.

Background: Butana are native Sudanese Bos indicus cattle that are well adapted to arid environments and valued for their relatively high milk performance and resilience under harsh conditions. Despite their adaptive advantages, Butana cattle face the risk of genetic erosion due to low production performance and the absence of structured breeding programs underscoring the urgent need to conserve their unique genetic potential for climate-resilient livestock development. Methods: In this study, we analyzed whole-genome sequencing data from 40 Butana cattle to assess their genetic diversity, population structure, signatures of selection, and potential pathogen load. Results: Butana cattle exhibited high nucleotide diversity and low levels of inbreeding, indicating a stable gene pool shaped by natural selection rather than by intensive breeding. Signatures of selection and functional variant analysis revealed candidate genes involved in heat stress adaptation (COL6A5, HSPA1L, TUBA8, XPOT), metabolic processes (G6PD, FAM3A, SLC10A3), and immune regulation (IKBKG, IRAK3, IL18RAP). Enrichment analyses and RoH island mapping consistently highlighted immune and thermoregulatory pathways as key selection targets, distinguishing Butana from both the geographically neighbored Kenana cattle and the specialized dairy cattle breed Holstein. Furthermore, metagenomic screening of unmapped reads detected the tick-borne parasite Theileria annulata and the opportunistic pathogen Burkholderia cenocepacia in all animals, underscoring the importance of integrating pathogen surveillance into genomic studies. Conclusions: Taken together, our findings highlight the distinct adaptive genomic profile of Butana cattle and reinforce their value in breeding programs aimed at improving climate resilience and disease resistance in livestock through the utilization of local breeds. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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27 pages, 3447 KB

Open AccessArticle

Genetic Insight into Expression-Defined Melanoma Subtypes and Network Mechanisms: An in Silico Study

by Desirèe Speranza, Mariapia Marafioti, Martina Musarra, Vincenzo Cianci, Cristina Mondello, Maria Francesca Astorino, Mariacarmela Santarpia, Natasha Irrera, Mario Vaccaro, Nicola Silvestris, Concetta Crisafulli, Marco Calabrò and Silvana Briuglia

Genes 2025, 16(12), 1428; https://doi.org/10.3390/genes16121428 - 30 Nov 2025

Abstract

Background: Melanoma is a highly heterogeneous neoplasia in which transcriptional profile encodes much of the biological diversity that determines tumor progression and therapeutic response. To refine its molecular stratification and profiles characterization, we conducted an in silico transcriptomic analysis. Methods: Public microarray datasets [...] Read more.

Background: Melanoma is a highly heterogeneous neoplasia in which transcriptional profile encodes much of the biological diversity that determines tumor progression and therapeutic response. To refine its molecular stratification and profiles characterization, we conducted an in silico transcriptomic analysis. Methods: Public microarray datasets from the GEO and ArrayExpress were examined, and the E-MTAB-6697 expression dataset was selected. We used a K-Means clustering algorithm to stratify 194 tumor samples into expression-driven subgroups and analyzed each one to define their transcriptional and biological profiles. Differential expression analysis between identified clusters and controls was performed. Additionally, we applied Weighted-Gene correlation analysis to identify coordinated expression hubs in the tumor dataset and tested the resulting modules for correlation with the identified clusters. Results: Unsupervised clustering of melanoma transcriptomic profiles identified three distinct molecular subtypes characterized by divergent biological programs. While all clusters shared the dysregulation of pathways involved in epidermal differentiation, immune response, and lipid metabolism, they diverged in proliferation, phenotypic plasticity, metabolic adaptation, and apoptotic regulation. Cluster A was characterized by enrichment in DNA replication, repair, and mitochondrial metabolism modules, suggesting a proliferative yet genomically stable state. Cluster B showed enrichment in immune and cytokine signaling pathways alongside reduced proliferative activity, consistent with a quiescent or transitional phenotype. Cluster C displayed coordinated enrichment in cell-cycle, DNA-maintenance, and neuroectodermal reprogramming pathways, indicating a highly plastic and proliferative subtype. Despite these molecular distinctions, all clusters retained an “immunologically hot” profile (IPS 7–8), indicating potential responsiveness to immunotherapy. Conclusions: These findings provide an overview of the functional characteristics of melanoma heterogeneity and identify biological processes that could be targeted by drugs for the development of tailored therapies for each subtype. Nevertheless, future studies in independent clinically annotated cohorts would be required. Full article

