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Editor’s Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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20 pages, 1884 KiB  
Article
Omics Data Integration Uncovers mRNA-miRNA Interaction Regions in Genes Associated with Chronic Venous Insufficiency
by Fatma Sarı-Tunel, Ayse Demirkan, Burcak Vural, Cenk Eray Yıldız and Evrim Komurcu-Bayrak
Genes 2025, 16(1), 40; https://doi.org/10.3390/genes16010040 - 31 Dec 2024
Viewed by 1296
Abstract
Background/Objectives: Chronic venous insufficiency (CVI), a chronic vascular dysfunction, is a common health problem that causes serious complications such as painful varicose veins and even skin ulcers. Identifying the underlying genetic and epigenetic factors is important for improving the quality of life of [...] Read more.
Background/Objectives: Chronic venous insufficiency (CVI), a chronic vascular dysfunction, is a common health problem that causes serious complications such as painful varicose veins and even skin ulcers. Identifying the underlying genetic and epigenetic factors is important for improving the quality of life of individuals with CVI. In the literature, many genes, variants, and miRNAs associated with CVI have been identified through genomic and transcriptomic studies. Despite molecular pathogenesis studies, how the genes associated with CVI are regulated by miRNAs and the effect of variants in binding regions on expression levels are still not fully understood. In this study, previously identified genes, variants, and miRNAs associated with CVI, common variants in the mRNA-miRNA binding regions, were investigated using in silico analyses. Methods: For this purpose, miRNA research tools, MBS (miRNA binding site) database, genome browsers, and the eQTL Calculator in the GTEx portal were used. Results: We identified SNVs associated with CVI that may play a direct role in the miRNA-mediated regulation of the ZNF664, COL1A2, HFE, MDN, MTHFR, SRPX, TDRD5, TSPYL4, VEGFA, and APOE genes. In addition, when the common SNVs in the mRNA binding region of 75 unique CVI related-miRNAs in five candidate genes associated with CVI were examined, seven miRNAs associated with the expression profiles of ABCA1, PIEZO1, and CASZ1 genes were identified. Conclusions: In conclusion, the relationship between genetic markers identified in the literature that play a role in the pathogenesis of the CVI and the expression profiles was evaluated for the first time in the mRNA-miRNA interaction axis. Full article
(This article belongs to the Special Issue Genetic and Genomic Research of Cardiovascular Diseases)
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10 pages, 3337 KiB  
Case Report
Typical Clinical Presentation of an Autosomal Dominant Polycystic Kidney Disease Patient with an Atypical Genetic Pattern
by Nenzi Marzano, Carlotta Caprara, Thiago Reis, Diego Pomarè Montin, Sofia Maria Pretto, Matteo Rigato, Anna Giuliani, Fiorella Gastaldon, Barbara Mancini, Claudio Ronco, Monica Zanella, Daniela Zuccarello and Valentina Corradi
Genes 2025, 16(1), 39; https://doi.org/10.3390/genes16010039 - 30 Dec 2024
Viewed by 1211
Abstract
Background: Autosomal Dominant Polycystic Kidney Disease (ADPKD) is mainly characterized by renal involvement with progressive bilateral development of renal cysts and volumetric increase in the kidneys, causing a loss of renal function, chronic kidney disease (CKD), and kidney failure. The occurrence of [...] Read more.
Background: Autosomal Dominant Polycystic Kidney Disease (ADPKD) is mainly characterized by renal involvement with progressive bilateral development of renal cysts and volumetric increase in the kidneys, causing a loss of renal function, chronic kidney disease (CKD), and kidney failure. The occurrence of mosaicism may modulate the clinical course of the disease. Mosaicism is characterized by a few cell populations with different genomes. In these special cases, a genetic diagnosis could be challenging. Methods: Herein, we describe the case of a 47-year-old woman presenting with typical ultrasound and computed tomography features of ADPKD. She had stage 3b CKD and hypertension. There was no family history of ADPKD, prompting an investigation with a genetic test. Target next-generation sequencing (NGS) did not detect the presence of any genomic variants. Therefore, we carried out second-level genetic analysis to investigate the presence of a large rearrangement through a multiple ligation-dependent probe amplification (MLPA) analysis of PKD1 and PKD2 genes. Results: MLPA showed a large deletion (portion including exons 2–34 of PKD1) present in the heterozygosis with a percentage of cells close to the resolution limits of the technique used (<25–30%). We concluded that the large deletion identified was mosaicism. This variant is not reported in major ADPKD databases, but due to the type of mutation and the patient’s clinical picture, it should be considered as likely pathogenic. Conclusions: A stepwise genetic approach might be useful in those cases where standard methods do not allow one to reach a definitive diagnosis. Full article
(This article belongs to the Special Issue Feature Papers in Human Genomics and Genetic Diseases 2024)
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16 pages, 19979 KiB  
Article
Overexpression of Cymbidium goeringii Cgo-miR159 Regulates Anther Dehiscence and Pollen Development in Arabidopsis and Tobacco
by Zihan Xu, Qian Liu, Yue Chen, Jinming Wang, Jianshuang Shen and Fengrong Hu
Genes 2025, 16(1), 35; https://doi.org/10.3390/genes16010035 - 29 Dec 2024
Viewed by 1014
Abstract
Background: MicroRNA159 (miR159) is a conserved miRNA found in various plant species. By regulating GAMYB-like transcription factors, miR159 is involved in diverse biological processes. Cymbidium goeringii, a significant traditional Chinese orchid, has unique flower shape and elegant fragrance. However, its development has [...] Read more.
Background: MicroRNA159 (miR159) is a conserved miRNA found in various plant species. By regulating GAMYB-like transcription factors, miR159 is involved in diverse biological processes. Cymbidium goeringii, a significant traditional Chinese orchid, has unique flower shape and elegant fragrance. However, its development has been several limited because of the low flower bud differentiation and the difficult reproduction. This research aims to provide guidance for the role of cgo-miR159 in reproductive organ development to enhance the ornamental and economic value of Cymbidium. Methods: In this study, miR159 was cloned and its expression was determined across different development stages and tissue types. The function of cgo-miR159 was identified using gene transformation in Arabidopsis and tobacco plants. Results: High expression levels of cgo-miR159 were detected in the leaves and stamens during reproductive growth and expression peaked during flower bud development when the flower was above 0.5 to 3 cm in length. In transgenic experiments, the ectopic expression of cgo-miR159 led to defective development in the stamens of model plants (Arabidopsis and tobacco), including earlier anther dehiscence and pollen deformity, which resulted in developmental abnormalities and reduced seeds count in fruits. Conclusions: In summary, cgo-miR159 affected the development of reproductive organs in model plants. This research complements previous studies on the function of miR159 and provide useful references for the genetic improvement of orchids. Full article
(This article belongs to the Special Issue Genetics and Breeding of Ornamental Plants)
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30 pages, 1775 KiB  
Systematic Review
The Immunoexpression and Prognostic Significance of Stem Cell Markers in Malignant Salivary Gland Tumors: A Systematic Review and Meta-Analysis
by Eleni-Marina Kalogirou, Athina Tosiou, Stavros Vrachnos, Vasileios L. Zogopoulos, Ioannis Michalopoulos, Theodora Tzanavari and Konstantinos I. Tosios
Genes 2025, 16(1), 37; https://doi.org/10.3390/genes16010037 - 29 Dec 2024
Viewed by 1382
Abstract
Background/Objectives: Salivary gland carcinomas encompass a broad group of malignant lesions characterized by varied prognoses. Stem cells have been associated with the potential for self-renewal and differentiation to various subpopulations, resulting in histopathological variability and diverse biological behavior, features that characterize salivary gland [...] Read more.
Background/Objectives: Salivary gland carcinomas encompass a broad group of malignant lesions characterized by varied prognoses. Stem cells have been associated with the potential for self-renewal and differentiation to various subpopulations, resulting in histopathological variability and diverse biological behavior, features that characterize salivary gland carcinomas. This study aims to provide a thorough systematic review of immunohistochemical studies regarding the expression and prognostic significance of stem cell markers between different malignant salivary gland tumors (MSGTs). Methods: The English literature was searched via the databases MEDLINE/PubMed, EMBASE via OVID, Web of Science, Scopus, and CINHAL via EBSCO. The Joanna Briggs Institute Critical Appraisal Tool was used for risk of bias (RoB) assessment. Meta-analysis was conducted for markers evaluated in the same pair of diseases in at least two studies. Results: Fifty-four studies reported the expression of stem cell markers, e.g., c-KIT, CD44, CD133, CD24, ALDH1, BMI1, SOX2, OCT4, and NANOG, in various MSGTs. Low, moderate, and high RoB was observed in twenty-five, eleven, and eighteen studies, respectively. Meta-analysis revealed an outstanding discriminative ability of c-KIT for adenoid cystic carcinoma (AdCC) over polymorphous adenocarcinoma [P(LG)A] but did not confirm the prognostic significance of stem cell markers in MSGTs. Conclusions: This study indicated a possible link between stem cells and the histopathological heterogeneity and diverse biological behavior that characterize the MSGTs. c-KIT might be of diagnostic value in discriminating between AdCC and P(LG)A. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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18 pages, 3071 KiB  
Article
Integrative Transcriptomic and Small RNA Analysis Uncovers Key Genes for Cold Resistance in Rice
by Fan Luo, Mengmeng Yin, Jianping Zhou, Xiaoli Zhou, Chunli Wang, Wenfeng Zhang, Lijuan Chen and Dongsun Lee
Genes 2025, 16(1), 38; https://doi.org/10.3390/genes16010038 - 29 Dec 2024
Viewed by 1011
Abstract
Background/Objectives: Cold stress is the main environmental factor that affects the growth and development of rice, leading to a decrease in its yield and quality. However, the molecular mechanism of rice’s low-temperature resistance remains incompletely understood. Methods: In this study, we conducted a [...] Read more.
