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Volume 17
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Genes, Volume 17, Issue 2 (February 2026) – 132 articles

Cover Story (view full-size image): Obsessive–compulsive disorder is a highly heritable yet biologically complex condition. This review integrates recent evidence from genomics and epigenomics, including GWAS, rare-variant studies, CNV analyses, methylation data, and miRNA research. Together, these findings support a model in which polygenic burden, rare functional variants, and regulatory mechanisms converge on synaptic, neurodevelopmental, immune, and cellular pathways. By connecting these signals to multilevel endophenotypes, the paper offers an updated framework for understanding OCD biology and for guiding future multidisciplinary and precision-based research. View this paper
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16 pages, 1565 KB  
Article
Genetic and Phenotypic Characterization of a Novel dull1 Allele Affecting Starch Accumulation in Maize
by Mingmin Zheng, Xiaowei Liu, Ziwen Shi, Xin Yuan, Yujiao Gao, Xian Zhao and Qiang Huang
Genes 2026, 17(2), 250; https://doi.org/10.3390/genes17020250 - 23 Feb 2026
Viewed by 450
Abstract
Background: Starch accumulation contributes substantially to maize grain yield and quality. Starch synthase III (SSIII) is a key component of the starch biosynthetic enzyme complex. However, its regulatory role in starch accumulation in maize endosperm remains incompletely understood. Methods: The du1-2018 mutant arose [...] Read more.
Background: Starch accumulation contributes substantially to maize grain yield and quality. Starch synthase III (SSIII) is a key component of the starch biosynthetic enzyme complex. However, its regulatory role in starch accumulation in maize endosperm remains incompletely understood. Methods: The du1-2018 mutant arose spontaneously during a conventional maize breeding program. Phenotypic characterization, storage compound contents, and starch structure were compared between the mutant and wild-type lines. BSA-seq, genetic linkage analysis, and transcriptomic analysis were employed to identify the candidate gene responsible for the mutant phenotype. Transcriptome sequencing was performed on developing kernels to evaluate the genome-wide effects of the du1-2018 mutation. Results: The du1-2018 mutant exhibited dull, glassy, and mildly shrunken kernels, with decreased starch levels and elevated soluble sugar and protein contents. The du1-2018 mutation disrupted starch accumulation, resulting in smaller, irregularly shaped starch granules and significant changes in starch composition and fine structure. This mutation was identified as a severe loss-of-function allele of the dull1 (du1) gene, evidenced by almost undetectable Du1 transcripts in developing kernels. Notably, transcriptomic analysis revealed that a substantial proportion of differentially expressed genes (DEGs) were involved in amino acid and protein metabolism. Conclusions: The novel du1 allelic variant, du1-2018, disrupts starch biosynthesis in maize endosperm, leading to reduced starch accumulation, altered starch structure, and transcriptional changes in nitrogen-related metabolic pathways. Our results provide new insights into the regulatory mechanisms underlying SSIII function in starch synthesis and endosperm development, and suggest potential links to carbon/nitrogen balance, with implications for future genetic improvement of maize grain quality. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)
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16 pages, 450 KB  
Article
Genetic Traces in Autism Spectrum Disorders: A Whole Exome Sequencing Study from Türkiye
by Gülsüm Kayhan, Ahmet Ozaslan, Elvan Işeri, Esra Guney, Hasan Huseyin Kazan, Dicle Buyuktaskin, Muhammed Fatih Mulayim, Mehmet Ali Ergun and Ferda Emriye Percin
Genes 2026, 17(2), 249; https://doi.org/10.3390/genes17020249 - 23 Feb 2026
Viewed by 783
Abstract
Background: Autism spectrum disorders (ASDs) are defined as a large spectrum of phenotypes whose basic definition is deficiency in social interactions, particularly during pediatric stages. Through clinical evaluations, it would be challenging to diagnose since the symptoms may be disregarded or controversial. Hence, [...] Read more.
Background: Autism spectrum disorders (ASDs) are defined as a large spectrum of phenotypes whose basic definition is deficiency in social interactions, particularly during pediatric stages. Through clinical evaluations, it would be challenging to diagnose since the symptoms may be disregarded or controversial. Hence, molecular approaches could be powerful for differential and certain diagnosis. Moreover, considering the possible genetic complexity of the disease, the rates of molecular diagnosis remain insufficient. Nevertheless, the number of newly identified ASD-monogenic inheritance relationships is escalating daily. This underscores the increasing importance of comprehensive molecular tests, such as whole exome sequencing (WES), which encompass all relevant genes. Furthermore, reporting population-specific variants is critical to validate already listed ones and decipher novel ones. In the present study, we aimed to document the disease-related variants in Turkish patients with ASD. Methods: This study evaluated the WES outcomes of 75 ASD patients with normal results in Fragile X testing, cytogenetic analysis, and molecular karyotyping. All patients were diagnosed with ASD based on the criteria from the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM-5). Results: The average age of the participants was 8.2 (±5.0) years. A higher percentage of the participants was male (73.3%) compared with female (26.7%). Eighteen patients (24%) had pathogenic or likely pathogenic (LP) variants, while 34 (45.3%) exhibited variants of unknown significance (VUS). In 30.7% of the cases, no clinically relevant variants were found. The MECP2 gene was most frequently affected, followed by EP300 and PTEN. Additionally, four patients carried novel de novo missense variants in the KMT2C, MECP2, PTEN, and TRRAP genes. Conclusions: Genetic diagnosis of ASD would be useful for confirming the underlying etiologies, devising personalized therapeutic strategies, and offering family counseling. Although WES has been employed in ASD patients for an extended period, the identification of gene and variant spectra across diverse cohorts and the discovery of novel variants continues to hold significant scientific importance. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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23 pages, 5493 KB  
Systematic Review
Genetic Mapping of the 22q11.2 Deletion Syndrome (DiGeorge Syndrome) Microdeletion Types Revealed Novel Candidate Breakpoints
by Louis Papageorgiou, Elena Nikolopoulou, Eleni Koniari, Kyriaki Hatziagapiou, Dimitrios Chaniotis, Apostolos Beloukas, George P. Chrousos, Elias Eliopoulos and Trias Thireou
Genes 2026, 17(2), 248; https://doi.org/10.3390/genes17020248 - 22 Feb 2026
Viewed by 957
Abstract
Background: 22q11.2 deletion syndrome (DiGeorge Syndrome) is a rare disorder that involves a de novo hemizygous microdeletion within the 22q11.2 chromosomal locus. Individuals affected by this condition display a wide array of clinical phenotypes as well as haplotype sequences, which render understanding [...] Read more.
Background: 22q11.2 deletion syndrome (DiGeorge Syndrome) is a rare disorder that involves a de novo hemizygous microdeletion within the 22q11.2 chromosomal locus. Individuals affected by this condition display a wide array of clinical phenotypes as well as haplotype sequences, which render understanding the genotype–phenotype relationship quite difficult. Additionally, the complex structure of the 22q11.2 low-copy repeats (LCRs), which usually inhibits sequencing efforts, has complicated the study of possible breakpoints that instigate the deletion events. In this study, 22q11.2 deletion syndrome is investigated on a genomic and phenotypic level for the purpose of determining the impact of each deletion type and identifying possible candidate breakpoints. Methods: In the present study, a systematic review combined with a secondary genomic analysis has been executed following PRISMA guidelines using PubMed and Scopus publications in order to estimate its holistic genomic map, genomic functional elements, and key genomic regions such as LCRs. A statistical content analysis of the affected chromosomal regions was also performed. Groups of functional elements with common traits were composed, and their contribution to the deletion events was investigated. Finally, the 22q11.2 repeat regions were screened for palindromic AT-rich repeats. Results: Of the 8202 unique publications studied in this work, only 65 met the inclusion criteria. The estimated genomic map of 22q11.2 deletion syndrome in the secondary genomic analysis revealed 11 distinct microdeletions occurring between eight LCRs, and a new repeat region within the CES region (CESRR), of which the LCR22A-LCR22D deletion was the most frequently reported. Last but not least, the palindromic analyses indicated eight critical groups as candidate breakpoints that potentially form four distinct patterns, and ten palindromic AT-rich repeat (PATRR) regions were identified amongst LCR22A, LCR22B, LCR22D, LCR22F and LCR22H. Conclusions: The study results validate the differentiating clinical contribution between the proximal and the distal segments. Eight novel candidate breakpoints and five new PATRRs were identified that require further study to establish their involvement in 22q11.2 microdeletion events. Full article
(This article belongs to the Special Issue Structural and Evolutionary Perspectives on Immunogenetic Variation in Autoimmune and Related Disorders)
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16 pages, 1988 KB  
Article
Clinical Insights into the Neurodevelopmental Impact of 16p CNVs in an Italian Clinical Cohort
by Ilaria La Monica, Maria Rosaria Di Iorio, Antonia Sica, Lucio Pastore and Barbara Lombardo
Genes 2026, 17(2), 247; https://doi.org/10.3390/genes17020247 - 21 Feb 2026
Viewed by 842
Abstract
Background: Neurodevelopmental disorders (NDDs) are a heterogeneous group of conditions characterized by cognitive, behavioral, and developmental impairments, frequently linked to structural genomic alterations. Copy number variants (CNVs) involving chromosome 16, particularly the short arm 16p, are recognized contributors to neurodevelopmental variability. Despite [...] Read more.