(This article belongs to the Section Bioinformatics)

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17 pages, 3500 KB

Open AccessArticle

Characterization of the Mitochondrial Genome of Cavariella salicicola: Insight into the Codon Usage Bias and Phylogenetic Implications in Aphidinae

by Tian-Xing Jing, Yan-Jin Zhang, Pei-Xuan Li, Qian Wang, Jin Yang, Hong-Hua Su and Shuai Zhang

Genes 2025, 16(12), 1427; https://doi.org/10.3390/genes16121427 - 29 Nov 2025

Abstract

Background: Cavariella salicicola (Hemiptera: Aphidinae) is a pest on Salix spp. and various Umbelliferae (Apiaceae) vegetables. However, the taxonomic status and phylogenetic relationship of the genus Cavariella within Aphidinae remain controversial due to the small body size and easily confused external morphology. [...] Read more.

Background: Cavariella salicicola (Hemiptera: Aphidinae) is a pest on Salix spp. and various Umbelliferae (Apiaceae) vegetables. However, the taxonomic status and phylogenetic relationship of the genus Cavariella within Aphidinae remain controversial due to the small body size and easily confused external morphology. Methods: The complete mitochondrial genome of C. salicicola collected from Oenanthe javanica was sequenced using the Illumina platform and compared with C. theobaldi. The codon usage bias of two Cavariella aphids was assessed through Enc plot, PR2 plot, and neutrality plot analyses. Furthermore, phylogenetic trees were constructed based on both Maximum Likelihood and Bayesian Inference analysis. Results: The C. salicicola mitochondrial genome comprises 15,720 bp and represents a typical circular DNA molecule with a high AT content of 83.8%. It contains the standard 37 genes, including 2 ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 long non-coding regions (control and repeat regions). Varying degrees of codon usage bias were found across different PCGs, and the bias was predominantly influenced by natural selection rather than mutational pressure. The ratio of nonsynonymous to synonymous substitutions (Ka/Ks) indicated that all PCGs in C. salicicola, as well as most other Aphidinae species, are under strong purifying selection. The phylogenetic analysis based on Maximum Likelihood and Bayesian Inference both strongly supported the monophyly of Aphidinae, Macrosiphini, and Aphidini. Crucially, the monophyletic genus Cavariella was resolved as a sister group to all other sampled species within the tribe Macrosiphini. Conclusions: This study provides new molecular data to support the sister relationship of the genus Cavariella to other Macrosiphini aphids. This study will enhance our understanding of phylogenetic relationships within the subfamily Aphidinae. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)

19 pages, 4517 KB

Open AccessArticle

The Methylation of the CYP11A1 Gene Affects the Expression Pattern in Different-Diameter Granulosa Cells of Qira Black Sheep

by Chunjie Liu, Peilin Guo, Linlin Pei, Wenhao Wang, Andi Qiao and Xin Xu

Genes 2025, 16(12), 1426; https://doi.org/10.3390/genes16121426 - 29 Nov 2025

Abstract

Background: CYP11A1 (a key enzyme in the process of progesterone synthesis) expression is a crucial factor that promotes the proliferation and progressive differentiation of granulosa cells (GCs) to support oocyte maturation and ovulation in livestock. Changes in its expression may be related to [...] Read more.