Background/Objectives: Cold stress is the main environmental factor that affects the growth and development of rice, leading to a decrease in its yield and quality. However, the molecular mechanism of rice’s low-temperature resistance remains incompletely understood. Methods: In this study, we conducted a joint analysis of miRNA and mRNA expression profiles in the cold-resistant material Yongning red rice and the cold-sensitive material B3 using high-throughput sequencing. Results: 194 differentially expressed miRNAs (DEMIs) and 14,671 differentially expressed mRNAs (DEMs) were identified. Among them, 19 DEMIs, including miR1437, miR1156, miR166, miR1861, and miR396_2 family members, showed opposite expression during the early or late stages of low-temperature treatment in two varieties, while 13 DEMIs were specifically expressed in Yongning red rice, indicating that these miRNAs are involved in rice’s resistance to low temperature. In the transcriptome analysis, 218 DEMs exhibited opposite expressions during the early or late stages of low-temperature treatment in two varieties. GO enrichment analysis indicated that these DEMs were enriched in biological processes such as a defense response to fungi, a defense response to bacteria, a plant-type cell wall modification, single-organism cellular processes, a response to chitin, and the regulation of a plant-type hypersensitive response, as well as in cellular components such as the apoplast, nucleus, vacuole, plasma membrane, and plasmodesma. Twenty-one genes were further selected as potential candidates for low-temperature resistance. The joint analysis of miRNA and mRNA expression profiles showed that 38 miRNAs corresponding to 39 target genes were candidate miRNA–mRNA pairs for low-temperature resistance. Conclusions: This study provides valuable resources for determining the changes in miRNA and mRNA expression profiles induced by low temperatures and enables the provision of valuable information for further investigating the molecular mechanisms of plant resistance to low temperatures and for the genetic improvement of cold-resistant varieties. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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21 pages, 7226 KiB  
Article
Genome-Wide Identification, Conservation, and Expression Pattern Analyses of the BBR-BPC Gene Family Under Abiotic Stress in Brassica napus L.
by Long Wang, Wei Chen, Zhi Zhao, Huaxin Li, Damei Pei, Zhen Huang, Hongyan Wang and Lu Xiao
Genes 2025, 16(1), 36; https://doi.org/10.3390/genes16010036 - 29 Dec 2024
Viewed by 1295
Abstract
Background: The BBR-BPC gene family is a relatively conservative group of transcription factors, playing a key role in plant morphogenesis, organ development, and responses to abiotic stress. Brassica napus L. (B. napus), commonly known as oilseed rape, is an allopolyploid plant [...] Read more.
Background: The BBR-BPC gene family is a relatively conservative group of transcription factors, playing a key role in plant morphogenesis, organ development, and responses to abiotic stress. Brassica napus L. (B. napus), commonly known as oilseed rape, is an allopolyploid plant formed by the hybridization and polyploidization of Brassica rapa L. (B. rapa) and Brassica oleracea L. (B. oleracea), and is one of the most important oil crops. However, little is known about the characteristics, conservation, and expression patterns of this gene family in B. napus, especially under abiotic stress. Methods: To explore the characteristics and potential biological roles of the BBR-BPC gene family members in B. napus, we conducted identification based on bioinformatics and comparative genomics methods. We further analyzed the expression patterns through RNA-seq and qRT-PCR. Results: We identified 25 BBR-BPC members, which were classified into three subfamilies based on phylogenetic analysis, and found them to be highly conserved in both monocots and dicots. The conserved motifs revealed that most members contained Motif 1, Motif 2, Motif 4, and Motif 8. After whole-genome duplication (WGD), collinearity analysis showed that BBR-BPC genes underwent significant purifying selection. The promoters of most BBR-BPC genes contained cis-acting elements related to light response, hormone induction, and stress response. RNA-seq and qRT-PCR further indicated that BnBBR-BPC7, BnBBR-BPC15, BnBBR-BPC20, and BnBBR-BPC25 might be key members of this family. Conclusions: This study provides a theoretical foundation for understanding the potential biological functions and roles of the BBR-BPC gene family, laying the groundwork for resistance breeding in B. napus. Full article
(This article belongs to the Special Issue Genes and Genomics of Plants Under Abiotic Stresses)
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19 pages, 1638 KiB  
Article
Expanding the Mutation Spectrum for Inherited Retinal Diseases
by Jacob Lynn, Samuel J. Huang, Grace K. Trigler, Ronald Kingsley, Razek G. Coussa and Lea D. Bennett
Genes 2025, 16(1), 32; https://doi.org/10.3390/genes16010032 - 28 Dec 2024
Viewed by 1675
Abstract
Background/Objectives: Inherited retinal diseases (IRDs) represent a diverse group of genetic disorders characterized by degeneration of the retina, leading to visual impairment and blindness. IRDs are heterogeneous, sharing common clinical features that can be difficult to diagnose without knowing the genetic basis of [...] Read more.
Background/Objectives: Inherited retinal diseases (IRDs) represent a diverse group of genetic disorders characterized by degeneration of the retina, leading to visual impairment and blindness. IRDs are heterogeneous, sharing common clinical features that can be difficult to diagnose without knowing the genetic basis of the disease. To improve diagnostic accuracy and advance understanding of disease mechanisms, genetic testing was performed for 103 unrelated patients with an IRD at a single clinical site between 30 August 2022 and 5 February 2024. Methods: Informed consent was obtained before buccal samples were collected for panel-based sequencing at BluePrint Genetics (BpG), sponsored by the Foundation Fighting Blindness MyRetina Tracker program. A retina specialist performed standard visit assessments, including visual acuity (Snellen chart), slit lamp examination, fundus photography (Optos®, Dunfermline, UK), and spectral-domain optical coherence tomography (SD-OCT; Zeiss). Results: From 103 patients, genetic findings were reported for 70 individuals. Among these included 20 novel variants. Conclusions: These results clarify and confirm clinical diagnoses, aid in counseling patients on prognosis and family planning, and guide treatment options. This study not only holds promise for affected individuals but also expands the mutation spectrum to guide understanding of IRD. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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17 pages, 2061 KiB  
Article
Development of a Polygenic Risk Score for Metabolic Dysfunction-Associated Steatotic Liver Disease Prediction in UK Biobank
by Panagiota Giardoglou, Ioanna Gavra, Athina I. Amanatidou, Ioanna Panagiota Kalafati, Panagiotis Symianakis, Maria Kafyra, Panagiotis Moulos and George V. Dedoussis
Genes 2025, 16(1), 33; https://doi.org/10.3390/genes16010033 - 28 Dec 2024
Cited by 3 | Viewed by 1688
Abstract
Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading cause of liver-related morbidity and mortality. Although the invasive liver biopsy remains the golden standard for MASLD diagnosis, Magnetic Resonance Imaging-derived Proton Density Fat Fraction (MRI-PDFF) is an accurate, non-invasive method for the [...] Read more.
Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading cause of liver-related morbidity and mortality. Although the invasive liver biopsy remains the golden standard for MASLD diagnosis, Magnetic Resonance Imaging-derived Proton Density Fat Fraction (MRI-PDFF) is an accurate, non-invasive method for the assessment of treatment response. This study aimed at developing a Polygenic Risk Score (PRS) to improve MRI-PDFF prediction using UK Biobank data to assess an individual’s genetic liability to MASLD. Methods: We iteratively sequestered 10% of MRI-PDFF samples as a validation set and split the rest of each dataset into base and target partitions, containing GWAS summary statistics and raw genotype data, respectively. PRSice2 was deployed to derive PRS candidates. Based on the frequency of SNP appearances along the PRS candidates, we generated different SNP sets according to variable frequency cutoffs. By applying the PRSs to the validation set, we identified the optimal SNP set, which was then applied to a Greek nonalcoholic fatty liver disease (NAFLD) study. Results: Data from 3553 UK Biobank participants yielded 49 different SNP sets. After calculating the PRS on the validation set for every SNP set, an optimal PRS with 75 SNPs was selected (incremental R2 = 0.025, p-value = 0.00145). Interestingly, 43 SNPs were successfully mapped to MASLD-related known genes. The selected PRS could predict traits, like LDL cholesterol and diastolic blood pressure in the UK Biobank, as also disease outcome in the Greek NAFLD study. Conclusions: Our findings provide strong evidence that PRS is a powerful prediction model for MASLD, while it can also be applied on populations of different ethnicity. Full article
(This article belongs to the Section Bioinformatics)
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13 pages, 1592 KiB  
Review
Snowflake Data Warehouse for Large-Scale and Diverse Biological Data Management and Analysis
by Tatsuya Koreeda, Hiroshi Honda and Jun-ichi Onami
Genes 2025, 16(1), 34; https://doi.org/10.3390/genes16010034 - 28 Dec 2024
Viewed by 2183
Abstract
With the increasing speed of genomic, transcriptomic, and metagenomic data generation driven by the advancement and widespread adoption of next-generation sequencing technologies, the management and analysis of large-scale, diverse data in the fields of life science and biotechnology have become critical challenges. In [...] Read more.
With the increasing speed of genomic, transcriptomic, and metagenomic data generation driven by the advancement and widespread adoption of next-generation sequencing technologies, the management and analysis of large-scale, diverse data in the fields of life science and biotechnology have become critical challenges. In this paper, we thoroughly discuss the use of cloud data warehouses to address these challenges. Specifically, we propose a data management and analysis framework using Snowflake, a SaaS-based data platform. We further demonstrate its convenience and effectiveness through concrete examples, such as disease variant analysis and in silico drug discovery. By introducing Snowflake, researchers can efficiently manage and analyze a wide array of biological data, enabling the discovery of new biological insights through integrated analysis. Through these specific methodologies and application examples, we aim to accelerate research progress in the field of bioinformatics. Full article
(This article belongs to the Section Bioinformatics)
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26 pages, 3585 KiB  
Article
Differential microRNA and Target Gene Expression in Scots Pine (Pinus sylvestris L.) Needles in Response to Methyl Jasmonate Treatment
by Baiba Krivmane and Dainis Edgars Ruņģis
Genes 2025, 16(1), 26; https://doi.org/10.3390/genes16010026 - 27 Dec 2024
Viewed by 716
Abstract
Background/objectives: Methyl jasmonate is a plant signaling molecule involved in a wide range of functions, including stress responses. This study investigates the relative differential expression of microRNAs and their target genes in response to methyl jasmonate treatment of Scots pine needles. Methods: A [...] Read more.