Background: Neurodevelopmental disorders (NDDs) are a heterogeneous group of conditions characterized by cognitive, behavioral, and developmental impairments, frequently linked to structural genomic alterations. Copy number variants (CNVs) involving chromosome 16, particularly the short arm 16p, are recognized contributors to neurodevelopmental variability. Despite increasing international evidence, data from Italian clinical cohorts are still limited. Methods: We investigated 1200 patients referred for genetic evaluation due to suspected NDDs, including autism spectrum disorder (ASD), intellectual disability (ID), global developmental delay, and language impairment. All individuals underwent array comparative genomic hybridization (a-CGH) analysis, and identified variants were correlated with detailed clinical, cognitive, and behavioral assessments. The analysis focused on recurrent CNVs at 16p11.2, 16p13.3, and 16p13.11, regions containing dosage-sensitive genes relevant to neurodevelopment. Results: CNVs involving the 16p region were identified in 96 patients (8% of the cohort), encompassing both deletions and duplications. Deletions were mainly associated with developmental delay, language deficits, and ASD-related features, whereas duplications were more frequently linked to behavioral dysregulation, attentional deficits, and variable cognitive impairment. Marked phenotypic variability was observed among individuals carrying similar CNVs, suggesting the contribution of modifying genetic or environmental factors. In a subset of patients, additional CNVs were identified, potentially exacerbating clinical severity, consistent with the two-hit model. Conclusions: This study confirms a strong association between recurrent 16p CNVs and a wide spectrum of neurodevelopmental phenotypes in an Italian clinical cohort. The findings emphasize the diagnostic utility of systematic genomic screening and the importance of an integrated genotype–phenotype approach to improve clinical interpretation, management, and genetic counseling in NDDs. Full article
(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)
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22 pages, 6202 KB  
Article
Integrated Transcriptomic Analysis Identifies Novel Candidate Genes Associated with Calcific Aortic Valve Disease
by Jing Chen, Shichao Guo, Junming Zhu, Haiou Hu, Bing Tang, Lingchen Huang, Chenhan Zhang, Suwei Chen, Sanbao Chai, Zhiyu Qiao and Hongfeng Jiang
Genes 2026, 17(2), 246; https://doi.org/10.3390/genes17020246 - 20 Feb 2026
Viewed by 712
Abstract
Background: Calcified aortic valve disease (CAVD) is a prevalent valvular disorder in the elderly and a major cause of aortic stenosis. Surgical and transcatheter aortic valve replacement remain the primary treatments for advanced CAVD; however, effective pharmacological therapies to prevent or slow disease [...] Read more.
Background: Calcified aortic valve disease (CAVD) is a prevalent valvular disorder in the elderly and a major cause of aortic stenosis. Surgical and transcatheter aortic valve replacement remain the primary treatments for advanced CAVD; however, effective pharmacological therapies to prevent or slow disease progression are lacking. Therefore, there is an urgent need to explore potential novel candidate biomarkers and therapeutic targets. Methods: In this study, transcriptomic data from multiple independent datasets were integrated to comprehensively characterize the transcriptional profile of CAVD. Feature genes were identified using complementary machine learning approaches, followed by functional pathway enrichment and protein–protein interaction (PPI) network analyses to uncover novel candidate genes associated with CAVD. Single-cell RNA sequencing (sc-RNA-Seq) data were further analyzed using pseudotime trajectory analysis to explore transcriptional dynamics during valve interstitial cells’ (VICs) osteogenic progression. Quantitative PCR and Western blot analyses of human calcified aortic valve tissues were used for validation. Results: A total of 119 CAVD-associated genes were identified, primarily involved in ossification, extracellular matrix organization, and cell–substrate adhesion. Among these, the ossification-associated genes BAMBI, HAND2, and MYOC exhibited potential discriminatory power between CAVD and control samples, with notable downregulation in calcified valves. Pseudotime analysis showed that the expression of these genes gradually decreased along the transcriptional trajectory associated with osteogenic differentiation. In addition, the analysis of relative immune signatures revealed negative correlations between these genes and multiple immune signatures. Conclusions: This study identifies novel candidate genes underlying CAVD pathogenesis and highlights BAMBI, HAND2, and MYOC as potential biomarkers and therapeutic targets, providing new insights into disease mechanisms and opportunities for novel interventions. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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17 pages, 2035 KB  
Article
Integrative Computational Analysis of TP53 Exon 5–6 Mutations in Oral Cavity, Prostate, and Breast Cancers in a Senegalese Population
by Mouhamed Mbaye, Fatimata Mbaye and Mbacke Sembene
Genes 2026, 17(2), 245; https://doi.org/10.3390/genes17020245 - 20 Feb 2026
Viewed by 559
Abstract
Background/Objectives: The tumor suppressor gene TP53 is one of the most frequently mutated genes in human cancers, with alterations predominantly affecting its DNA-binding domain (DBD). However, the mutational landscape and functional consequences of TP53 variants remain poorly characterized in African populations. This [...] Read more.
Background/Objectives: The tumor suppressor gene TP53 is one of the most frequently mutated genes in human cancers, with alterations predominantly affecting its DNA-binding domain (DBD). However, the mutational landscape and functional consequences of TP53 variants remain poorly characterized in African populations. This study aimed to characterize mutations in exons 5–6 of TP53 in oral cavity cancer (OCC), prostate cancer (PC), and breast cancer (BC) in a Senegalese population, and to assess their structural effects, functional consequences, and impact on protein–protein interactions with BCL-2. Methods: Seventy-eight archived tumor DNA samples from Senegalese patients with OCC, PC, and BC were analyzed. Variants were annotated using COSMIC and dbSNP databases. Functional impact was evaluated with PolyPhen-2. Structural stability changes (ΔΔG) were predicted using FoldX, conformational dynamics (ΔΔSvib) were assessed with ENCoM, and effects on the p53–BCL-2 interaction were analyzed using DDMut-PPI. Statistical analyses were also performed. Results: BC exhibited the highest TP53 mutation frequency, whereas OCC showed greater mutational diversity. Exon-level analysis revealed a significant enrichment of exon 6 mutations in BC. Structural analyses indicated that exon 5 mutations across all cancers and mutations in OCC were predominantly destabilizing and associated with loss-of-function effects. In contrast, recurrent exon 6 mutations in PC and BC, particularly V217L and V218M, were predicted to stabilize the p53 structure. Conformational dynamics differences between exons were significant only in PC. All analyzed mutations were predicted to stabilize the p53–BCL-2 interaction. Conclusions: This integrative in silico study identified cancer and exon-specific TP53 mutation patterns in a Senegalese population, highlighting exon 6 as a context-dependent hotspot with potential oncogenic implication in PC and BC. Despite its computational nature, the study provides valuable insights that merit further investigation. Full article
(This article belongs to the Special Issue Computational Genomics and Bioinformatics of Cancer)
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17 pages, 2577 KB  
Article
Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Celaenorrhinus victor (Lepidoptera: Hesperiidae)
by Yaping Hu, Site Luo, Zhentian Yan, Xiaomin Ge, Le Wang, Xu Zhou, Bin Chen, Hui Ding and Xiao Zheng
Genes 2026, 17(2), 244; https://doi.org/10.3390/genes17020244 - 19 Feb 2026
Viewed by 478
Abstract
Background: Skipper butterflies (Hesperiidae) are a morphologically distinctive lineage within Papilionoidea, yet relationships among many groups remain difficult to resolve, and mitochondrial genomic resources remain limited for some tribes, including Celaenorrhinini. Methods: We sequenced and characterized the complete mitochondrial genome of [...] Read more.