Background: CYP11A1 (a key enzyme in the process of progesterone synthesis) expression is a crucial factor that promotes the proliferation and progressive differentiation of granulosa cells (GCs) to support oocyte maturation and ovulation in livestock. Changes in its expression may be related to DNA methylation, but the specific regulatory mechanism of this remains unclear. Methods: The qRT-PCR, western-blot, CCK-8 assay, RNAi, dual-luciferase activity assay and sulfite sequening were used to explore the effect of the activity and methylation level of the CYP11A promoter on the proliferation of GCs. Results: Our studies first identified that the activity of CYP11A1 promoted the core genes that affected the superior growth of follicles in Qira Black sheep, and activity changes were related to the degree of DNA methylation. We further revealed that the DNA methylation of GCs at different developmental stages was mainly regulated by the promoter region, and also clearly defined the optimal window period for CYP11A1 to affect the proliferation of GCs. Conclusion: In summary, our data reveals the epigenetic regulatory mechanism of GCs in follicle development provides a new perspective for understanding the molecular basis of reproductive cell differentiation, and offers important theoretical support for future research and basic application in the field of livestock reproduction. Discussion: This not only helps to improve the efficient breeding and production system of sheep and the process of genetic improvement, but also provides a theoretical basis for fundamentally accelerating the expansion, breeding, and genetic quality innovation of superior sheep breeds in China, and also offers accurate targets for sheep genetic breeding. Full article

(This article belongs to the Special Issue Genetics and Breeding Improvements in Sheep and Goat)

17 pages, 3501 KB

Open AccessArticle

Identification of the FLA Gene Family in Soybean and Preliminary Functional Analysis of Its Drought-Responsive Candidate Genes

by Jiyue Zhang, Lina Yang, Jingxuan Dou, Cong Wang and Zhengpei Yao

Genes 2025, 16(12), 1425; https://doi.org/10.3390/genes16121425 - 29 Nov 2025

Abstract

Background/Objectives: Fasciclin-like arabinogalactan proteins (FLAs) are critical components of the plant cell wall, playing vital roles in development and abiotic stress responses. However, a systematic genome-wide analysis of the FLA family in soybean (Glycine max L.), a major legume crop susceptible to [...] Read more.

Background/Objectives: Fasciclin-like arabinogalactan proteins (FLAs) are critical components of the plant cell wall, playing vital roles in development and abiotic stress responses. However, a systematic genome-wide analysis of the FLA family in soybean (Glycine max L.), a major legume crop susceptible to drought, is lacking. This study aimed to comprehensively identify GmFLA members and investigate their potential functions in drought tolerance. Methods: We identified GmFLA genes via BLASTP (v2.16.0) and Hidden Markov Model (HMM) searches against the soybean genome. Subsequent analyses encompassed their physicochemical properties, chromosomal distribution, gene structure, phylogenetic relationships, conserved domains, cis-acting elements, and subcellular localization. Drought-responsive candidates were screened using a Gene Expression Omnibus (GEO) dataset, and their expression profiles were validated under drought stress using quantitative real-time PCR (qRT-PCR). Results: A total of 55 GmFLA genes were identified and unevenly distributed across 14 chromosomes. Most genes featured a single-exon structure and contained a conserved Fasciclin domain, with predicted localization primarily to the chloroplast. Phylogenetic analysis grouped them into three distinct subclasses with Arabidopsis homologs, suggesting lineage-specific expansion. Promoter analysis revealed an abundance of stress- and hormone-related cis-elements. Expression analysis identified five candidate genes (GmFLA5, GmFLA15, GmFLA40, GmFLA47, and GmFLA54) that showed tissue-specific expression changes under drought treatment. Conclusions: This study provides the first comprehensive genomic characterization of the GmFLA gene family and identifies candidate GmFLAs with drought-responsive expression patterns. Our findings establish a foundation for future functional research to investigate their potential roles in soybean drought response. Furthermore, these candidates serve as potential targets for further investigation in strategies aimed at improving soybean drought tolerance. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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16 pages, 4097 KB

Open AccessArticle

Transcriptome Analysis of Paeonia ostii ‘Fengdan’ Seeds Uncovers Starch and Sucrose Metabolism Conferring High Yield Under Brassinosteroid Treatment

by Shixi Yu, Ruixue Xiao, Xiaopeng Li, Renjie Li, Chengwei Song, Yuying Li, Jingyi Zhao and Xiaogai Hou

Genes 2025, 16(12), 1424; https://doi.org/10.3390/genes16121424 - 29 Nov 2025

Abstract

Background: Tree peony (Paeonia section Moutan DC.) seeds, renowned for their rich content of unsaturated fatty acids, hold significant medicinal and nutritional value. Despite their potential, their yield is relatively low, which constrains economic gains and health benefits. Brassinosteroids (BRs), emerging [...] Read more.