Background/objectives: Methyl jasmonate is a plant signaling molecule involved in a wide range of functions, including stress responses. This study investigates the relative differential expression of microRNAs and their target genes in response to methyl jasmonate treatment of Scots pine needles. Methods: A combined strategy of high-throughput sequencing and in silico prediction of potential target genes was implemented. Results: a total of 58 differentially expressed (DE) microRNAs (miRNAs) (43 up-regulated and 15 down-regulated), belonging to 29 miRNA families, were identified. The 41 DE miRNAs from 17 families were conifer-specific miRNA families—miR946, miR947, miR950, miR1312, miR1313, miR1314, miR3693, miR3107, miR11452, miR11466, miR11487, miR11490, miR11504, miR11511, miR11532, miR11544, and miR11551. The other DE miRNAs (miR159, miR164, miR169, miR396, miR397, miR398, miR408, miR535) were conserved miRNAs, which are also found in angiosperm species. Transcriptome analysis identified 389 gene transcripts with 562 miRNA-target sites targeted by 57 of the 58 DE miRNAs. Of these, 250 target genes with 138 different GO annotations were found for the 41 DE conifer-specific conserved miRNAs. Conclusions: The 26 DE miRNAs from 14 DE miRNA families, of which almost all (12 families, 24 miRNAs) are conifer specific, and were associated with 68 disease resistance and TMV resistance proteins, TIR-NBS-LRR, LRR receptor-like serine/threonine-protein kinase, putative CC-NBS-LRR protein, and putative NBS-LRR protein target transcripts with 29 target gene GO term descriptions. Some of the genes targeted by conifer-specific miRNAs have been previously reported to be targeted by other miRNAs in angiosperms, indicating that the miRNA-target gene regulation system can vary between species. Full article
(This article belongs to the Special Issue Plant Small RNAs: Biogenesis and Functions)
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16 pages, 21287 KiB  
Article
Comparative Transcriptome Analysis of Gene Expression Between Female and Monoecious Spinacia oleracea L.
by Yingjie Zhao, Zhiyuan Liu, Hongbing She, Zhaosheng Xu, Helong Zhang, Shaowen Zheng and Wei Qian
Genes 2025, 16(1), 24; https://doi.org/10.3390/genes16010024 - 27 Dec 2024
Viewed by 1148
Abstract
Background: Spinach (Spinacia oleracea L.) is an important leafy vegetable with dioecious and occasional monoecious plants. Monoecious lines are more suitable for hybrid production than dioecious lines due to their extended flowering period. However, genetic research on the sex determination of monoecism [...] Read more.
Background: Spinach (Spinacia oleracea L.) is an important leafy vegetable with dioecious and occasional monoecious plants. Monoecious lines are more suitable for hybrid production than dioecious lines due to their extended flowering period. However, genetic research on the sex determination of monoecism remains limited. Methods: In this study, RNA-seq analysis of monoecious and female spinach plants was performed at two distinct flowering stages. In total, we identified 4586 differentially expressed genes (DEGs), which were primarily involved in biological processes such as hormone signaling, cell wall biosynthesis, photosynthesis, and flower development, based on Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Results: Among these DEGs, 354 transcription factors, including 27 genes associated with the ABCDE gene, were discovered. Furthermore, a co-expression gene regulatory network was built, identifying nine key genes that play important roles in regulating sex differentiation between female and monoecious plants. Conclusions: Our findings provide crucial molecular insights into the mechanisms of monoecism in spinach and offer a scientific basis for future spinach breeding. Full article
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17 pages, 2526 KiB  
Article
Genome-Wide Patterns of Homozygosity and Heterozygosity and Candidate Genes in Greek Insular and Mainland Native Goats
by Valentina Tsartsianidou, Antonis Otapasidis, Spiros Papakostas, Nikoleta Karaiskou, Sotiria Vouraki and Alexandros Triantafyllidis
Genes 2025, 16(1), 27; https://doi.org/10.3390/genes16010027 - 27 Dec 2024
Cited by 1 | Viewed by 1278
Abstract
Background: Runs of homozygosity (ROHs) and heterozygosity (ROHets) serve for the identification of genomic regions as candidates of selection, local adaptation, and population history. Methods: The present study aimed to comprehensively explore the ROH and ROHet patterns and hotspots in Greek native dairy [...] Read more.
Background: Runs of homozygosity (ROHs) and heterozygosity (ROHets) serve for the identification of genomic regions as candidates of selection, local adaptation, and population history. Methods: The present study aimed to comprehensively explore the ROH and ROHet patterns and hotspots in Greek native dairy goats, Eghoria and Skopelos, genotyped with the Illumina Goat SNP50 BeadChip. SNP and functional enrichment analyses were conducted to further characterize hotspots and the candidate genes located within these genomic regions. Genetic relationships between and within breeds and inbreeding coefficients were also evaluated. Results: Clear genetic differentiation and diversified management practices were depicted between the two native populations. The ROH and ROHet average genome coverage for Skopelos (65.35 and 35 Mb) and Eghoria (47.64 and 43 Mb) indicated differences in mainland and insular goats, with Skopelos showing more long ROH fragments, reflecting its geographic isolation and small population size. An ROH hotspot (CHR12: 43.59–44.61 Mb) detected in the Skopelos population has been also reported across European goats and co-localizes with a selection signal detected in the Egyptian Barki goats and sheep adapted to hot–arid conditions. A novel ROH hotspot (CHR18: 60.12–61.81 Mb), shared among the Greek breeds, harbors candidate genes enriched in biosynthesis, metabolism, and immune response. Two well-conserved ROHet islands were detected in Greek goats on chromosomes 1 and 18, with genes participating in development and embryogenesis. The Eghoria population showed the highest number of ROHet islands, potentially reflecting its adaptability to diverse environments. Conclusions: These findings offer new insights into the environmental adaptation and artificial selection in Greek goats and could be utilized in future breeding strategies for sustainable goat farming. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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13 pages, 222 KiB  
Article
Relevance of Next-Generation Sequencing in the Diagnosis of Thalassemia and Hemoglobinopathies: The Experience of Four Italian Diagnostic Hubs
by Rita Selvatici, Valentina Guida, Massimo Maffei, Milena Agata Irrera, Alice Margutti, Paola Bisceglia, Massimo Mogni, Erica Melchionda, Giuseppina Stoico, Nicoletta Grifone, Laura Bocciardo, Simone Salerio, Vittoria Nagliati, Angela Alberico, Giusy Tringali, Cristina Melles, Alessandro De Luca, Alessandra Ferlini, Domenico Coviello and Cristina Curcio
Genes 2025, 16(1), 28; https://doi.org/10.3390/genes16010028 - 27 Dec 2024
Viewed by 1527
Abstract
Thalassemias and hemoglobinopathies are among the most common genetic diseases worldwide and have a significant impact on public health. The decreasing cost of next-generation sequencing (NGS) has quickly enabled the development of new assays that allow for the simultaneous analysis of small nucleotide [...] Read more.
Thalassemias and hemoglobinopathies are among the most common genetic diseases worldwide and have a significant impact on public health. The decreasing cost of next-generation sequencing (NGS) has quickly enabled the development of new assays that allow for the simultaneous analysis of small nucleotide variants (SNVs) and copy number variants (CNVs) as deletions/duplications of α- and β-globin genes. Background/Objectives: This study highlighted the efficacy and rapid identification of all types of mutations in the α- and β-globin genes, including silent variants, using the Devyser Thalassemia NGS kit. Furthermore, we report the frequency of mutations identified in a total population of 2649 individuals recruited from four Italian Medical Genetics Laboratories. Methods: All samples were first hematologically characterized, and sequence analysis was conducted by using the Devyser Thalassemia NGS kit. All variants were also validated in an independent sample by a conventional molecular test. Results: A total of 1789 subjects were identified with genetic variants in the globin genes, of which 966 (53.9%) had variations in the β-gene, 480 (26.8%) had variations in the α-gene; and 307 (17.1%) had variations in both α- and β-genes. Variant analysis evidenced a heterogeneous mutation spectrum enriched with variants not usually observed in the Italian population. Conclusions: This study showed the high effectiveness and the rapid identification of all mutation types in both α- and β-globin genes, including silent variants. It should be emphasized that the NGS approach greatly shortens turnaround reporting times, overcoming the classic diagnostic flowchart which envisages multistep, subsequent, diagnostic approaches, often requiring long resolution times. Full article
(This article belongs to the Section Bioinformatics)
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17 pages, 4217 KiB  
Article
Novel Splice-Altering Variants in the CHM and CACNA1F Genes Causative of X-Linked Choroideremia and Cone Dystrophy
by Anna R. Ridgeway, Ciara Shortall, Laura K. Finnegan, Róisín Long, Evan Matthews, Adrian Dockery, Ella Kopčić, Laura Whelan, Claire Kirk, Giuliana Silvestri, Jacqueline Turner, David J. Keegan, Sophia Millington-Ward, Naomi Chadderton, Emma Duignan, Paul F. Kenna and G. Jane Farrar
Genes 2025, 16(1), 25; https://doi.org/10.3390/genes16010025 - 27 Dec 2024
Viewed by 1152
Abstract
Background: An estimated 10–15% of all genetic diseases are attributable to variants in noncanonical splice sites, auxiliary splice sites and deep-intronic variants. Most of these unstudied variants are classified as variants of uncertain significance (VUS), which are not clinically actionable. This study investigated [...] Read more.