Background: Skipper butterflies (Hesperiidae) are a morphologically distinctive lineage within Papilionoidea, yet relationships among many groups remain difficult to resolve, and mitochondrial genomic resources remain limited for some tribes, including Celaenorrhinini. Methods: We sequenced and characterized the complete mitochondrial genome of Celaenorrhinus victor using Illumina short-read sequencing. Gene content and organization were annotated, codon-usage patterns were assessed across Celaenorrhinus using relative synonymous codon usage and multiple compositional/selection tests (ENC–GC3s, neutrality, and PR2 analyses), selective constraints were evaluated using Ka/Ks for 13 protein-coding genes, and phylogenetic relationships were inferred with a partitioned maximum-likelihood analysis of 66 complete hesperiid mitogenomes. Results: The circular mitogenome of C. victor is 15,180 bp and contains the typical 37 genes (13 protein-coding genes, 22 tRNAs, and two rRNAs) plus an A + T-rich control region, with an overall A + T content of 79.64%. Gene order and orientation match those of other Celaenorrhinus and hesperiid mitogenomes. All protein-coding genes use standard invertebrate mitochondrial start codons (with cox1 initiating with TTG) and terminate with complete TAA stop codons. Codon usage is strongly biased toward A/U-ending codons and is broadly similar among five sampled Celaenorrhinus mitogenomes; ENC–GC3s, neutrality, and PR2 analyses indicate a predominant influence of A + T-directed mutational pressure with additional effects beyond base composition. Ka/Ks values for all 13 protein-coding genes were <1, consistent with pervasive purifying selection; cox genes were the most conserved, whereas several NADH dehydrogenase subunit genes evolved comparatively faster. The phylogeny recovered monophyletic Celaenorrhinini and a well-supported Celaenorrhinus clade, placing C. victor as sister to Celaenorrhinus consanguineus, while deeper nodes among major hesperiid lineages showed only moderate support in parts of the tree. Conclusions: This study provides a new mitogenomic resource for Celaenorrhinini and a comparative reference for codon usage and selective constraints within Celaenorrhinus, supporting the placement of C. victor within Hesperiidae while highlighting remaining uncertainty at deeper hesperiid divergences. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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15 pages, 4641 KB  
Article
The Mitochondrial Genome of Curcuma longa: A Large and Structurally Complex Genome with Extensive Intracellular DNA Transfer
by Bing Xu, Minlong Jia, Jiali Kong, Liyun Nie, Jie Wang, Luke R. Tembrock, Zhiqiang Wu, Sen Li and Xuezhu Liao
Genes 2026, 17(2), 243; https://doi.org/10.3390/genes17020243 - 19 Feb 2026
Cited by 1 | Viewed by 568
Abstract
Background: Plant mitochondrial genomes exhibit extreme variation in size and structure while maintaining a conserved set of core protein-coding genes. This combination of structural diversity and functional conservation provides valuable insights into evolutionary processes such as genome expansion, rearrangement, and intracellular DNA [...] Read more.
Background: Plant mitochondrial genomes exhibit extreme variation in size and structure while maintaining a conserved set of core protein-coding genes. This combination of structural diversity and functional conservation provides valuable insights into evolutionary processes such as genome expansion, rearrangement, and intracellular DNA transfer. Curcuma longa, an economically and medicinally important species in the genus Curcuma (Zingiberaceae), has not yet been studied in terms of the organization and evolution of its mitochondrial genome. Methods: In this study, we assembled and annotated the mitochondrial and plastid genomes of C. longa using third-generation HiFi sequencing data, systematically analyzing their genomic structure, repetitive sequence content, and features of sequence transfer between nuclear and organellar genomes. Results: The mitochondrial genome of C. longa was assembled as a complex, network-like structure consisting of 12 contigs with a total length of approximately 7.7 Mb, making it one of the largest mitochondrial genomes reported in monocots to date. Comparative analysis revealed significant differences in repeat types, abundance, and length distribution between the two organellar genomes. Additionally, extensive intracellular DNA transfer events were identified among the nuclear, mitochondrial, and plastid genomes. Conclusions: Overall, this study provides the first comprehensive report on the giant mitochondrial genome of C. longa, detailing its structural organization, repeat content, and intergenomic transfers. These findings lay a foundation for understanding mitochondrial genome evolution in Curcuma and offer broader insights into the mechanisms driving extreme mitochondrial genome expansion in angiosperms and monocots specifically. Full article
(This article belongs to the Special Issue Genetic and Breeding Improvement of Horticultural Crops)
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29 pages, 13047 KB  
Article
Integrated Analysis of Transcriptome and Metabolome Profiles in Astragslus membranaceus (Fisch.) Bge. var. mongholicus (Bge.) Hsiao Seedlings Under Drought Stress
by Aihuan Ma, Kamila Abudourexiti, Zhen Liu, Saideaihemaiti Wulamu, Danye Zhao and Kuerban Tusong
Genes 2026, 17(2), 242; https://doi.org/10.3390/genes17020242 - 18 Feb 2026
Viewed by 660
Abstract
Background: Astragalus membranaceus is a traditional Chinese medicinal herb with significant pharmacological value. Drought stress adversely affects its biomass accumulation and medicinal quality. Methods: In this study, we performed physiological profiling, transcriptomics, and metabolomics analyses on A. membranaceus (Fisch.) Bge. var. mongholicus [...] Read more.
Background: Astragalus membranaceus is a traditional Chinese medicinal herb with significant pharmacological value. Drought stress adversely affects its biomass accumulation and medicinal quality. Methods: In this study, we performed physiological profiling, transcriptomics, and metabolomics analyses on A. membranaceus (Fisch.) Bge. var. mongholicus (Bge.) Hsiao seedlings to elucidate the response mechanisms in both aboveground and root tissues under varying drought stress intensities (Control, CK; Light Drought LD; Moderate Drought MD; Severe Drought SD). Results: Our findings indicate that LD primarily activated antioxidant enzymes, whereas severe stress led to the dominance of osmotic adjustment. Compared with CK, drought treatments resulted in 2987 differentially expressed genes (DEGs; 1674 up-regulated and 1313 down-regulated) and 921 differentially accumulated metabolites (DAMs)—562 in positive ionization mode (224 up, 338 down) and 359 in negative ionization mode (166 up, 193 down). Both gene expression and metabolite accumulation exhibited pronounced stress intensity-dependent patterns, suggesting that A. mongholicus initiates a broad, gene activation-led “active coping” strategy and mobilizes increasingly extensive metabolic pathways as drought intensifies. Conclusions: Integrated transcriptomic and metabolomic analyses revealed a tissue-specific “shoot–root partitioned coordination” mechanism: aboveground tissues activated a glutathione metabolism-centered “antioxidant–osmotic adjustment” defense, while root tissues reconfigured amino acid metabolism to maintain energy supply and signaling. This synergistic coordination represents a core adaptive strategy of A. mongholicus under drought conditions. Our study provides deeper insights into the drought resistance mechanisms of Astragalus and offers valuable references for breeding drought-tolerant varieties of Astragalus and other medicinal plants. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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15 pages, 10132 KB  
Article
Regulatory Potential of piRNAs Targeting Klotho and Other Genes
by Anna Pyrkova, Kyrmyzy Akhmetova, Murat Zhanuzakov, Makpal Tauassarova, Aizhan Rakhmetulina, Raigul Niyazova, Saltanat Orazova, Piotr Zielenkiewicz and Anatoliy Ivashchenko
Genes 2026, 17(2), 241; https://doi.org/10.3390/genes17020241 - 18 Feb 2026
Viewed by 583
Abstract
Background/Objectives: piRNAs (PIWI-interacting RNAs) can significantly modify the expression of protein-coding genes by suppressing the translation process. The aim of this work was to computationally evaluate the potential interactions between piRNAs and the mRNA of the Klotho gene, as well as other genes [...] Read more.
Background/Objectives: piRNAs (PIWI-interacting RNAs) can significantly modify the expression of protein-coding genes by suppressing the translation process. The aim of this work was to computationally evaluate the potential interactions between piRNAs and the mRNA of the Klotho gene, as well as other genes involved in key metabolic pathways related to health and lifespan regulation. Methods: Bioinformatic analysis was conducted using the MirTarget program, which determines the quantitative characteristics of predicted nucleotide interactions between piRNAs and mRNA targets. Results: Several piRNAs (piR-44682, piR-1940042, piR-3008660, piR-3215034, piR-6885965, and piR-7980636) were predicted to bind within a single cluster of binding sites on the KL mRNA. In addition, piR-6890096 was predicted to interact with the KL mRNA through full complementarity. The mRNAs of AFF2, BCL2L11, CPT1A, DAZAP1, NDRG3, SKIDA1, WBP4, ZIC5, and ZSWIM6 were predicted to interact with piR-3215034 and piR-6885965, forming clusters of binding sites located in the 5′ untranslated region (5′UTR), coding sequence (CDS), and 3′ untranslated region (3′UTR). Additionally, piR-576442, piR-1501557, piR-1845735, piR-2069834, and piR-3029987 were predicted to bind only within the 3′UTR of FGF23 mRNA. These results suggest that piRNAs are potential regulators of KL and other genes involved in key metabolic processes. Conclusions: The findings provide a basis for further experimental validation of predicted piRNA–mRNA interactions and their possible roles in gene regulation. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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16 pages, 3575 KB  
Article
Assembly of the Delphinium densiflorum Chloroplast Genome and Comparative Genomics Within Delphinium
by Siqi Chen, Min Wang, Xinhang Lu, Yuying Sun and Min Ma
Genes 2026, 17(2), 240; https://doi.org/10.3390/genes17020240 - 17 Feb 2026
Viewed by 458
Abstract
Background/Objectives: Chloroplast genomes are essential for understanding the systematics and adaptive evolution of alpine plants, yet genomic data for high-altitude Delphinium species remain scarce. Delphinium densiflorum, a medicinal plant endemic to the Qinghai-Tibet Plateau, exhibits notable high-altitude adaptations, but its plastome [...] Read more.