Background: Tree peony (Paeonia section Moutan DC.) seeds, renowned for their rich content of unsaturated fatty acids, hold significant medicinal and nutritional value. Despite their potential, their yield is relatively low, which constrains economic gains and health benefits. Brassinosteroids (BRs), emerging as potent plant growth regulators, have demonstrated efficacy in boosting plant productivity. Methods: This study employed Paeonia ostii ‘Fengdan’ and administered either water (control group, CKs) or 0.05 mg/L BRs through foliar application during the seed enrichment and conversion phase to assess the effects of BR treatment on seed yield. Results: The BR treatment notably enhanced the protein, starch, and sugar content and yield of P. ostii ‘Fengdan’ seeds, surpassing those of the CKs. Transcriptome profiling identified a plethora of differentially expressed genes in P. ostii ‘Fengdan’ in response to BR treatment, which are implicated in biological processes associated with nutrient reservoir activity. KEGG analysis highlighted the pivotal role of starch and sucrose metabolism in the BR treatment response. WGCNA revealed key gene expression modules that correlate with physiological traits in P. ostii ‘Fengdan’. Furthermore, the quantitative real-time PCR (qRT-PCR) validation of key genes in this pathway revealed that BR treatment enhances yield through a dual mechanism: accelerating the seed-filling process and optimizing developmental timing for earlier maturation. Conclusions: Collectively, these findings offer inaugural comprehensive genomic resources delineating the transcriptional regulatory mechanisms of BRs in P. ostii ‘Fengdan’ seeds. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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10 pages, 826 KB

Open AccessArticle

DNA Barcoding Protocol for Masdevallia Orchids: A Tool for CITES-Based Identification and Trade Control

by Małgorzata Karbarz, Eliza Lebioda and Agnieszka Leśko

Genes 2025, 16(12), 1423; https://doi.org/10.3390/genes16121423 - 29 Nov 2025

Abstract

Background: Orchids of the Masdevallia genus are characterized by their beautiful esthetic qualities. However, they are vulnerable to habitat destruction, illegal harvesting, tourism and climate change. These extinction threats have led to the listing of all Masdevallia species in Appendix II of [...] Read more.

Background: Orchids of the Masdevallia genus are characterized by their beautiful esthetic qualities. However, they are vulnerable to habitat destruction, illegal harvesting, tourism and climate change. These extinction threats have led to the listing of all Masdevallia species in Appendix II of CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) and their selection by the IUCN (International Union for Conservation of Nature). Orchids are sold in various forms, e.g., stems or tubers, rendering them impossible to identify based on morphology alone. DNA barcoding is a method that enables reliable identification of organisms using DNA barcodes, and it offers an excellent solution to the need for efficient identification of Masdevallia orchids. The aim of this study was to determine the most effective locus for DNA barcode identification of Masdevallia orchids in order to develop a quick and practical identification method for this genus. Such a method can be used by CITES verification authorities to detect illegal trade. This is the first focused study to validate a DNA barcoding protocol for Masdevallia for CITES enforcement purposes. Methods: Three genetic regions were analyzed: matK, rbcL, and ITS. The effectiveness of identification was verified based on results obtained from the new version of the BOLD Systems v.5 reference database. Results: Although Masdevallia is not well represented in this database, successful identification to the genus level was achieved. Conclusions: The highest identification efficiency at the genus level was achieved for the ITS region (91%). Full article

(This article belongs to the Section Plant Genetics and Genomics)