Background: An estimated 10–15% of all genetic diseases are attributable to variants in noncanonical splice sites, auxiliary splice sites and deep-intronic variants. Most of these unstudied variants are classified as variants of uncertain significance (VUS), which are not clinically actionable. This study investigated two novel splice-altering variants, CHM NM_000390.4:c.941-11T>G and CACNA1F NM_005183.4:c.2576+4_2576+5del implicated in choroideremia and cone dystrophy (COD), respectively, resulting in significant visual loss. Methods: Next-generation sequencing was employed to identify the candidate variants in CHM and CACNA1F, which were confirmed using Sanger sequencing. Cascade analysis was undertaken when additional family members were available. Functional analysis was conducted by cloning genomic regions of interest into gateway expression vectors, creating variant and wildtype midigenes, which were subsequently transfected into HEK293 cells. RNA was harvested and amplified by RT-PCR to investigate the splicing profile for each variant compared to the wildtype. Novel variants were reclassified according to ACMG/AMP and ClinGen SVI guidelines. Results: Midigene functional analysis confirmed that both variants disrupted splicing. The CHM NM_000390.4:c.941-11T>G variant caused exon 8 skipping, leading to a frameshift and the CACNA1F NM_005183.4:c.2576+4_2576+5del variant caused a multimodal splice defect leading to an in-frame insertion of seven amino acids and a frameshift. With this evidence, the former was upgraded to likely pathogenic and the latter to a hot VUS. Conclusions: This study adds to the mutational spectrum of splicing defects implicated in retinal degenerations by identifying and characterising two novel variants in CHM and CACNA1F. Our results highlight the importance of conducting functional analysis to investigate the consequences of intronic splice-altering variants and the significance of reclassifying VUS to confirm a genetic diagnosis. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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10 pages, 2261 KiB  
Brief Report
Systematic Analysis of UFMylation Family Genes in Tissues of Mice with Metabolic Dysfunction-Associated Steatotic Liver Disease
by Mingdi Jiang, Chenlu Zhang, Zhengyao Zhang, Yingying Duan, Shuaiyong Qi, Qingyu Zeng, Jiabao Wang, Jiawen Zhang, Yu Jiang, Ying Wang, Yi Chen and Jiang Liu
Genes 2025, 16(1), 31; https://doi.org/10.3390/genes16010031 - 27 Dec 2024
Viewed by 1409
Abstract
Background/Objectives: UFMylation, a newly identified ubiquitin-like modification, modulates a variety of physiological processes, including endoplasmic reticulum homeostasis maintenance, DNA damage response, embryonic development, and tumor progression. Recent reports showed that UFMylation plays a protective role in preventing liver steatosis and fibrosis, serving as [...] Read more.
Background/Objectives: UFMylation, a newly identified ubiquitin-like modification, modulates a variety of physiological processes, including endoplasmic reticulum homeostasis maintenance, DNA damage response, embryonic development, and tumor progression. Recent reports showed that UFMylation plays a protective role in preventing liver steatosis and fibrosis, serving as a defender of liver homeostasis in the development of metabolic dysfunction-associated steatotic liver disease (MASLD). However, the regulation of UFMylation in MASLD remains unclear. This study aimed to determine the expressed patterns of UFMylation components in multiple tissues of leptin-deficient ob/ob mice and high-fat diet (HFD)-fed mice, which are mimicking the conditions of MASLD. Methods: The ob/ob mice and HFD-fed mice were sacrificed to collect tissues indicated in this study. Total RNA and proteins were extracted from tissues to examine the expressed patterns of UFMylation components, including UBA5, UFC1, UFL1, DDRGK1, UFSP1, UFSP2 and UFM1, by real-time PCR and western blot analysis. Results: The protein levels of UBA5, UFC1 and UFL1 were down-regulated in liver, brown adipose tissue (BAT) and inguinal white adipose tissue (iWAT), whereas the messenger RNA (mRNA) levels of Ufl1 and Ufsp1 were both decreased in skeletal muscle, BAT, iWAT and epididymal white adipose tissue (eWAT) of ob/ob mice. In contrast, the mRNA levels of Ufsp1 in skeletal muscle, BAT, iWAT and heart, and the protein levels of UFL1 were decreased in BAT, iWAT, heart and cerebellum of HFD-fed mice. Conclusions: Our findings established the expressed profiles of UFMylaiton in multiple tissues of mice mimicking MASLD, indicating an important regulation for UFMylation in these tissues’ homeostasis maintenance. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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15 pages, 243 KiB  
Article
AI-Powered Neurogenetics: Supporting Patient’s Evaluation with Chatbot
by Stefania Zampatti, Juliette Farro, Cristina Peconi, Raffaella Cascella, Claudia Strafella, Giulia Calvino, Domenica Megalizzi, Giulia Trastulli, Carlo Caltagirone and Emiliano Giardina
Genes 2025, 16(1), 29; https://doi.org/10.3390/genes16010029 - 27 Dec 2024
Cited by 2 | Viewed by 1258
Abstract
Background/Objectives: Artificial intelligence and large language models like ChatGPT and Google’s Gemini are promising tools with remarkable potential to assist healthcare professionals. This study explores ChatGPT and Gemini’s potential utility in assisting clinicians during the first evaluation of patients with suspected neurogenetic disorders. [...] Read more.
Background/Objectives: Artificial intelligence and large language models like ChatGPT and Google’s Gemini are promising tools with remarkable potential to assist healthcare professionals. This study explores ChatGPT and Gemini’s potential utility in assisting clinicians during the first evaluation of patients with suspected neurogenetic disorders. Methods: By analyzing the model’s performance in identifying relevant clinical features, suggesting differential diagnoses, and providing insights into possible genetic testing, this research seeks to determine whether these AI tools could serve as a valuable adjunct in neurogenetic assessments. Ninety questions were posed to ChatGPT (Versions 4o, 4, and 3.5) and Gemini: four questions about clinical diagnosis, seven about genetic inheritance, estimable recurrence risks, and available tests, and four questions about patient management, each for six different neurogenetic rare disorders (Hereditary Spastic Paraplegia type 4 and type 7, Huntington Disease, Fragile X-associated Tremor/Ataxia Syndrome, Becker Muscular Dystrophy, and FacioScapuloHumeral Muscular Dystrophy). Results: According to the results of this study, GPT chatbots demonstrated significantly better performance than Gemini. Nonetheless, all AI chatbots showed notable gaps in diagnostic accuracy and a concerning level of hallucinations. Conclusions: As expected, these tools can empower clinicians in assessing neurogenetic disorders, yet their effective use demands meticulous collaboration and oversight from both neurologists and geneticists. Full article
(This article belongs to the Special Issue Molecular Genetics of Neurodegenerative Diseases and Neuromuscular Diseases)
23 pages, 5931 KiB  
Article
Transcriptional Analysis of Tissues in Tartary Buckwheat Seedlings Under IAA Stimulation
by Yingying Gao, Jialing Lai, Chenglu Feng, Luyang Li, Qihang Zu, Juan Li and Dengxiang Du
Genes 2025, 16(1), 30; https://doi.org/10.3390/genes16010030 - 27 Dec 2024
Cited by 1 | Viewed by 663
Abstract
Background: Fagopyrum tataricum, commonly referred to as tartary buckwheat, is a cultivated medicinal and edible crop renowned for its economic and nutritional significance. Following the publication of the buckwheat genome, research on its functional genomics across various growth environments has gradually [...] Read more.
Background: Fagopyrum tataricum, commonly referred to as tartary buckwheat, is a cultivated medicinal and edible crop renowned for its economic and nutritional significance. Following the publication of the buckwheat genome, research on its functional genomics across various growth environments has gradually begun. Auxin plays a crucial role in many life processes. Analyzing the expression changes in tartary buckwheat after IAA treatment is of great significance for understanding its growth and environmental adaptability. Methods: This study investigated the changes in auxin response during the buckwheat seedling stage through high-throughput transcriptome sequencing and the identification and annotation of differentially expressed genes (DEGs) across three treatment stages. Results: After IAA treatment, there are 3355 DEGs in leaves and 3974 DEGs in roots identified. These DEGs are significantly enriched in plant hormone signaling, MAPK signaling pathways, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways. This result suggests a notable correlation between these tissues in buckwheat and their response to IAA, albeit with significant differences in response patterns. Additionally, the identification of tissue-specific expression genes in leaves and other tissues revealed distinct tissue variations. Conclusions: Following IAA treatment, an increase in tissue-specific expression genes observed, indicating that IAA significantly regulates the growth of buckwheat tissues. This study also validated certain genes, particularly those in plant hormone signaling pathways, providing a foundational dataset for the further analysis of buckwheat growth and tissue development and laying the groundwork for understanding buckwheat growth and development. Full article
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16 pages, 6152 KiB  
Article
Genome-Wide Identification and Analysis of the MYC Gene Family in Cotton: Evolution and Expression Profiles During Normal Growth and Stress Response
by Jingxi Chen, Long Wang, Xiufang Wang, Lu Lu, Peng Han, Caidie Zhang, Min Han, Siyu Xiang, Haibiao Wang, Lizhong Xuan, Zhibo Li, Hairong Lin, Xinhui Nie and Yuanlong Wu
Genes 2025, 16(1), 20; https://doi.org/10.3390/genes16010020 - 26 Dec 2024
Cited by 1 | Viewed by 1057
Abstract
Background: The gene family of myelomatosis (MYC), serving as a transcription factor in the jasmonate (JA) signaling pathway, displays a significant level of conservation across diverse animal and plant species. Cotton is the most widely used plant for fiber production. Nevertheless, there is [...] Read more.
Background: The gene family of myelomatosis (MYC), serving as a transcription factor in the jasmonate (JA) signaling pathway, displays a significant level of conservation across diverse animal and plant species. Cotton is the most widely used plant for fiber production. Nevertheless, there is a paucity of literature reporting on the members of MYCs and how they respond to biotic stresses in cotton. Methods: Bioinformatics analysis was used to mine the MYC gene family in cotton based on InterPro, cottongen, etc. Results: The gene structure, conserved motifs, and upstream open reading frames of 32 GhMYCs in Gossypium hirsutum were identified. Moreover, it was anticipated that the GT1-motif is the most abundant in GhMYCs, indicating that the GT1-motif plays a significant role in light-responsive GhMYCs. The expression patterns of GhMYCs under biotic stresses including V. dahliae and Aphid gossypii were evaluated, suggesting that GhMYCs in class-1 and -3 GhMYCs, which function as negative regulators, are involved in resistance to verticillium wilt and aphids. The class-3 GhMYCs genes were found to be mostly expressed in female tissues. Interestingly, it was also determined that the homeologous expression bias within GhMYCs in cotton was uncovered, and results showed that the gene expression of class-1A and class-2 GhMYCs in the Dt sub-genome may have a direct impact on gene function. Conclusions: This study provides a research direction for researchers and breeders to enhance cotton traits through manipulating individual or multiple homeologs, which laid a foundation for further study of the molecular characteristics and biological functions of GhMYC gene. Full article
(This article belongs to the Section Bioinformatics)
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19 pages, 3783 KiB  
Article
Whole Genome Sequencing and Comparative Genomics Analysis of Goat-Derived Klebsiella oxytoca
by Yu Zhang, Zhenxing Zhang, Ziying Wang, Yimei Chen, Lianjie Liao, Li Du, Hongyan Gao, Qiaoling Chen, Churiga Man, Si Chen and Fengyang Wang
Genes 2025, 16(1), 13; https://doi.org/10.3390/genes16010013 - 26 Dec 2024
Viewed by 988
Abstract
Background: This research aims to enhance the genomic database of Klebsiella oxytoca by identifying virulence genes through the whole genome sequencing and comparative analysis of a goat-derived K. oxytoca (KOHN1) strain, while clarifying the relationship between its genetic evolution and virulence, ultimately providing [...] Read more.