Background/Objectives: Chloroplast genomes are essential for understanding the systematics and adaptive evolution of alpine plants, yet genomic data for high-altitude Delphinium species remain scarce. Delphinium densiflorum, a medicinal plant endemic to the Qinghai-Tibet Plateau, exhibits notable high-altitude adaptations, but its plastome features and evolutionary position are still unclear. This study aims to assemble and characterize its complete chloroplast genome and clarify its phylogenetic placement within Delphinium. Methods: Using Illumina NovaSeq data, we de novo assembled the D. densiflorum plastome, annotated it with CPGAVAS2, and compared it with 12 published Ranunculaceae plastomes. We analyzed IR-boundary dynamics, genome-wide sequence variation, and codon-usage bias and constructed a maximum-likelihood phylogeny based on 69 shared protein-coding genes. Results: The plastome is 154,161 bp (GC 38.24%) with a canonical quadripartite structure, encoding 131 genes (87 CDS, 8 rRNA, 37 tRNA). An IR expansion into the SSC region yields the shortest SSC reported among the compared Delphinium species and produces unique structural variants. Photosynthetic genes are extremely conserved (nucleotide diversity Pi ≤ 0.01), whereas several loci (e.g., ycf1 and psaC) are highly divergent (Pi ≥ 0.05). Codon usage shows a strong bias toward AU-ending triplets. Phylogenetically, D. densiflorum forms a 100%-bootstrap clade with other high-altitude congeners, supporting the non-monophyly of Delphinium. Conclusions: This study delineates the plastome architecture and putative adaptive signatures of D. densiflorum, identifies robust candidate loci for DNA barcoding, and provides molecular evidence for taxonomic revision and conservation strategies in Delphinium. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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19 pages, 24066 KB  
Article
Identification of a Tertiary Lymphoid Structure Signature for Predicting Tumor Outcomes Through Transcriptomics Analysis
by Mengdi Zhou, Fangliangzi Meng, Fan Wu and Chi Zhou
Genes 2026, 17(2), 239; https://doi.org/10.3390/genes17020239 - 16 Feb 2026
Viewed by 781
Abstract
Background: Tertiary lymphoid structures (TLSs) play a crucial role in regulating tumor invasion and metastasis and serve as a promising prognostic biomarker in immunotherapy, influencing survival and immune response in multiple cancers. However, existing studies rely on limited gene signatures to assess TLSs, [...] Read more.
Background: Tertiary lymphoid structures (TLSs) play a crucial role in regulating tumor invasion and metastasis and serve as a promising prognostic biomarker in immunotherapy, influencing survival and immune response in multiple cancers. However, existing studies rely on limited gene signatures to assess TLSs, and there remains a lack of comprehensive TLS-related features for pan-cancer prognosis or immunotherapy response prediction. Methods: Based on published TLS gene signatures, mutation data, and expression profiles from 33 tumor types in TCGA, along with data from 15 immune checkpoint blockade (ICB) cohorts, we first systematically evaluated six TLS gene signatures in relation to immune-related indicators and assessed their predictive and prognostic performance across tumors and immunotherapy. Subsequently, using meta-analysis, we constructed a de novo TLS-related gene feature set, termed predictTLS, designed to predict ICB efficacy and prognosis. The rationality and effectiveness of predictTLS were validated using internal validation sets, single-cell transcriptomic, and spatial transcriptomic data. Results: The evaluation revealed associations between TLS gene signatures and key immune-related indicators. The newly constructed predictTLS feature set demonstrated effectiveness in predicting both ICB therapy outcomes and patient prognosis across the analyzed cohorts. Validation across internal datasets, single-cell profiles, and spatial transcriptomics supported the robustness and biological relevance of predictTLS. Conclusions: This study provides a systematically validated, de novo TLS-related gene signature that can serve as a clinical biomarker for predicting immunotherapy response and prognosis in pan-cancer settings. These findings offer new tools for risk stratification and potential therapeutic targeting in tumor immunotherapy. Full article
(This article belongs to the Special Issue Computational Genomics and Bioinformatics of Cancer)
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14 pages, 1511 KB  
Case Report
Xp22.33 Duplication Encompassing PAR1 in a Male with Syndromic Neurodevelopmental Disorder and Tall Stature
by Dibyendu Dutta, Xi Luo and Ria Garg
Genes 2026, 17(2), 238; https://doi.org/10.3390/genes17020238 - 15 Feb 2026
Viewed by 1516
Abstract
Background: Duplications involving Xp22.33, particularly within the pseudoautosomal region 1 (PAR1), are rare. While copy number variants (CNVs) involving SHOX, a dosage-sensitive gene in PAR1, are known to cause growth disorders, large duplications encompassing the entire PAR1 region and beyond show variable [...] Read more.
Background: Duplications involving Xp22.33, particularly within the pseudoautosomal region 1 (PAR1), are rare. While copy number variants (CNVs) involving SHOX, a dosage-sensitive gene in PAR1, are known to cause growth disorders, large duplications encompassing the entire PAR1 region and beyond show variable associations with skeletal and neurodevelopmental abnormalities. Duplication of the near-complete, isolated PAR1 with a comprehensive clinical description has not been reported. Case Presentation: We report a male patient with a 2.49 Mb duplication encompassing nearly the entire PAR1 region (chrX:200854–2692897, GRCh37). Clinical features included global developmental delay (GDD), autism spectrum disorder (ASD), recurrent seizures, hypotonia with joint hypermobility, dysmorphic features, and proportionate tall stature. The duplicated segment contains 30 genes, including 15 protein-coding genes that escape X-inactivation. Among these, SHOX, DHRSX, ASMT, and CSF2RA are notable candidates contributing to the observed phenotype. Conclusions: This report presents a detailed clinical characterization of a rare, near-complete, isolated PAR1 duplication in a male individual. The co-occurrence of tall stature, GDD, ASD, and seizures raises the possibility of a dosage-related phenotypic effect involving one or more genes within the duplicated interval. While causality cannot be definitively established, these observations contribute to the emerging understanding of the functional consequences of Xp22.33 duplications and suggest that increased copy number within this region may be associated with a clinically significant neurodevelopmental phenotype. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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20 pages, 1913 KB  
Article
Transcriptome-Based Selection and Validation of Reference Genes for Gene Expression Analysis in Roegneria ciliaris ‘Liao Sheng’ Across Various Tissues and Under Drought Stress
by Qianyun Luo, Yue Liu, Yifan Wang, Guanghao Zhang, Jiafen Liu, Hongxin Li, Zhen Liang, Ying Liu, Long Bai and Sijia Liu
Genes 2026, 17(2), 237; https://doi.org/10.3390/genes17020237 - 14 Feb 2026
Viewed by 429
Abstract
Backgrounds: Roegneria ciliaris is a perennial tetraploid wild relative of wheat that is widely distributed in China. It can be used both as a forage crop and ecological grass (the grasses specifically bred for ecological restoration) due to its strong stress tolerance, early [...] Read more.
Backgrounds: Roegneria ciliaris is a perennial tetraploid wild relative of wheat that is widely distributed in China. It can be used both as a forage crop and ecological grass (the grasses specifically bred for ecological restoration) due to its strong stress tolerance, early green-up, vigorous seedling growth in spring, and great palatability. Methods: It is necessary to select and validate appropriate reference genes (RGs) for gene expression normalization by qRT-PCR in order to decipher the stress tolerance mechanism of this grass species. Therefore, eight candidate RGs were identified from transcriptome data of R. ciliaris ‘Liao sheng’ in response to drought stress. The expression stability of these RGs was evaluated by five algorithms (∆Ct, geNorm, NormFinder, Bestkeeper and ReFinder) using samples from different tissues and drought stress. Results: The results showed that MDH and RPL19 were the most stable RGs among all samples, while GAPDH and TUBA presented the lowest expression stability. These representative RGs were further used to normalize the expression level of the pyrroline-5-carboxylate synthase (P5CS) and protein phosphatase 2C (PP2C) genes in different tissues and under drought stress. The results of P5CS and PP2C expression were consistent with transcriptome data. Conclusion: Our study provided the first systematic evaluation of the most stable RG selection for qRT-PCR normalization in R. ciliaris, which will promote further research on its tissue-specific gene expression and mechanism of drought tolerance. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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27 pages, 2051 KB  
Review
Environmental Substances Associated with Neurodegeneration: An Overview of Parkinson’s Disease and Related Genotoxic Endpoints
by Mohammad Shoeb, Breanna Alman, Harpriya Kaur, Moon Han, Fahim Atif, William Wu Kim, Siddhi Desai, Patricia Ruiz and Gregory M. Zarus
Genes 2026, 17(2), 236; https://doi.org/10.3390/genes17020236 - 13 Feb 2026
Viewed by 1565
Abstract
Parkinson’s disease (PD) is a complex neurodegenerative disorder influenced by age, genetic predispositions, and environmental exposures, with a growing global incidence. This review aims to summarize findings from ATSDR Toxicological Profiles, EPA Risk Assessments, and other sources of peer-reviewed literature to examine the [...] Read more.