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15 pages, 2792 KB

Open AccessCase Report

A Novel Variant of the ACTRT1 Gene Is Potentially Associated with Oligoasthenoteratozoospermia, Acrosome Detachment, and Fertilization Failure

by Olga Solovova, Sabina Khayat, Sergey Bogolyubov, Elizaveta Bragina, Tatiana Cherevatova and Vyacheslav Chernykh

Genes 2025, 16(12), 1422; https://doi.org/10.3390/genes16121422 - 28 Nov 2025

Abstract

Background: Male infertility is a common reproductive disorder, affecting about 7% of men in the general population. Despite its prevalence, the cause of infertility is often unknown. This case report presents the results of a comprehensive evaluation of a patient with severe oligoasthenoteratozoospermia [...] Read more.

Background: Male infertility is a common reproductive disorder, affecting about 7% of men in the general population. Despite its prevalence, the cause of infertility is often unknown. This case report presents the results of a comprehensive evaluation of a patient with severe oligoasthenoteratozoospermia and primary infertility. Methods: The patient underwent clinical, andrological, and genetic examinations, including semen analysis, transmission electron microscopy, cytogenetic examination, molecular analysis of the AZF locus and the CFTR gene, whole-exome sequencing, and Sanger sequencing. Results: Semen analysis revealed severe oligoasthenoteratozoospermia. Transmission electron microscopy showed acrosome detachment from the nucleus in 49% of the spermatozoa. A high percentage (54%) of spermatozoa with insufficiently condensed (“immature”) chromatin was also observed. No chromosomal abnormalities, Y chromosome microdeletions, or pathogenic CFTR gene variants were identified. Whole-exome sequencing revealed a novel c.821G>C variant (chrX:127185365G>C; NM_138289.4) in the ACTRT1 gene (Xq25). This variant was hemizygous in the patient and heterozygous in his mother, as determined by Sanger sequencing. According to the ACMG guidelines (PM2, PP3), this missense variant in the ACTRT1 gene was classified as a variant of uncertain clinical significance (VUS). Amino acid conservation and 3D protein modeling predict that the identified variant has a deleterious effect on the protein. Conclusions: This study suggests a potential link between a novel ACTRT1 variant and a specific teratozoospermia phenotype. Further functional studies are needed to confirm this association and determine the role of the gene in X-linked male infertility. Full article

(This article belongs to the Special Issue The Genetics of Male Infertility and Clinical Implications)

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10 pages, 2891 KB

Open AccessArticle

The Interference of RNA Preservative and Post-Collection Interval on RNA Integrity from Different Mice Tissues

by Ting Xie, Hui Zhu, Xiaoxi Wang, Fangyuan Li, Anqi Wang, Yaran Zhang, Sumei Zhang and Dan Guo

Genes 2025, 16(12), 1421; https://doi.org/10.3390/genes16121421 - 28 Nov 2025

Abstract

Background: For precise and reliable gene expression analysis, the acquisition of high-quality RNA is contingent upon excellent tissue preparation and handling. The optimal method for preserving tissues after surgical resection remains challenging due to the delays in delivery or the absence of cold [...] Read more.

Background: For precise and reliable gene expression analysis, the acquisition of high-quality RNA is contingent upon excellent tissue preparation and handling. The optimal method for preserving tissues after surgical resection remains challenging due to the delays in delivery or the absence of cold storage equipment. Although RNAlater has been extensively adopted for tissue preservation, few studies have systematically evaluated the effects of various tissue preservation solutions and post-collection intervals on RNA integrity across a range of tissue types. Methods: Ten types of mouse tissues, representing common tissue species in biobanks, were collected after resection. Tissues were either flash-frozen in liquid nitrogen as controls or immersed in one of three RNA preservatives—TRIzol and two commercial RNAlater solutions—and stored at room temperature (RT) for 0, 4, or 8 h before being frozen. Total RNA was extracted using TRIzol method, and its integrity was assessed using the RNA Integrity Number (RIN). Results: The results indicated that both the post-collection interval and the type of RNA preservative significantly impact RNA integrity. Pancreatic tissue showed the poorest RNA integrity (RIN < 5.5), whereas heart and ovary tissue yielded high-quality RNA (RIN > 7) even without any preservatives after 8 h at RT. To maintain baseline RNA integrity (RIN > 5.5), tissues including brain, kidney, muscle, liver, intestine, and uterus should be immersed in preservative and frozen within 8 h. For lung tissue preserved in RNAlater, the maximum recommended time at RT was 4 h. Conclusions: Robust, high-quality RNA can be obtained from most mouse tissues stored in RNA preservatives for up to 8 h at RT, with only minor variations observed across the different preservatives tested. Full article