Background: This research aims to enhance the genomic database of Klebsiella oxytoca by identifying virulence genes through the whole genome sequencing and comparative analysis of a goat-derived K. oxytoca (KOHN1) strain, while clarifying the relationship between its genetic evolution and virulence, ultimately providing a theoretical foundation for clinical prevention and diagnosis. Methods: Third-generation Oxford Nanopore Technologies (ONT) sequencing and second-generation Illumina sequencing were used to sequence the strain and analyze the database annotations. Screening for 10 virulence genes was conducted using PCR. Comparative genomic analyses of the strain KOHN1 with four human-derived K. oxytoca model strains were performed using collinearity analysis, taxonomy classification through ANI analysis, and gene function family analysis. Results: The genome size of the KOHN1 strain was 5,817,806 bp, and the GC content was 55.14%. It contained 5227 predicted coding genes, including 25 rRNA genes, 85 tRNA genes, and 53 sRNA genes. A total of 14 type VI secretion system effector proteins and 146 virulence factor-related genes were annotated. Additionally, eight virulence genes—fimA, fimH, entB, mrkD, clpV, rmpA, vgrG, and hcp—were detected through PCR identification. The strain has 448 drug resistance genes, mainly against β-lactams and fosfomycins. Comparative genomic analysis indicated that its closest relation is the human isolate ASM338647. Conclusions: In this study, the whole genome sequence of a goat-derived K. oxytoca (KOHN1) strain was obtained, revealing its evolutionary relationship with domestic and foreign isolates and providing a reference for future studies on the mechanisms of antimicrobial resistance and the pathogenicity of K. oxytoca. Full article
(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)
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11 pages, 3634 KiB  
Article
EDA Mutations Causing X-Linked Recessive Oligodontia with Variable Expression
by Ye Ji Lee, Youn Jung Kim, Wonseon Chae, Seon Hee Kim and Jung-Wook Kim
Genes 2025, 16(1), 12; https://doi.org/10.3390/genes16010012 - 26 Dec 2024
Viewed by 844
Abstract
Background/Objectives: The ectodysplasin A (EDA) gene, a member of the tumor necrosis factor ligand superfamily, is involved in the early epithelial–mesenchymal interaction that regulates ectoderm-derived appendage formation. Numerous studies have shown that mutations in the EDA gene can cause X-linked ectodermal [...] Read more.
Background/Objectives: The ectodysplasin A (EDA) gene, a member of the tumor necrosis factor ligand superfamily, is involved in the early epithelial–mesenchymal interaction that regulates ectoderm-derived appendage formation. Numerous studies have shown that mutations in the EDA gene can cause X-linked ectodermal dysplasia (ED) and non-syndromic oligodontia (NSO). Accordingly, this study aimed to identify the causative genetic mutations of the EDA gene. Methods: We investigated EDA gene mutations in two X-linked oligodontia families using candidate gene sequencing and whole-exome sequencing, with a single proband identified and studied for each family. The first family included a patient with NSO, while the second family had a patient exhibiting variable expression of ED. Results: Mutational analysis identified two missense mutations in the EDA gene (NM_001399.5): one novel mutation, c.787A>C p.(Lys263Gln), in family 2; and one previously reported mutation, c.457C>T p.(Arg153Cys), in family 1. All mutated residues are evolutionarily highly conserved amino acids. The p.(Arg153Cys) mutation would destroy the furin recognition site and affect the cleavage of EDA. The p.(Lys263Gln) mutation in a TNF homology domain would interfere with the binding of the EDA receptor. The p.(Lys263Gln) mutation was associated with NSO, while the other mutation demonstrated ED. Conclusions: This study helps to better understand the nature of EDA-related ED and NSO and their pathogenesis, and it expands the mutational spectrum of EDA mutations. Full article
(This article belongs to the Special Issue Genetic, Epigenetic and Environmental Factors in Dental Development and Pathologies: Genes, Interactions and Dental Development)
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15 pages, 2158 KiB  
Article
Exploring the Potential of Genome-Wide Hybridization Capture Enrichment for Forensic DNA Profiling of Degraded Bones
by Christian Haarkötter, Xavier Roca-Rada, María Saiz, Diana C. Vinueza-Espinosa, Xiomara Gálvez, María Isabel Medina-Lozano, Daniel Díaz-Ruiz, Juan Carlos Álvarez, Bastien Llamas, Jose Antonio Lorente and Jeremy Austin
Genes 2025, 16(1), 23; https://doi.org/10.3390/genes16010023 - 26 Dec 2024
Cited by 1 | Viewed by 1779
Abstract
In many human rights and criminal contexts, skeletal remains are often the only available samples, and they present a significant challenge for forensic DNA profiling due to DNA degradation. Ancient DNA methods, particularly capture hybridization enrichment, have been proposed for dealing with severely [...] Read more.
In many human rights and criminal contexts, skeletal remains are often the only available samples, and they present a significant challenge for forensic DNA profiling due to DNA degradation. Ancient DNA methods, particularly capture hybridization enrichment, have been proposed for dealing with severely degraded bones, given their capacity to yield results in ancient remains. Background/Objectives: This paper aims to test the efficacy of genome-wide capture enrichment on degraded forensic human remains compared to autosomal STRs analysis. Methods: Six highly degraded human bones from the Spanish Civil War (1936–1939) were quantified with Quantifiler™ Trio and amplified with GlobalFiler™. Independently, partially UDG-treated double-stranded DNA libraries were generated and shotgun sequenced to screen for endogenous human DNA content. Subsequently, libraries were enriched with the Twist Bioscience “Twist Ancient DNA” reagent enrichment kit, which had not been previously tested for forensic purposes. Results: The results show that the samples behave similarly with both approaches (well-preserved samples yield good results). However, capture enrichment provides some new relevant insights, suggesting that its implementation in current NGS forensic platforms could be beneficial. Conclusions: Shotgun results show that the analyzed samples exhibit the same characteristics as ancient DNA samples in terms of DNA fragmentation and molecular damage, which may enhance the value of this approach when authenticating the endogenous DNA of forensic samples. Full article
(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods, 2nd Edition)
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20 pages, 8209 KiB  
Article
Genome-Wide Identification and Comprehensive Analysis of the PPO Gene Family in Glycine max and Glycine soja
by Ziye Song, Bo Wang, Jia Liu, Nianxi Liu, Zhigang Yi, Zhi Li, Zhimin Dong, Chunbao Zhang, Yingshan Dong and Yuqiu Li
Genes 2025, 16(1), 17; https://doi.org/10.3390/genes16010017 - 26 Dec 2024
Viewed by 962
Abstract
Background: Polyphenol oxidases (PPOs) form a multigene family that is widely distributed in plants, animals, and insects. To date, PPOs have been identified in plants such as Populus L. and Solanum tuberosum L., but studies on PPOs in soybean (Glycine [...] Read more.
Background: Polyphenol oxidases (PPOs) form a multigene family that is widely distributed in plants, animals, and insects. To date, PPOs have been identified in plants such as Populus L. and Solanum tuberosum L., but studies on PPOs in soybean (Glycine max (L.) Merr.) and wild soybean (Glycine soja Sieb. and Zucc.) remain limited. Methods: To clarify the nature, structure, evolution, expression pattern, and interaction network of PPOs in these plants, we performed bioinformatics analysis and evaluated the expression patterns of PPOs in soybean and wild soybean throughout the growth period and under salt stress. Results: We identified 17 and 15 genes belonging to the PPO family. These genes were distributed across chromosomes 7 and 6 and could be divided into three groups. Most of these genes only contained one coding sequence (CDS), and their gene structure, conserved motifs, and 3D structures were very similar. Although there were a few intraspecies gene duplications, 75 gene replication pairs between soybean and wild soybean were detected. A Ka/Ks analysis showed that the PPOs in these plants were mainly subjected to purity selection. Moreover, the expression of the PPO genes varied greatly during different stages of the growth period and under salt stress, showing high temporal and spatial specificity. The protein interaction networks of these genes appeared to be quite distinct. Through the interaction analysis of the candidate gene GmPPO2 selected under salt stress, Glyma.07G059000, Glyma.10G279000, and Glyma.03G167900 were identified as the candidate genes regulating salt stress tolerance in soybean. Conclusions: These findings provide a foundation for further research on the evolution of soybean and wild soybean, as well as the functions of the PPO gene family. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Crop Breeding)
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12 pages, 1116 KiB  
Article
Metallothionein-1A (MT1A) Gene Variability May Play a Role in Female Frailty: A Preliminary Study
by Paolina Crocco, Francesco De Rango, Rossella La Grotta, Giuseppe Passarino, Giuseppina Rose and Serena Dato
Genes 2025, 16(1), 15; https://doi.org/10.3390/genes16010015 - 26 Dec 2024
Viewed by 967
Abstract
Background/Objectives: Frailty is a complex geriatric syndrome resulting in decreased physiological reserve. While genetics plays a role, the underlying mechanisms remain unsolved. Metallothioneins (MTs), metal-binding proteins with high affinity for zinc, an essential mineral for many physiological functions, are involved in processes including [...] Read more.