Parkinson’s disease (PD) is a complex neurodegenerative disorder influenced by age, genetic predispositions, and environmental exposures, with a growing global incidence. This review aims to summarize findings from ATSDR Toxicological Profiles, EPA Risk Assessments, and other sources of peer-reviewed literature to examine the potential associations between PD and select metals, pesticides, and chlorinated organic compounds. Additionally, it explores using computational toxicology methods to elucidate the interactions between specific chemicals, associated genes, and their possible roles in PD. A total of 29 substances were identified to be neurotoxic with direct or probable association with PD. Risk of disease onset or symptom exacerbation of PD has been linked to exposures to neurodegenerative metals, pesticides, chlorinated organic compounds, and other environmental toxicants, alongside intrinsic factors such as genetic predisposition and aging. Supporting evidence from neurotoxicological studies directly or possibly associated with PD are summarized in referenced toxicological profiles and EPA risk assessments. Genotoxic endpoints evaluated in exposure-induced neurodegeneration including oxidative stress, DNA strand breaks, mitochondrial dysfunction, impaired DNA repair, and telomere alterations may play a critical role in linking environmental exposures to PD pathogenesis. Although these endpoints represent imperative data gaps between environmental and genetic risk factors for PD, isolating individual substances may not be necessary for prevention, as many co-occur at contaminated sites or within certain occupations. Further research is needed to clarify causal relationships between environmental exposure and genotoxic endpoints seen in neurodegenerative processes that can also be seen in PD for consideration in the development of preventive and therapeutic strategies. Full article
(This article belongs to the Section Neurogenomics)
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18 pages, 1613 KB  
Article
Antibiotic-Driven Evolutionary Engineering in Salmonella Heidelberg Reveals Genomic Signatures of Attenuation
by Ruy D. Chacón, Manuel Ramírez, Claudete S. Astolfi-Ferreira and Antonio J. Piantino Ferreira
Genes 2026, 17(2), 235; https://doi.org/10.3390/genes17020235 - 12 Feb 2026
Viewed by 787
Abstract
Background/Objectives: Salmonella Heidelberg (SH) is a globally distributed pathogen associated with gastrointestinal disease in humans and animals and frequently affects poultry. Among the classic strategies used in vaccine development, evolutionary engineering enables the generation of attenuated bacterial strains through exposure to selective [...] Read more.
Background/Objectives: Salmonella Heidelberg (SH) is a globally distributed pathogen associated with gastrointestinal disease in humans and animals and frequently affects poultry. Among the classic strategies used in vaccine development, evolutionary engineering enables the generation of attenuated bacterial strains through exposure to selective pressures such as antibiotics. In this study, spontaneous antibiotic-resistant mutant strains of SH were generated by exposure to high concentrations of streptomycin and rifampicin, after which their phenotypic and genotypic characteristics were evaluated. Methods: The wild-type strain SA628 wt was subjected to continuous and discontinuous selection under antibiotic pressure. Phenotypic characterization included biochemical profiling and antibiotic susceptibility testing. Whole-genome sequencing was performed to identify genetic changes affecting virulence- and resistance-associated genes, plasmid content, and point mutations using variant calling approaches. The potential functional relationships of the mutated genes were further analyzed through genetic network analysis. Results: The mutant strains SA628 mut1 and SA628 mut3 were obtained through discontinuous selection, whereas strain SA628 mut2 was generated under continuous selection. Phenotypically, all the mutant strains exhibited resistance to streptomycin, whereas SA628 mut2 and SA628 mut3 also exhibited resistance to rifampicin. Genomic analyses revealed mutations in rpoS, ascD, ynfE, rpoB, and cyaA associated with discontinuous selection and in iscU, ybiO, rpoB, and rsmG associated with continuous selection. Network analysis indicated that these genes are functionally connected within regulatory and metabolic interaction networks, including global transcriptional regulation, anaerobic metabolism, cAMP-mediated signaling, translation, and iron–sulfur cluster biogenesis. Conclusions: Collectively, these findings suggest that antibiotic-driven selection promotes coordinated genetic changes affecting stress responses and metabolism, which may contribute to reduced virulence. This work provides insights into bacterial adaptation under antibiotic stress and supports the potential use of evolutionary engineering for the development of attenuated strains. Full article
(This article belongs to the Special Issue Unraveling Genomic Mechanisms of Stress Tolerance and Antimicrobial Resistance in Foodborne Pathogens)
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17 pages, 514 KB  
Article
Diagnostic Value of Karyotype, Microarray, RASopathy Gene Testing and Ultrasound in Fetuses with Nuchal Translucency 3.0–3.4 mm: A Single-Center Cohort Retrospective Study
by Silvia Andrietti, Giuseppe Gullo, Diliana Beleva, Alessia Maccarrone, Lina De Paola, Chiara Roberta Gaggero, Chiara Calcagno, Maria Lucia Furnari and Pierangela De Biasio
Genes 2026, 17(2), 234; https://doi.org/10.3390/genes17020234 - 12 Feb 2026
Viewed by 845
Abstract
Background: Increased nuchal translucency (NT) is associated with an elevated risk of genetic abnormalities and structural malformations. The clinical utility of invasive testing and the optimal diagnostic approach in mildly increased NT (3.0–3.4 mm) is debated. This study aimed to evaluate genetic [...] Read more.
Background: Increased nuchal translucency (NT) is associated with an elevated risk of genetic abnormalities and structural malformations. The clinical utility of invasive testing and the optimal diagnostic approach in mildly increased NT (3.0–3.4 mm) is debated. This study aimed to evaluate genetic and ultrasound findings in this subgroup and to assess the diagnostic yield of advanced genetic testing. Methods: We retrospectively included a total of 107 fetuses with NT between 3.0 and 3.4 mm from a single fetal medicine unit. Complete outcome data were available for 97 pregnancies. Invasive prenatal testing with standard karyotype, chromosomal microarray analysis (CMA) and RASopathy panel testing were offered. All patients underwent detailed ultrasound examination to detect structural abnormalities at 16 and 20 weeks, regardless of whether invasive testing was performed. Results: Invasive prenatal testing, amniocentesis or chorionic villus sampling, (CVS), was performed in 77/97 cases (79.4%). Genetic abnormalities were detected in 28/97 (28.9%). Overall, five rare genetic anomalies were identified; none would have been detected by quantitative fluorescent polymerase chain reaction (QF-PCR) or non-invasive prenatal testing (NIPT). Two anomalies were detectable by standard karyotype, two exclusively by CMA and one exclusively by RASopathy panel. When considering all cases undergoing advanced genetic testing (CMA or RASopathy panel, n = 35) the overall diagnostic yield was 8.5% (3/35). When calculated across the entire cohort with complete follow-up, the additional diagnostic yield was 3.1% (3/97). Major structural malformations were identified in 17/97 cases (17.5%), of which 10 (58.8%) were associated with genetic abnormalities. Conclusions: Fetuses with NT measurements between 3.0 and 3.4 mm show a substantially increased risk of genetic abnormalities and structural malformations. These findings support a comprehensive prenatal evaluation, including invasive testing with advanced genetic analysis and detailed ultrasound assessment, to optimize diagnosis and counseling. Full article
(This article belongs to the Section Genetic Diagnosis)
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26 pages, 506 KB  
Review
Alzheimer’s 2030: From Precision Genomics to Artificial Intelligence
by Valeria D’Argenio, Rossella Tomaiuolo, Silvia Bargeri and Giulia Sancesario
Genes 2026, 17(2), 233; https://doi.org/10.3390/genes17020233 - 12 Feb 2026
Viewed by 1112
Abstract
Alzheimer’s disease (AD) represents a critical global health challenge, with its prevalence and associated costs expected to double significantly by 2030 and 2050. While lifestyle interventions are crucial, sporadic late-onset AD has a substantial genetic component (40–80% heritability), though known variants limit the [...] Read more.
Alzheimer’s disease (AD) represents a critical global health challenge, with its prevalence and associated costs expected to double significantly by 2030 and 2050. While lifestyle interventions are crucial, sporadic late-onset AD has a substantial genetic component (40–80% heritability), though known variants limit the scope of traditional precision medicine. Crucially, sex and gender are significant risk determinants, with women accounting for two-thirds of cases due to a complex interplay of biological and sociocultural factors. This review focuses on the influence of genetic and gender-related factors, examining large-scale genome-wide association studies (GWASs) and their role in developing advanced genetic risk scores (GRS) for precision genomics. We also explore the potential of Artificial Intelligence (AI) for multimodal big data analysis and digital health tools to promote personalized prevention and emerging concerns about ethics, privacy and data treatment. The convergence of these findings underscores the urgent need for a genetic-, sex- and gender-informed precision-medicine approach to AD. Full article
(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)
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21 pages, 446 KB  
Perspective
Conversation with Future Clinical Cytogeneticists: The New Frontiers
by Jing Christine Ye, Rishi Chowdhury and Henry H. Heng
Genes 2026, 17(2), 232; https://doi.org/10.3390/genes17020232 - 12 Feb 2026
Viewed by 882
Abstract
The post-genomic era has transformed medical genetics, raising renewed debate over the role of medical cytogenetics in clinical practice. High-throughput sequencing and chromosomal microarray technologies now dominate cancer diagnostics, prenatal testing, and rare disease evaluation by enabling rapid detection of gene-level variation, often [...] Read more.