(This article belongs to the Section RNA)

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14 pages, 702 KB

Open AccessArticle

Genetic Diversity of Apis cerana cerana in the Lüliang Mountain Area Based on Molecular Markers

by Chang Song, Ke Sun, Yanting Song, Qiyan Su, Xueyan Yi, Lina Guo and Yuan Guo

Genes 2025, 16(12), 1420; https://doi.org/10.3390/genes16121420 - 28 Nov 2025

Abstract

Objectives: This study presents a comprehensive molecular investigation of Apis cerana cerana populations inhabiting the Lüliang Mountain region, aiming to evaluate their genetic diversity and population structure using polymorphic microsatellite and mitochondrial DNA (mtDNA) markers. Methods: A total of 23 microsatellite loci and [...] Read more.

Objectives: This study presents a comprehensive molecular investigation of Apis cerana cerana populations inhabiting the Lüliang Mountain region, aiming to evaluate their genetic diversity and population structure using polymorphic microsatellite and mitochondrial DNA (mtDNA) markers. Methods: A total of 23 microsatellite loci and three mtDNA fragments (COI–COII, COI, Cytb) were successfully amplified, of which 21 loci were polymorphic and used for subsequent genetic analyses. Measures of genetic variability, population differentiation, and molecular variance were computed to assess intra- and interpopulation diversity. Results: High levels of genetic variation were detected (mean PIC = 0.349), with observed heterozygosity (Ho = 0.827) exceeding expected heterozygosity (He = 0.608). Analysis of molecular variance (AMOVA) revealed that 95.28% of total genetic variation occurred within populations, while 4.72% was attributed to among-population differences. Mitochondrial analyses identified 20 polymorphic sites forming 19 haplotypes, with high haplotype (Hd = 0.884) and nucleotide diversity (π = 0.00157). Conclusions: These results indicate substantial gene flow and interpopulation connectivity among A. c. cerana populations in the Lüliang region. Collectively, the findings provide critical molecular evidence supporting the conservation and sustainable management of A. c. cerana genetic resources in this area. Full article

(This article belongs to the Section Population and Evolutionary Genetics and Genomics)

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29 pages, 4628 KB

Open AccessArticle

Integrated Multi-Omics and Independent Validation Reveal MPO and TREM2 as Secretory Biomarkers for Non-Healing Diabetic Foot Ulcers

by Boya Li, Tianbo Li, Jiangning Wang and Lei Gao

Genes 2025, 16(12), 1419; https://doi.org/10.3390/genes16121419 - 28 Nov 2025

Abstract

Background: Diabetic foot ulcers (DFUs) are chronic wounds with high morbidity and mortality. Secretory proteins coordinate intercellular communication and may regulate inflammation, tissue repair and regeneration, but their contributions to DFU pathogenesis remain unclear. Aim: To discover and validate secretory protein–linked biomarkers that [...] Read more.