Background/Objectives: Frailty is a complex geriatric syndrome resulting in decreased physiological reserve. While genetics plays a role, the underlying mechanisms remain unsolved. Metallothioneins (MTs), metal-binding proteins with high affinity for zinc, an essential mineral for many physiological functions, are involved in processes including oxidative stress and inflammation. We investigated the impact of genetic variations in MTs on frailty. Methods: 448 subjects (235 females and 213 males, median age of 76 years) were categorized into three frailty groups (non-frail/pre-frail/frail), by hierarchical cluster analysis based on cognitive status (MMSE), functional capacity (ADL), and physical strength (HGS). Subjects were analyzed for selected SNPs in MT1A, MT1B, MT2A, and MT3 genes by PCR-RFLP. Results: An association was found between the rs8052394-A/G (Lys51Arg) polymorphism in the MT1A gene and frailty in females both in binary (OR = 0.345, p = 0.037) and multinomial logistic regression (OR = 0.343, p = 0.036) corrected for age and sex, with carriers of the minor G-allele less likely to transition from non-frail to pre-frail status. Additionally, a significant association with albumin levels (beta = 0.231; p = 0.027) and a trend of association with CRP levels (beta = −1.563; p = 0.097) were observed for this SNP in non-frail females, both indicative of a low inflammatory status. However, Bonferroni correction for multiple SNPs and physiological parameters tested renders these results statistically non-significant. Conclusions: Although its associations do not survive Bonferroni correction, this exploratory study suggests a sex-specific influence of MT1A variability in frailty, likely affecting zinc availability, aligning with ongoing research on sex differences in frailty risk and progression. Larger studies are needed to validate these findings and clarify the mechanisms behind MTs’ variability in frailty progression. Full article
(This article belongs to the Special Issue Genetic Variation in Age-Related Changes)
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15 pages, 3221 KiB  
Article
Genome-Wide Identification and Characterization of HSP70 Gene Family in Tausch’s Goatgrass (Aegilops tauschii)
by Yongmei Xu, Yue Liu, Yanjun Yi and Jiajia Liu
Genes 2025, 16(1), 19; https://doi.org/10.3390/genes16010019 - 26 Dec 2024
Cited by 3 | Viewed by 813
Abstract
Background: Aegilops tauschii, a winter annual grass weed native to Eastern Europe and Western Asia, has become a widespread invasive species in the wheat-growing regions of China due to its high environmental adaptability. This study aims to explore the molecular mechanisms underlying [...] Read more.
Background: Aegilops tauschii, a winter annual grass weed native to Eastern Europe and Western Asia, has become a widespread invasive species in the wheat-growing regions of China due to its high environmental adaptability. This study aims to explore the molecular mechanisms underlying the stress resistance of Tausch’s goatgrass, focusing on the HSP70 gene family. Methods: A genome-wide analysis was conducted to identify and characterize the HSP70 gene family in A. tauschii. Afterward, their physicochemical properties, phylogenetic relationships, gene structures, and chromosomal distributions were analyzed. Additionally, cis-acting regulatory elements were predicted to understand their potential role in stress resistance. Results: A total of 19 identified HSP70 family genes were classified into four subfamilies and distributed across all chromosomes. The syntenic analysis revealed extensive homology between Tausch’s goatgrass and wheat HSP70 genes. Segmental duplication was found to play a crucial role in the expansion of the HSP70 gene family. The prediction of cis-acting elements suggested that these genes are involved in stress resistance to various environmental conditions. Conclusions: This study provides a comprehensive overview of the HSP70 gene family in A. tauschii, offering insights into their role in stress resistance and their potential application in understanding invasive species behavior and improving wheat resilience. Further research is needed to validate their functional roles in stress adaptation. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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18 pages, 2505 KiB  
Review
From Species to Varieties: How Modern Sequencing Technologies Are Shaping Medicinal Plant Identification
by Mingcheng Wang, Haifeng Lin, Hongqiang Lin, Panyue Du and Shuqiao Zhang
Genes 2025, 16(1), 16; https://doi.org/10.3390/genes16010016 - 26 Dec 2024
Cited by 17 | Viewed by 1858
Abstract
Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing [...] Read more.
Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing the accuracy and reliability of plant identification. Additionally, the integration of multi-omics approaches is examined to provide a comprehensive understanding of medicinal plant identity. Methods: The literature search for this review was conducted across databases such as Google Scholar, Web of Science, and PubMed, using keywords related to plant taxonomy, genomics, and biotechnology. Inclusion criteria focused on peer-reviewed studies closely related to plant identification methods and techniques that contribute significantly to the field. Results: The review highlights that while sequencing technologies offer substantial improvements, challenges such as high costs, technical expertise, and the lack of standardized protocols remain barriers to widespread adoption. Potential solutions, including AI-driven data analysis and portable sequencers, are discussed. Conclusions: This review provides a comprehensive overview of molecular techniques, their transformative impact, and future perspectives for more accurate and efficient medicinal plant identification. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants: 2nd Edition)
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18 pages, 13184 KiB  
Article
Lactate Promotes Hypoxic Granulosa Cells’ Autophagy by Activating the HIF-1α/BNIP3/Beclin-1 Signaling Axis
by Yitong Pan, Gang Wu, Min Chen, Xiumei Lu, Ming Shen, Hongmin Li and Honglin Liu
Genes 2025, 16(1), 14; https://doi.org/10.3390/genes16010014 - 26 Dec 2024
Viewed by 1453
Abstract
Background/Objectives: The avascular nature of the follicle creates a hypoxic microenvironment, establishing a niche where granulosa cells (GCs) rely on glycolysis to produce energy in the form of lactate (L-lactate). Autophagy, an evolutionarily conserved stress-response process, involves the formation of autophagosomes to encapsulate [...] Read more.
Background/Objectives: The avascular nature of the follicle creates a hypoxic microenvironment, establishing a niche where granulosa cells (GCs) rely on glycolysis to produce energy in the form of lactate (L-lactate). Autophagy, an evolutionarily conserved stress-response process, involves the formation of autophagosomes to encapsulate intracellular components, delivering them to lysosomes for degradation. This process plays a critical role in maintaining optimal follicular development. However, whether hypoxia regulates autophagy in GCs via lactate remains unclear. Methods: In this study, we investigated lactate-induced autophagy under hypoxia by utilizing glycolysis inhibitors or silencing related genes. Results: We observed a significant increase in autophagy in ovarian GCs under hypoxic conditions, indicated by elevated LC3II levels and reduced P62 levels. Suppressing lactate production through glycolytic inhibitors (2-DG and oxamate) or silencing lactate dehydrogenase (LDHA/LDHB) effectively reduced hypoxia-induced autophagy. Further investigation revealed that the HIF1-α/BNIP3/Beclin-1 axis is essential for lactate-induced autophagy under hypoxic conditions. Inhibiting HIF-1α activity using siRNAs or PX-478 downregulated BNIP3 expression and subsequently suppressed autophagy. Similarly, BNIP3 silencing with siRNAs repressed lactate-induced autophagy in hypoxic conditions. Mechanistically, immunoprecipitation experiments showed that BNIP3 disrupted pre-existing Bcl-2/Beclin-1 complexes by competing with Bcl-2 to form Bcl-2/BNIP3 complexes. This interaction released Beclin-1, which subsequently triggered lactate-induced autophagy under hypoxic conditions. Conclusions: These findings unveil a novel mechanism by which hypoxia regulates GC autophagy through lactate production, highlighting its potential role in sustaining follicular development under hypoxic conditions. Full article
(This article belongs to the Special Issue Gene Regulation of Development and Evolution in Mammals)
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10 pages, 3856 KiB  
Case Report
Novel LYST Variants Lead to Aberrant Splicing in a Patient with Chediak–Higashi Syndrome
by Maxim Aleksenko, Elena Vlasova, Amina Kieva, Ruslan Abasov, Yulia Rodina, Michael Maschan, Anna Shcherbina and Elena Raykina
Genes 2025, 16(1), 18; https://doi.org/10.3390/genes16010018 - 26 Dec 2024
Viewed by 1091
Abstract
Background: The advent of next-generation sequencing (NGS) has revolutionized the analysis of genetic data, enabling rapid identification of pathogenic variants in patients with inborn errors of immunity (IEI). Sometimes, the use of NGS-based technologies is associated with challenges in the evaluation of the [...] Read more.
Background: The advent of next-generation sequencing (NGS) has revolutionized the analysis of genetic data, enabling rapid identification of pathogenic variants in patients with inborn errors of immunity (IEI). Sometimes, the use of NGS-based technologies is associated with challenges in the evaluation of the clinical significance of novel genetic variants. Methods: In silico prediction tools, such as SpliceAI neural network, are often used as a first-tier approach for the primary examination of genetic variants of uncertain clinical significance. Such tools allow us to parse through genetic data and emphasize potential splice-altering variants. Further variant assessment requires precise RNA assessment by agarose gel electrophoresis and/or cDNA Sanger sequencing. Results: We found two novel heterozygous variants in the coding region of the LYST gene (c.10104G>T, c.10894A>G) in an individual with a typical clinical presentation of Chediak–Higashi syndrome (CHS). The SpliceAI neural network predicted both variants as probably splice-altering. cDNA assessment by agarose gel electrophoresis revealed the presence of abnormally shortened splicing products in each variant’s case, and cDNA Sanger sequencing demonstrated that c.10104G>T and c.10894A>G substitutions resulted in a shortening of the 44 and 49 exons by 41 and 47 bp, respectively. Both mutations probably lead to a frameshift and the formation of a premature termination codon. This, in turn, may disrupt the structure and/or function of the LYST protein. Conclusions: We identified two novel variants in the LYST gene, predicted to be deleterious by the SpliceAI neural network. Agarose gel cDNA electrophoresis and cDNA Sanger sequencing allowed us to verify inappropriate splicing patterns and establish these variants as disease-causing. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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10 pages, 571 KiB  
Article
Sleep Genetics and Cognitive Changes over Time: The Moderating Effect of Age and the Role of Brain
by Angeliki Tsapanou, Seonjoo Lee, Silvia Chapman, Niki Mourtzi, Christian Habeck and Yaakov Stern
Genes 2025, 16(1), 21; https://doi.org/10.3390/genes16010021 - 26 Dec 2024
Viewed by 1787
Abstract
Background: Sleep plays a crucial role in cognitive performance and cognitive changes in aging. In the current study, we investigated the role of sleep duration genetics in cognitive changes over time and the moderating effect of age. Methods: Participants were drawn from the [...] Read more.