The post-genomic era has transformed medical genetics, raising renewed debate over the role of medical cytogenetics in clinical practice. High-throughput sequencing and chromosomal microarray technologies now dominate cancer diagnostics, prenatal testing, and rare disease evaluation by enabling rapid detection of gene-level variation, often leading to the perception that cytogenetics is obsolete. However, this view overlooks the unique and complementary strengths of cytogenetic analysis. Although the relationship between cytogenetics and current NGS technologies can be compared to that between forests and trees versus leaves—both of which are necessary for clinical diagnosis—cytogenetic methods uniquely enable direct in situ visualization of chromosomes, allowing detection of large-scale structural and numerical genome alterations at the level of individual cells and cell populations. These system-level features that are frequently invisible or difficult to interpret using sequencing-based approaches alone yet are critical in disease contexts where genome architecture itself carries biological and clinical significance beyond individual genes. This article, therefore, advances a new perspective based on Genome Architecture Theory: that karyotype-level information organizes gene-level function and that many previous gene-centric genetic concepts require reexamination within a unified framework of clinical genomics. Rather than being replaced, cytogenetics is increasingly integrated with sequencing within a unified framework of clinical genomics that combines high-resolution molecular detail with system-level insight into genome organization. Reassessing the role of cytogenetics, therefore, has important implications for medical education, diagnostic strategy, and healthcare policy, as cytogenetics provides the appropriate platform for understanding system-level inheritance through karyotype coding and for advancing molecular medicine from a genome systems perspective. Full article
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
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18 pages, 2894 KB  
Article
Reassessing Benign ASXL1 Variants in Bohring–Opitz Syndrome: The Role of Population Databases in Variant Reinterpretation
by Liliana Fernández-Hernández, Sergio Enríquez-Flores, Nancy L. Hernández-Martínez, Melania Abreu-González, Esther Lieberman-Hernández, Gerardo Rodríguez-González, Sinuhé Reyes-Ruvalcaba and Miriam E. Reyna-Fabián
Genes 2026, 17(2), 231; https://doi.org/10.3390/genes17020231 - 12 Feb 2026
Viewed by 520
Abstract
Background/Objectives: ASXL1 is a chromatin-associated gene implicated in both hematologic malignancies and neurodevelopmental disorders, including Bohring–Opitz syndrome (BOS). Although many ASXL1 variants are well classified, a substantial proportion remain variants of uncertain significance (VUS), complicating molecular diagnosis and genetic counseling. The objective [...] Read more.
Background/Objectives: ASXL1 is a chromatin-associated gene implicated in both hematologic malignancies and neurodevelopmental disorders, including Bohring–Opitz syndrome (BOS). Although many ASXL1 variants are well classified, a substantial proportion remain variants of uncertain significance (VUS), complicating molecular diagnosis and genetic counseling. The objective of this study was to evaluate whether structural context can inform the interpretation of selected ASXL1 missense variants in a clinical setting. Methods: We describe a 17-year-old female with clinical features consistent with BOS carrying the heterozygous ASXL1 variant p.Q1448R, currently classified as benign under ACMG/AMP guidelines. Three-dimensional in silico structural modeling was performed using AlphaFold3 and available crystallographic data. Three additional ASXL1 missense variants classified as VUS in ClinVar (p.R265H, p.T297M, and p.Y358C) were also analyzed. Evolutionary conservation, domain localization, and residue-level interactions were assessed. Results: Structural modeling indicated that the p.Q1448R substitution alters polar interactions and introduces a steric constraint near a conserved PHD-type zinc finger domain. Variants p.R265H and p.T297M affected stabilizing interactions within the DEUBAD, which is involved in BAP1 activation, while p.Y358C altered a polar microenvironment adjacent to a chromatin-interacting region. All analyzed variants, except p.T297M, localized to evolutionarily conserved regions. Conclusions: This study demonstrates that in silico structural analysis can provide complementary, domain-level insights for the interpretation of ASXL1 missense variants that remain classified as benign, likely benign or VUS under current frameworks. Such approaches may assist in prioritizing variants for further functional evaluation and refining molecular interpretation when experimental data are limited. Full article
(This article belongs to the Collection Genetics and Genomics of Rare Disorders)
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28 pages, 1118 KB  
Review
CRISPR-Mediated Silkworm: The Oncoming Agricultural Revolutions and a Rising Model Organism
by Qiaoling Sun, Yongkang Guo, Liting Wang, Ling Jia, Peng Wei and Sanyuan Ma
Genes 2026, 17(2), 230; https://doi.org/10.3390/genes17020230 - 12 Feb 2026
Viewed by 1355
Abstract
The silkworm (Bombyx mori) is essential to sericulture and is also becoming a key model organism in genomics and agriculture. For decades, genetic studies of the silkworm were limited by inefficient and inflexible genome tools. CRISPR genome editing allows precise and [...] Read more.
The silkworm (Bombyx mori) is essential to sericulture and is also becoming a key model organism in genomics and agriculture. For decades, genetic studies of the silkworm were limited by inefficient and inflexible genome tools. CRISPR genome editing allows precise and scalable alterations to genes regulating development, physiology, and industrial traits. This review summarizes silkworm genome-editing breakthroughs, highlighting CRISPR’s evolution from simple gene knockouts to large-scale genome-wide screening. We highlight how these advancements contribute to disease resistance, higher yields, and the development of new silk-based materials, as well as how they influence the development and growth rate of the sericulture. The creation of high-quality reference genomes, pangenomes, and genome-wide screening systems has made the silkworm a major model for integrating multiple biological datasets and approaches, such as genomic, transcriptomic, and proteomic. By considering the unique biological characteristics of the silkworm, this provides new insights for research on silk biology, piRNA synthetic biology, and hormonal signaling regulation. Finally, we examine new areas at the intersection of CRISPR, pangenomics, and artificial intelligence (AI) and suggest future paths for molecular breeding, pest control, and synthetic biology. Moreover, AI-assisted prediction of CRISPR outcomes is utilized to inform the design of targeted trait modifications, representing an approach to enhancing biomanufacturing efficiency and eco-friendly silk production. Together, these advances have made the silkworm a flexible genetic platform and an important part of sustainable agriculture and biomanufacturing. Full article
(This article belongs to the Special Issue Application of CRISPR/Cas9 Technology in Insects)
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23 pages, 2413 KB  
Article
Next-Generation Sequencing Defines a Molecularly Confirmed ARPKD Core Within the Broader PKHD1-Associated Disease Spectrum
by Paloma Lapunzina-Soler, Amir Shabaka, Ramón Peces, Ángel Alonso, Emilio Cuesta, Rocío Mena, Laura Espinosa-Román, Marta Melgosa, Gema Fernández, Yolanda Muñoz-GᵃPorrero, Jair Tenorio-Castaño, Pablo Lapunzina and Julián Nevado
Genes 2026, 17(2), 229; https://doi.org/10.3390/genes17020229 - 11 Feb 2026
Viewed by 674
Abstract
Background/Objectives: Autosomal recessive polycystic kidney disease (ARPKD) is a severe ciliopathy caused by biallelic pathogenic variants in PKHD1, characterized by variable renal and hepatobiliary involvement. The widespread use of next-generation sequencing (NGS) has revealed a large number of rare PKHD1 variants, [...] Read more.
Background/Objectives: Autosomal recessive polycystic kidney disease (ARPKD) is a severe ciliopathy caused by biallelic pathogenic variants in PKHD1, characterized by variable renal and hepatobiliary involvement. The widespread use of next-generation sequencing (NGS) has revealed a large number of rare PKHD1 variants, creating major challenges in distinguishing molecularly confirmed ARPKD from a broader spectrum of PKHD1-associated disease. Methods: We performed an integrated clinical and molecular analysis of 68 individuals referred for suspected ARPKD. Using phase-aware and family-informed ACMG classification, patients were stratified into three genetically defined groups: 40 with molecularly confirmed ARPKD (biallelic pathogenic, likely pathogenic or segregation-supported VUS-LP variants in trans), 10 with biallelic PKHD1 variants of uncertain pathogenicity, and 18 monoallelic carriers. Genotype–phenotype correlations were restricted to the molecularly confirmed ARPKD group. Results: Among the 40 molecularly confirmed ARPKD patients, 17 (42.5%) carried two loss-of-function (LoF) alleles, 16 (40%) carried one LoF allele, and 7 (17.5%) carried only non-LoF alleles. A strong allele-dose effect was observed. Neonatal or infantile onset occurred in 88% of LoF/LoF patients, compared with 56% of LoF/non-LoF and 29% of non-LoF/non-LoF individuals (p < 0.001). Progression to renal replacement therapy occurred in 65%, 31%, and 0% of patients (p = 0.002). In contrast, hepatobiliary disease was highly prevalent across all genotype classes and showed no significant association with LoF burden. Conclusions: Phase-aware and family-informed interpretation of PKHD1 variants distinguishes a molecularly confirmed ARPKD core from a broader PKHD1 variant spectrum. Within confirmed ARPKD, loss-of-function allele burden is the primary determinant of renal and perinatal severity, whereas hepatic disease is largely independent of truncating allele burden. These findings refine diagnosis, prognosis, and genetic counseling in the genomic era. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Rare Genetic Diseases)
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16 pages, 1054 KB  
Review
DNA Methylation in the Ovary and Uterus of Mammalian Animal Models: Implications for Reproductive Function
by Oliwia Serej, Magdalena K. Kowalik and Robert Rekawiecki
Genes 2026, 17(2), 228; https://doi.org/10.3390/genes17020228 - 11 Feb 2026
Viewed by 653
Abstract
DNA methylation is a key epigenetic modification that regulates gene expression and maintains genome stability, particularly in mammalian reproductive tissues. This review summarizes the current knowledge of DNA methylation and demethylation fluctuations with a specific focus on the regulation of ovarian development and [...] Read more.