Background: Diabetic foot ulcers (DFUs) are chronic wounds with high morbidity and mortality. Secretory proteins coordinate intercellular communication and may regulate inflammation, tissue repair and regeneration, but their contributions to DFU pathogenesis remain unclear. Aim: To discover and validate secretory protein–linked biomarkers that distinguish non-healing DFUs and to explore their potential utility for diagnosis and therapy. Methods: We integrated bulk RNA-sequencing datasets (GSE199939 training set; GSE80178 and GSE143735 validation sets) and a single-cell RNA-sequencing dataset (GSE223964). Differentially expressed genes, secretory protein lists, and weighted gene co-expression networks were intersected to select candidates. Functional enrichment, protein interaction networks and support vector machine–recursive feature elimination identified key markers. We visualized their cell-type distribution at single-cell resolution and validated their expression in external cohorts. Pathway enrichment, gene co-expression networks, ceRNA regulatory analysis and qRT-PCR in patient samples were used for further characterization. Results: Among 4803 differentially expressed genes, 743 overlapped with known secretory proteins. WGCNA highlighted modules strongly associated with DFUs, yielding 386 candidates. SVM-RFE combined with protein interaction analysis pinpointed four secretory proteins—LYZ, MPO, SLCO2B1 and TREM2—as putative biomarkers. Single-cell analyses showed that MPO, LYZ, SLCO2B1 and TREM2 transcripts are detectable in multiple skin-resident and immune cell populations, and that the DFU-associated upregulation of MPO and LYZ is most pronounced within keratinocyte clusters, while MPO and TREM2 remained consistently dysregulated in independent bulk cohorts. MPO-associated genes were enriched for immune and inflammatory pathways, whereas TREM2-linked genes implicated cell cycle and cytoskeletal regulation. GeneMANIA and ceRNA analyses revealed extensive interaction networks. qRT-PCR confirmed differential expression of MPO and TREM2 in clinical DFU tissues. Conclusions: Integrated multi-modal analysis identifies secretory proteins, particularly MPO and TREM2, as central determinants of impaired healing in DFUs. These molecules and their regulatory networks represent promising biomarkers and therapeutic targets for precision management of diabetic wounds. Full article

(This article belongs to the Section Bioinformatics)

28 pages, 6018 KB

Open AccessArticle

The Complete Chloroplast Genome of Encyclia tampensis (Orchidaceae): Structural Variation and Heterogeneous Evolutionary Dynamics in Epidendreae

by Bing Liu, Ju Huang, Zishuo Wang, Dong Li, Zhangxi Yuan and Yi Yao

Genes 2025, 16(12), 1418; https://doi.org/10.3390/genes16121418 - 28 Nov 2025

Abstract

Background: The epiphytic orchids of the tribe Epidendreae represent a remarkably evolutionary radiation, yet their phylogenetic relationships and plastome evolutionary dynamics are still not fully resolved. Methods: This study has sequenced, assembled, and annotated the complete chloroplast genome of Encyclia tampensis. Through [...] Read more.

Background: The epiphytic orchids of the tribe Epidendreae represent a remarkably evolutionary radiation, yet their phylogenetic relationships and plastome evolutionary dynamics are still not fully resolved. Methods: This study has sequenced, assembled, and annotated the complete chloroplast genome of Encyclia tampensis. Through comparative analyses of a curated dataset of 40 Epidendreae plastomes, we investigated codon usage bias, evolutionary selection pressures (Ka/Ks), and phylogenetic relationships. Results: The plastome of E. tampensis (160,650 bp) has a typical quadripartite structure, with a significant AT bias (62.09%), and contains 124 annotated genes. Comparative genomic analysis across 40 Epidendreae species revealed substantial plastome size variation (123,455 to 160,650 bp), pronounced small single copy (SSC) contraction in E. tampensis (608 bp), and atypical long simple sequence repeats (SSRs) accumulation. Natural selection dominated codon usage, with strongest purifying selection in rbcL (average Ka/Ks = 0.205). Phylogenetic analyses confirmed subtribal monophyly and detected evolutionary rate heterogeneity correlated with life history strategies. Conclusions: These results establish that plastome evolution in Epidendreae has been principally driven by structural reorganization through SSC contraction and long SSR accumulation, selective constraints maintaining functional genes under purifying selection, and life history-strategy-mediated evolutionary rate diversification. These processes collectively account for the tribe’s extensive genomic diversity and phylogenetic complexity, thereby providing a theoretical framework for understanding orchid plastome evolution and a molecular basis for the systematic classification and conservation of this economically significant plant group. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in the “Plant Genetics and Genomics” Section)

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