Background: Sleep plays a crucial role in cognitive performance and cognitive changes in aging. In the current study, we investigated the role of sleep duration genetics in cognitive changes over time and the moderating effect of age. Methods: Participants were drawn from the Reference Abilities Neural Network and the Cognitive Reserve studies of Columbia University. Each participant underwent an evaluation of sleep function and an extensive neuropsychological assessment. Published GWAS summary statistics from a polygenic score for sleep duration (Sleep PGI) were used to derive Sleep PGI in our study. We examined whether this Sleep PGI is associated with cognitive changes over a 5-year follow-up and if age moderates this effect. Analysis was performed after first being adjusted for age group (young: 20–44; middle: 45–64; old: 65–80), sex, education, the first four principal components, intracranial volume (ICV), mean cortical thickness, and total gray matter volume. We included ICV, mean thickness, and total gray matter volumes as time-varying covariates. We further included interactions of time with age and the first four PCs. Results: A total of 96 white-only participants were included, aged 24 to 78 years old. In the fully adjusted model, age-specific analysis showed that in younger individuals, higher Sleep PGI was associated with lower rates of cognitive decline in speed of processing. Conclusion: Genetic variants associated with sleep duration significantly influence performance in speed of processing, with age playing a critical moderating role, over and above brain morphometry. A genetic predisposition for longer sleep duration can work as a protective factor against decline in the speed of processing in young adults. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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20 pages, 2285 KiB  
Review
Advances in the Structure, Function, and Regulatory Mechanism of Plant Plasma Membrane Intrinsic Proteins
by Xueting Li, Yirong Guo, Qiuping Ling, Zhejun Guo, Yawen Lei, Xiaomin Feng, Jiayun Wu and Nannan Zhang
Genes 2025, 16(1), 10; https://doi.org/10.3390/genes16010010 - 25 Dec 2024
Viewed by 1439
Abstract
Plasma membrane intrinsic proteins (PIPs), as members of the aquaporin (AQPs) family, can transport not only water but also urea, CO2, H2O2, metal ions, and trace elements. They are crucial for maintaining water balance, substance transport, and [...] Read more.
Plasma membrane intrinsic proteins (PIPs), as members of the aquaporin (AQPs) family, can transport not only water but also urea, CO2, H2O2, metal ions, and trace elements. They are crucial for maintaining water balance, substance transport, and responding to various stresses. This article delves into the structure, function, response mechanism, molecular mechanism, and regulatory mechanism of PIPs as a result of biological and abiotic stresses. It also summarizes current research trends surrounding PIPs and highlights potential research directions for further exploration. The aim is to assist researchers in related fields in gaining a more comprehensive understanding and precise insight into the advancements in PIP research. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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14 pages, 781 KiB  
Article
Model Organisms in Aging Research: Evolution of Database Annotation and Ortholog Discovery
by Elizaveta Sarygina, Anna Kliuchnikova, Svetlana Tarbeeva, Ekaterina Ilgisonis and Elena Ponomarenko
Genes 2025, 16(1), 8; https://doi.org/10.3390/genes16010008 - 25 Dec 2024
Viewed by 1155
Abstract
Background: This study aims to analyze the exploration degree of popular model organisms by utilizing annotations from the UniProtKB (Swiss-Prot) knowledge base. The research focuses on understanding the genomic and post-genomic data of various organisms, particularly in relation to aging as an integral [...] Read more.
Background: This study aims to analyze the exploration degree of popular model organisms by utilizing annotations from the UniProtKB (Swiss-Prot) knowledge base. The research focuses on understanding the genomic and post-genomic data of various organisms, particularly in relation to aging as an integral model for studying the molecular mechanisms underlying pathological processes and physiological states. Methods: Having characterized the organisms by selected parameters (numbers of gene splice variants, post-translational modifications, etc.) using previously developed information models, we calculated proteome sizes: the number of possible proteoforms for each species. Our analysis also involved searching for orthologs of human aging genes within these model species. Results: Our findings indicate that genomic and post-genomic data for more primitive species, such as bacteria and fungi, are more comprehensively characterized compared to other organisms. This is attributed to their experimental accessibility and simplicity. Additionally, we discovered that the genomes of the most studied model organisms allow for a detailed analysis of the aging process, revealing a greater number of orthologous genes related to aging. Conclusions: The results highlight the importance of annotating the genomes of less-studied species to identify orthologs of marker genes associated with complex physiological processes, including aging. Species that potentially possess unique traits associated with longevity and resilience to age-related changes require comprehensive genomic studies. Full article
(This article belongs to the Special Issue Genes and Pathway Regulating Longevity in Model Organisms)
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15 pages, 1033 KiB  
Case Report
Utilization of RT-PCR and Optical Genome Mapping in Acute Promyelocytic Leukemia with Cryptic PML::RARA Rearrangement: A Case Discussion and Systemic Literature Review
by Giby V. George, Murad Elsadawi, Andrew G. Evans, Sarmad Ali, Bin Zhang and M. Anwar Iqbal
Genes 2025, 16(1), 7; https://doi.org/10.3390/genes16010007 - 25 Dec 2024
Cited by 1 | Viewed by 1301
Abstract
Background: Acute promyelocytic leukemia (APL) is characterized by abnormal promyelocytes and t(15;17)(q24;q21) PML::RARA. Rarely, patients may have cryptic or variant rearrangements. All-trans retinoic acid (ATRA)/arsenic trioxide (ATO) is largely curative provided that the diagnosis is established early. Methods: We present the case [...] Read more.
Background: Acute promyelocytic leukemia (APL) is characterized by abnormal promyelocytes and t(15;17)(q24;q21) PML::RARA. Rarely, patients may have cryptic or variant rearrangements. All-trans retinoic acid (ATRA)/arsenic trioxide (ATO) is largely curative provided that the diagnosis is established early. Methods: We present the case of a 36-year-old male who presented with features concerning for disseminated intravascular coagulation. Although the initial diagnostic work-up, including pathology and flow cytometry evaluation, suggested a diagnosis of APL, karyotype and fluorescence in situ hybridization (FISH), using the PML/RARA dual fusion and RARA breakapart probes, were negative. We performed real-time polymerase chain reaction (RT-PCR) and optical genome mapping (OGM) to further confirm the clinicopathological findings. Results: RT-PCR revealed a cryptic PML::RARA fusion transcript. OGM further confirmed the nature and orientation of a cryptic rearrangement with an insertion of RARA into PML at intron 3 (bcr3). In light of these findings, we performed a systematic literature review to understand the prevalence, diagnosis, and prognosis of APL with cryptic PML::RARA rearrangements. Conclusions: This case, in conjunction with the results of our systematic literature review, highlights the importance of performing confirmatory testing in FISH-negative cases of suspected APL to enable prompt diagnosis and appropriate treatment. Full article
(This article belongs to the Special Issue Clinical Cytogenetics: Current Advances and Future Perspectives)
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14 pages, 2743 KiB  
Article
Determination of Stable Reference Genes for Gene Expression Analysis in Black Rockfish (Sebastes schlegeli) Under Hypoxia Stress
by Xiatian Chen, Yujie Yu, Tao Gao, Zhifei Liu, Shuaiyu Chen and Yudong Jia
Genes 2025, 16(1), 9; https://doi.org/10.3390/genes16010009 - 25 Dec 2024
Cited by 1 | Viewed by 978
Abstract
Background: Hypoxia triggers stress, leading to significant alterations in gene expression patterns, which in turn affect fish’s growth and development. Real-time quantitative PCR (RT-qPCR) is a pivotal technique for assessing changes in gene expression. However, its accuracy is highly contingent upon the stable [...] Read more.
Background: Hypoxia triggers stress, leading to significant alterations in gene expression patterns, which in turn affect fish’s growth and development. Real-time quantitative PCR (RT-qPCR) is a pivotal technique for assessing changes in gene expression. However, its accuracy is highly contingent upon the stable expression of reference genes. Ribosomal RNA (18s), β-actin (actb), elongation factor 1-α (ef1a), α tubulin (tuba), and ribosomal protein L17 (rpl17) are the widely used reference genes, but their expression stability in the tissues of black rockfish under hypoxic conditions remains unclear. Methods: The expression of genes was detected by RT-qPCR and the stability was assessed by Delta Ct, geNorm, NormFinder, and BestKeeper algorithms. Results: Results showed that tuba exhibited stable expression in liver, heart, gill tissues under normoxic conditions, and in the liver and head kidney under hypoxic conditions. Ef1a was identified as the most stably expressed gene in gill tissue under hypoxia. For hypoxic heart studies, rpl17 and tuba were recommended as reference genes. 18s showed high stability in spleen tissue under hypoxic conditions. Actb was the most stably expressed gene in spleen and head kidney tissues under normoxic conditions. Conclusions: The identified reference genes exhibited tissue-specific stability, and it was necessary to select appropriate reference genes based on the specific tissue type for gene expression studies under hypoxic conditions. These findings help in enhancing the accuracy of gene expression analysis in the mechanism of hypoxia for black rockfish. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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24 pages, 6167 KiB  
Article
Transcriptomic Evidence Reveals the Dysfunctional Mechanism of Synaptic Plasticity Control in ASD
by Chao Kong, Zhitong Bing, Lei Yang, Zigang Huang, Wenxu Wang and Celso Grebogi
Genes 2025, 16(1), 11; https://doi.org/10.3390/genes16010011 - 25 Dec 2024
Cited by 1 | Viewed by 1311
Abstract
Background/Objectives: A prominent endophenotype in Autism Spectrum Disorder (ASD) is the synaptic plasticity dysfunction, yet the molecular mechanism remains elusive. As a prototype, we investigate the postsynaptic signal transduction network in glutamatergic neurons and integrate single-cell nucleus transcriptomics data from the Prefrontal Cortex [...] Read more.