DNA methylation is a key epigenetic modification that regulates gene expression and maintains genome stability, particularly in mammalian reproductive tissues. This review summarizes the current knowledge of DNA methylation and demethylation fluctuations with a specific focus on the regulation of ovarian development and uterine function during pregnancy. This modification primarily occurs at CpG-rich regions and is catalyzed by DNA methyltransferases (DNMTs): DNMT1 maintains existing patterns during replication, while DNMT3A and DNMT3B establish de novo methylation. Demethylation is mediated by ten-eleven translocation enzymes (TET1, TET2, and TET3), which oxidize 5-methylcytosine, ultimately replacing it with unmethylated cytosine. These processes play essential roles in folliculogenesis, oocyte maturation, steroidogenesis, and tissue-specific gene regulation. Understanding these epigenetic mechanisms provides important insights into veterinary medicine and offers potential applications in fertility preservation across diverse mammalian species. Consequently, further research is essential to elucidate the clinical implications of these epigenetic processes for improving reproductive health outcomes in animals. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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13 pages, 4655 KB  
Article
Characterisation of a Missense Variant of the Alström Syndrome Centrosome and Basal Body Associated Protein (ALMS1) Gene Associated with Cardiomyopathy Using Induced Pluripotent Stem Cells
by Tanushri Dargar, Alexandre Janin, Valérie Risson, Estèle Lafont, Camille Valla, Vincent Gache and Marie Abitbol
Genes 2026, 17(2), 227; https://doi.org/10.3390/genes17020227 - 11 Feb 2026
Viewed by 653
Abstract
Background/Objectives: Human induced pluripotent stem cell (hiPSC) models provide a unique platform for testing the effect of genomic variants identified in patients with inherited diseases. In Alström syndrome, a rare multisystem disorder mainly caused by nonsense mutations in the ALMS1 gene, patients often [...] Read more.
Background/Objectives: Human induced pluripotent stem cell (hiPSC) models provide a unique platform for testing the effect of genomic variants identified in patients with inherited diseases. In Alström syndrome, a rare multisystem disorder mainly caused by nonsense mutations in the ALMS1 gene, patients often present with infantile cardiomyopathy, retinal dystrophy, type 2 diabetes, and hearing loss in addition to obesity. These diverse clinical manifestations highlight the pleiotropic functions of ALMS1 in cellular processes such as ciliary signalling, cell cycle regulation, and tissue homeostasis. In cats, the ALMS1:c.7384G>C missense variant has been associated with cardiomyopathy in the absence of other symptoms of Alström syndrome, raising questions regarding the impact of this variant on cardiac pathology. Methods: To answer these questions, we generated an hiPSC line carrying the human ALMS1:c.10004G>C missense variant, homologous to the ALMS1:c.7384G>C feline variant, as well as an isogenic control, to investigate the impact of this variant on cardiomyocyte differentiation and function. Results: The introduction of the ALMS1:c.10004G>C variant in the homozygous state in hiPSCs resulted in a significant reduction in cardiomyocyte differentiation efficiency. However, the variant did not affect contractile frequency, sarcomere organisation, sarcomere length, or cardiomyocyte cell size. Together, these results suggest that while the ALMS1:c.10004G>C variant impairs cardiomyocyte differentiation, it does not disrupt the structural or functional properties of the hiPSC-derived cardiomyocytes that do form. Conclusions: We have generated and initiated the characterisation of the third ALMS1 mutant hiPSC line and the first line based on a missense variant, but further research is needed on its relevance in modelling ALMS1-related changes. Our results also support the previous recommendation not to use ALMS1:c.7384G>C for the selection of breeding cats until further data confirm its intrinsic pathogenicity. Full article
(This article belongs to the Special Issue Hereditary Traits and Diseases in Companion Animals)
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17 pages, 1952 KB  
Article
ABCC6 Heterozygosity as Genetic Predisposition to Cerebrovascular Disease Across Ages
by Giulia Amico, Mariasavina Severino, Marta Bertamino, Rosario Pascarella, Domenico Tortora, Sara Signa, Marta Rusmini, Andrea Rossi, Isabella Ceccherini and Marialuisa Zedde
Genes 2026, 17(2), 226; https://doi.org/10.3390/genes17020226 - 11 Feb 2026
Viewed by 656
Abstract
Background: Heterozygosity for pathogenic variants in the ABCC6 gene has been associated with an increased incidence of cerebrovascular diseases. This study aims to characterize the prevalence and clinical and neuroradiological phenotypes associated with monoallelic and biallelic ABCC6 variants in pediatric and adult [...] Read more.
Background: Heterozygosity for pathogenic variants in the ABCC6 gene has been associated with an increased incidence of cerebrovascular diseases. This study aims to characterize the prevalence and clinical and neuroradiological phenotypes associated with monoallelic and biallelic ABCC6 variants in pediatric and adult patients presenting with arterial ischemic stroke or cerebral small vessel disease (CSVD). Methods: We conducted a retrospective observational study on 143 consecutive patients (48 pediatric, 24 juvenile, 71 adult) diagnosed with ischemic stroke or CSVD of unknown etiology. Clinical and neuroradiological data were collected and analyzed in relation to the identified genetic variants through next-generation sequencing. Results: Among the patients, 16 (11.2%) tested positive for causative variants in the ABCC6 gene, with 11 subjects carrying monoallelic variants and 5 carrying biallelic variants. Patients with biallelic variants exhibited severe and complex vasculopathy, with a high incidence of early ischemic events. In contrast, monoallelic carriers predominantly presented with microvascular disease manifestations, including lacunar strokes and signs of CSVD. Conclusions: The results suggest a significant age-dependent phenotypic divergence in patients with ABCC6 variants, highlighting the impact of heterozygosity on cerebrovascular health. Identifying these variants may enhance risk stratification and inform management strategies in patients with traditional vascular risk factors. Full article
(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)
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18 pages, 1346 KB  
Review
Redox Imbalance and Genetic Mutations in Heart Failure: Synergistic Mechanisms and Therapeutic Strategies
by Vinod Kumar Balakrishnan, Abinayaa Rajkumar, Monisha K. G. Ganesh, Harilalith Reddy Kovvuri, Durgadevi Selvam, Preetam Krishnamurthy, Sandhya Sundaram, Kalaiselvi Periandavan, Sankaran Ramesh, Muralidharan Thoddi Ramamurthy and Namakkal S. Rajasekaran
Genes 2026, 17(2), 225; https://doi.org/10.3390/genes17020225 - 11 Feb 2026
Viewed by 654
Abstract
Heart failure (HF) is a significant global health challenge, with rising prevalence and a complex, multifactorial pathophysiology. Emerging evidence suggests that disruptions in redox signaling pathways and genetic mutations play critical, synergistic roles in the development and progression of HF. This comprehensive review [...] Read more.
Heart failure (HF) is a significant global health challenge, with rising prevalence and a complex, multifactorial pathophysiology. Emerging evidence suggests that disruptions in redox signaling pathways and genetic mutations play critical, synergistic roles in the development and progression of HF. This comprehensive review synthesizes current knowledge on how redox imbalance and genetic alterations interact to drive cardiac dysfunction and critically evaluates the therapeutic strategies targeting these mechanisms. We begin by introducing the basic concepts of redox biology and its role in maintaining cardiac homeostasis. Next, we examine the specific redox signaling pathways and genetic mutations implicated in HF pathogenesis, highlighting the latest mechanistic insights and findings from human studies. The complex interplay between redox dysregulation and genetic factors is explored, including their synergistic effects, compensatory mechanisms, and illustrative case studies. We also review current therapeutic strategies aimed at restoring redox balance and correcting underlying genetic mutations, discussing their progress and limitations. Finally, we present the latest research advances, identify critical knowledge gaps, and propose future directions for both basic and translational research. Understanding the redox–genetic axis is key to developing novel, targeted therapies to address the growing HF epidemic. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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19 pages, 3457 KB  
Article
Core Ferroptosis-Related Biomarkers and miRNA Regulatory Networks in Alzheimer’s Disease
by Wenjia Liu, Xin Rao and Liyang Yu
Genes 2026, 17(2), 224; https://doi.org/10.3390/genes17020224 - 11 Feb 2026
Viewed by 545
Abstract
Background: The exact pathogenesis of Alzheimer’s disease (AD), a neurodegenerative disorder, remains unclear. Ferroptosis is a form of cell death characterized by intracellular iron accumulation, and has emerged as a potential contributor to the pathological cascade of AD. Therefore, this study aims [...] Read more.
Background: The exact pathogenesis of Alzheimer’s disease (AD), a neurodegenerative disorder, remains unclear. Ferroptosis is a form of cell death characterized by intracellular iron accumulation, and has emerged as a potential contributor to the pathological cascade of AD. Therefore, this study aims to identify core genes that may function as reliable biomarkers for AD through an in-depth analysis of the genetic relationship between ferroptosis-related genes and AD. Methods: This study first obtained the gene expression profiles (GSE140831, GSE63060 and GSE63061 expression profiles). The GSE140831 dataset served as the discovery cohort, and the GSE63060 and GSE63061 datasets were used as independent validation cohorts. R language 4.4.1 was used for standardizing and identifying differentially expressed genes (DEGs) in AD patients in all datasets. Secondly, the ferroptosis-related genes were obtained. By integrating the ferroptosis-related genes, ferroptosis-related DEGs (FRDEGs) were detected. Then, the FRDEGs were verified and evaluated, and the biological functions of the core genes were analyzed. Finally, miRNAs interacting with these core FRDEGs were explored. Results: The study identified nine FRDEGs (ACVR1B, BRPF1, G6PD, KLHDC3, LAMP2, MTCH1, P4HB, PTPN6, RBMS1), which are potentially related and may serve as biomarkers for AD. All nine genes demonstrated statistically significant differential expression (up-regulation) in both independent validation cohorts and in the combined analysis (p < 0.05). Although the area under the curve (AUC) values of these nine genes ranged from 0.61 to 0.71, indicating moderate discriminatory power, these findings suggest that they may be involved in pathways related to AD and are worthy of further investigation as potential auxiliary biomarkers. Finally, a network of hub FRDEGs-miRNAs interaction was constructed. There were 11 miRNAs that may regulate these hub FRDEGs simultaneously. Conclusions: This study showed the significant association of the identified FRDEGs with AD. Also, a core ferroptosis-related biomarker network for miRNAs regulation of AD was constructed. The specific regulatory mechanism is worthy of further investigation. Full article
(This article belongs to the Special Issue Novel Biomarkers of Neurodegenerative Diseases)
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15 pages, 1551 KB  
Article
The Association Between Estrogen Receptor-α and PIWIL3/piR-651/piR-823 Complex Regulates MI to MII Transposition in Normoresponder and Diminished Ovarian Reserve Cases
by Çağrı Öner, Damla Kolcuoğlu, Senem Aslan Öztürk, Nergis Özlem Kılıç, Duygu Kütük, Belgin Selam, İbrahim Orçun Olcay and Ertuğrul Çolak
Genes 2026, 17(2), 223; https://doi.org/10.3390/genes17020223 - 11 Feb 2026
Viewed by 676
Abstract
Background: Diminished ovarian reserve is characterized by a decrease in oocyte count and estrogen levels, which leads to infertility. The genetic and epigenetic mechanisms in MI to MII transition or complete MII phase in the oocyte maturation process estrogen receptor alpha and piRNA [...] Read more.
Background: Diminished ovarian reserve is characterized by a decrease in oocyte count and estrogen levels, which leads to infertility. The genetic and epigenetic mechanisms in MI to MII transition or complete MII phase in the oocyte maturation process estrogen receptor alpha and piRNA relationship were evaluated. Methods: This study analyzed 100 cumulus oophorous complex samples from normoresponder and DOR patients undergoing IVF, subdivided into metaphase I and metaphase II stages. To elucidate the ER-α, PIWIL3, piR-651, and piR-823 genes qRT-PCR was used and qualitative ER-α protein expressions were determined by immunohistochemistry. Pearson’s correlation analysis was utilized to evaluate the interactions between genes within each experimental group. Results: The DOR samples exhibited significant downregulation of ER-α gene and protein expression compared to the NOR controls. PIWIL3 gene, piR-651, and piR-823 expressions reduced in DOR MI and MII. Strong positive correlations among ER-α, PIWIL3, piR-651, and piR-823 were observed in NOR, whereas DOR showed weaker correlations and immunohistochemistry verified lower ER-α protein levels in DOR. Conclusions: The disruption of ER-α and piRNA-related gene networks in DOR may underlie the suboptimal maturation of oocytes, and monitoring ER-α, PIWIL3, piR-651, and piR-823 expressions could facilitate early determination of maturation stages and improve assessment of ovarian reserve. The potential for transposition to MII in NOR and DOR oocytes was observed in relation to the association between ER-α protein/gene expression and PIWIL3, which regulates ER-α. Moreover, piR-651 and piR-823, whose expressions depend on estrogen level, indirectly regulate oocyte maturation from MI to MII in both NOR and DOR epigenetically. We suggest that the MI and MII stages of oocytes could be determined earlier in NOR and DOR cases by controlling ER-α, PIWIL3, piR-651 and piR-823 expressions. These molecular markers indicate promise for diagnostic applications in reproductive medicine, warranting further validation in larger cohorts. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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29 pages, 2194 KB  
Article
Cross-Species Exome Sequencing Reveals Recurrent Genomic Alterations in California Sea Lion (Zalophus californianus) Urogenital Carcinoma and Highlights a Recurrent PD-L1 Variant
by Isabella G. Livingston, Catherine F. Wise, Allison N. Dickey, Rachael Thomas, Alissa C. Deming, Barbie Halaska, Frances M. D. Gulland, Kathleen M. Colegrove, Pádraig Duignan and Matthew Breen
Genes 2026, 17(2), 222; https://doi.org/10.3390/genes17020222 - 10 Feb 2026
Viewed by 893
Abstract
Background/Objectives: Human-driven environmental change can promote cancer development in wild species, yet the pathophysiology of wildlife cancers remain largely unexplored. Urogenital carcinoma (UGC) in the California sea lion (CSL) (Zalophus californianus) is one of the most common cancer types documented in [...] Read more.
Background/Objectives: Human-driven environmental change can promote cancer development in wild species, yet the pathophysiology of wildlife cancers remain largely unexplored. Urogenital carcinoma (UGC) in the California sea lion (CSL) (Zalophus californianus) is one of the most common cancer types documented in any wild mammal. The pathogenesis of UGC in CSLs is known to be multifactorial, with links to environmental contaminant exposure and infection by Otarine Herpesvirus-1 (OtHV-1); however, the genomic features of these cancers have not been thoroughly explored. Understanding UGC pathogenesis in the CSL has important implications for the health of humans and other species that share environment and diet. Methods: We leveraged the evolutionary conservation between the domestic dog and CSL genomes to perform cross-species whole-exome sequencing (WES) of CSL UGC tumors and matched normal tissue pairs. We also used PCR and Sanger sequencing to investigate the prevalence of DNA from OtHV-1. Results: Bioinformatic analyses identified shared somatic variants and DNA copy number aberrations in UGC tumor samples, including recurrent exonic single-nucleotide variants in CD274/PD-L1, and recurrent copy number gains in CD274/PD-L1, TNFRSF14, CD200, CDK4, and PLCG2. In an extended cohort of 70 CSLs (tumor, matched normals, and controls), a recurrent C > T single-nucleotide variant in exon 4 of CD274/PD-L1 was identified in 54 of 68 (79.4%) CSLs with diagnosed UGC. OtHV-1 DNA was detected in 67 of 70 individuals (95.8%). Conclusions: These results demonstrate that cross-species exome capture provides a means to identify genomic alterations that may play a role in the molecular pathogenesis of UGC in the CSL and adds to the body of evidence for an association between OtHV-1 and UGC in this species. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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11 pages, 242 KB  
Article
SIRT1 rs7069102 Polymorphism Confers Increased Risk of Diabetic Retinopathy in T2DM
by Melina Bešić, Jernej Letonja, Mojca Globočnik Petrovič, Ana Peterlin, Ema Šuligoj, Stella Stare and Daniel Petrovič
Genes 2026, 17(2), 221; https://doi.org/10.3390/genes17020221 - 10 Feb 2026
Viewed by 609
Abstract
Background: The incidence and prevalence of type 2 diabetes mellitus (T2DM) has been increasing worldwide recently. Diabetic retinopathy (DR) is a major ocular complication of diabetes mellitus, and it is the leading cause of blindness and visual impairment. Sirtuin 1 (SIRT 1) is [...] Read more.
Background: The incidence and prevalence of type 2 diabetes mellitus (T2DM) has been increasing worldwide recently. Diabetic retinopathy (DR) is a major ocular complication of diabetes mellitus, and it is the leading cause of blindness and visual impairment. Sirtuin 1 (SIRT 1) is a NAD+-dependent deacetylase and is involved in stress responses such as hypoxic and genotoxic stress, inflammation and heat shock. Tumor necrosis factor α (TNF-α) is an important inflammatory mediator that is involved in the pathogenesis of T2DM. The purpose of our study was to investigate the relationship between the SIRT1 rs7069102 polymorphism and TNF- α rs1800629 polymorphisms and diabetic retinopathy (DR) in patients with type 2 diabetes mellitus (T2DM). Materials and Methods: We analyzed 1554 Slovenian (Caucasian) patients with T2DM of at least 10 years’ duration, stratifying them into two groups: 577 patients with diabetic retinopathy (DR) and 977 patients without DR. Genotyping of SIRT1 rs7069102 and TNF-α rs1800629 polymorphisms was performed using the StepOne real-time PCR System with TaqMan SNP Genotyping Assays. Results and Conclusions: A significant difference in the distribution of SIRT1 rs7069102 genotypes and alleles was observed between the groups. Under the dominant inheritance model, patients with CC or CG genotypes were more likely to develop DR than those with the GG genotype (OR = 1.30; 95% CI = 1.02–1.65; p = 0.036). No significant association was found between TNF-α rs1800629 and DR. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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