Background/Objectives: A prominent endophenotype in Autism Spectrum Disorder (ASD) is the synaptic plasticity dysfunction, yet the molecular mechanism remains elusive. As a prototype, we investigate the postsynaptic signal transduction network in glutamatergic neurons and integrate single-cell nucleus transcriptomics data from the Prefrontal Cortex (PFC) to unveil the malfunction of translation control. Methods: We devise an innovative and highly dependable pipeline to transform our acquired signal transduction network into an mRNA Signaling-Regulatory Network (mSiReN) and analyze it at the RNA level. We employ Cell-Specific Network Inference via Integer Value Programming and Causal Reasoning (CS-NIVaCaR) to identify core modules and Cell-Specific Probabilistic Contextualization for mRNA Regulatory Networks (CS-ProComReN) to quantitatively reveal activated sub-pathways involving MAPK1, MKNK1, RPS6KA5, and MTOR across different cell types in ASD. Results: The results indicate that specific pivotal molecules, such as EIF4EBP1 and EIF4E, lacking Differential Expression (DE) characteristics and responsible for protein translation with long-term potentiation (LTP) or long-term depression (LTD), are dysregulated. We further uncover distinct activation patterns causally linked to the EIF4EBP1-EIF4E module in excitatory and inhibitory neurons. Conclusions: Importantly, our work introduces a methodology for leveraging extensive transcriptomics data to parse the signal transduction network, transforming it into mSiReN, and mapping it back to the protein level. These algorithms can serve as potent tools in systems biology to analyze other omics and regulatory networks. Furthermore, the biomarkers within the activated sub-pathways, revealed by identifying convergent dysregulation, illuminate potential diagnostic and prognostic factors in ASD. Full article
(This article belongs to the Section Bioinformatics)
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14 pages, 877 KiB  
Review
Hypoxia-Inducible Factor in Renal Cell Carcinoma: From Molecular Insights to Targeted Therapies
by Giandomenico Roviello, Irene De Gennaro, Ismaela Vascotto, Giulia Venturi, Alberto D’Angelo, Costanza Winchler, Adriana Guarino, Salvatore Cacioppo, Mikol Modesti, Marinella Micol Mela, Edoardo Francini, Laura Doni, Virginia Rossi, Elisabetta Gambale, Roberta Giorgione, Lorenzo Antonuzzo, Gabriella Nesi and Martina Catalano
Genes 2025, 16(1), 6; https://doi.org/10.3390/genes16010006 - 24 Dec 2024
Cited by 1 | Viewed by 2028
Abstract
Mutations of the von Hippel–Lindau (VHL) tumor suppressor gene occur frequently in clear cell renal cell carcinoma (RCC), the predominant histology of kidney cancer, and have been associated with its pathogenesis and progression. Alterations of VHL lead to impaired degradation of [...] Read more.
Mutations of the von Hippel–Lindau (VHL) tumor suppressor gene occur frequently in clear cell renal cell carcinoma (RCC), the predominant histology of kidney cancer, and have been associated with its pathogenesis and progression. Alterations of VHL lead to impaired degradation of hypoxia-inducible factor 1α (HIF1α) and HIF2α promoting neoangiogenesis, which is pivotal for cancer growth. As such, targeting the VHL-HIF axis holds relevant potential for therapeutic purposes. Belzutifan, an HIF-2α inhibitor, has been recently indicated for metastatic RCC and other antiangiogenic drugs directed against HIF-2α are currently under investigation. Further, clinical and preclinical studies of combination approaches for metastatic RCC including belzutifan with cyclin-dependent kinase 4–6 inhibitors, tyrosine kinase inhibitors, or immune checkpoint inhibitors achieved promising results or are ongoing. This review aims to summarize the existing evidence regarding the VHL/HIF pathway, and the approved and emerging treatment strategies that target this pivotal molecular axis and their mechanisms of resistance. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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11 pages, 3326 KiB  
Article
Construction of Promoter Elements for Strong, Moderate, and Weak Gene Expression in Drosophila melanogaster
by Ksenia S. Kudryashova, Irina O. Deriglazova, Igor S. Osadchiy, Pavel Georgiev and Oksana Maksimenko
Genes 2025, 16(1), 3; https://doi.org/10.3390/genes16010003 - 24 Dec 2024
Viewed by 1380
Abstract
Background/Objectives: Transcriptional promoters play an essential role in regulating protein expression. Promoters with weak activity generally lead to low levels of expression, resulting in fewer proteins being produced. At the same time, strong promoters are commonly used in studies using transgenic organisms as [...] Read more.
Background/Objectives: Transcriptional promoters play an essential role in regulating protein expression. Promoters with weak activity generally lead to low levels of expression, resulting in fewer proteins being produced. At the same time, strong promoters are commonly used in studies using transgenic organisms as model systems. This approach can have various negative consequences for the organism, as many regulatory proteins need to be expressed in small quantities, and excessive expression can have harmful effects on cells and organisms. Therefore, it is important to select the right promoter when creating transgenic organisms for research and practical applications. Methods: In this study, we used the Drosophila melanogaster genome as a source of natural promoter sequences for RNA polymerase II. These sequences were extracted and used to create a set of promoters that are suitable for practical application. The promoters were tested in a model system using fluorescent reporter genes in S2 cells and transgenic lines of Drosophila. Results: We assessed the expression levels of fluorescent reporter genes to rank the tested promoters from strongest to weakest. Six individual promoters of different sizes were established and compared. Additionally, we designed and tested three pairs of bidirectional promoters that could be used to simultaneously express two proteins. Conclusions: Based on our findings, we grouped the tested promoters into three categories: strong, moderate, and weak. These promoters can be utilized in transgenic model systems for protein production at different levels, from high to low. Bidirectional promoters, constructed “head-to-head”, meaning oppositely directed with the minimum distance between them, represent a novel tool for the co-expression of proteins. Full article
(This article belongs to the Section Technologies and Resources for Genetics)
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15 pages, 6261 KiB  
Article
Metabolomics and WGCNA Analyses Reveal the Underlying Mechanisms of Resistance to Botrytis cinerea in Hazelnut
by Jun Sun, Liyuan Lu, Juanjuan Liu, Yanhong Cui, Hanqi Liu, Yue Zhang, Zeyang Zheng and Weicong Yang
Genes 2025, 16(1), 2; https://doi.org/10.3390/genes16010002 - 24 Dec 2024
Viewed by 1118
Abstract
Background: Hazelnut (Corylus), a significant woody oil tree species in economic forests, faces production constraints due to biotic stresses, with Hazelnut Husk Brown Rot, caused by the pathogenic necrotrophic fungus Botrytis cinerea (B. cinerea), being the most severe. To [...] Read more.
Background: Hazelnut (Corylus), a significant woody oil tree species in economic forests, faces production constraints due to biotic stresses, with Hazelnut Husk Brown Rot, caused by the pathogenic necrotrophic fungus Botrytis cinerea (B. cinerea), being the most severe. To date, limited information is available regarding the resistance of hazelnuts to B. cinerea. To better understand the mechanisms of resistance to B. cinerea. in hazelnut, we conducted metabolomics and WGCNA analyses of a B. cinerea-resistant Ping’ou hybrid hazelnut variety (Dawei; DW) and a susceptible variety (Qiuxiang; QX). Methods: In this study, metabolomics and weighted gene co-expression network analysis (WGCNA, weighted correlation network analysis) were applied to elucidate the resistance mechanisms underlying different hazelnut varieties to B. cinerea. Our study focused on the metabolome profiles of DW and QX plants after 72 h of B. cinerea infection. Results: Venn analysis of QX_0 vs. DW_0 and QX_72 vs. DW_72 revealed 120 differential accumulation metabolites (DAMs) that were upregulated. Among these metabolites, the concentrations of flavonoids and phenolic acids in DW were significantly higher than those in QX, respectively, suggesting that the elevated levels of these compounds contribute substantially to the resistance of hazelnut against B. cinerea. 3,4-hydroxyphenyllactic acid and phloretin were significantly more abundant in accumulation in DW than in QX after infection by B. cinerea. Conclusions: This study provides that the elevated levels of these compounds (flavonoids and phenolic acids) contribute substantially to the resistance of hazelnut against B. cinerea. Furthermore, 3,4-hydroxyphenyllactic acid and phloretin were identified as pivotal metabolites in modulating the resistance of hazelnut to B. cinerea. Through WGCNA analyses, we identified four transcription factors (WRKY19, HSFC1, ERF071, and RAP2-1) that are most likely to regulate the synthesis of 3,4-dihydroxyphenyllactic acid and phloretin. This study provides crucial insights for further investigation into the regulatory network of metabolites associated with hazelnut resistance to B. cinerea. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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22 pages, 1322 KiB  
Review
Genetic Etiology in Pelvic Organ Prolapse: Role of Connective Tissue Homeostasis, Hormone Metabolism, and Oxidative Stress
by Wenxuan Jiang, Rachel Yau Kar Cheung, Cheuk Yan Chung, Symphorosa Shing Chee Chan and Kwong Wai Choy
Genes 2025, 16(1), 5; https://doi.org/10.3390/genes16010005 - 24 Dec 2024
Cited by 1 | Viewed by 1523
Abstract
Background: Pelvic organ prolapse (POP) has become a common health problem among the aging population and affects an increasing number of elderly women worldwide. Studies within family and twin pairs provided strong evidence for the contribution of genetic factors to POP. Given [...] Read more.
Background: Pelvic organ prolapse (POP) has become a common health problem among the aging population and affects an increasing number of elderly women worldwide. Studies within family and twin pairs provided strong evidence for the contribution of genetic factors to POP. Given the incomplete penetrance, polygenic traits, and small effect sizes of each variant in complex diseases, it is not always easy to evaluate the genetic susceptibility and molecular mechanisms involved in POP. Objectives: This review intends to comprehensively summarize the current studies on genetic variants associated with POP. Methods: We performed a comprehensive review to summarize the genetic findings from genome-linkage studies, genome-wide association studies, candidate association studies, and gene expression analyses. Results: We summarized genetic variants associated with connective tissue homeostasis, hormone metabolism, and oxidative stress, which were potentially related to the pathophysiology of POP. We also reviewed the limited polygenic risk score (PRS) studies generated for each individual’s genetic risk stratification and its integration into clinical risk factors for disease prediction. Conclusions: This pooled analysis provides moderate epidemiological credibility for associations of these genetic variants with POP to bridge the gap between genetic research and clinical medicine towards understanding the genetic etiology of POP. It also highlights the potential of PRS as a risk prediction model. Full article
(This article belongs to the Special Issue Genetic Advances and Challenges in Complex Diseases)
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16 pages, 569 KiB  
Article
Maximal Fat Oxidation During Exercise in Healthy Individuals: Lack of Genetic Association with the FTO rs9939609 Polymorphism
by Teresa García-Pastor, Iván Muñoz-Puente, Miriam Pérez-Pelayo, Isabel Púa, Justin D. Roberts and Juan Del Coso
Genes 2025, 16(1), 4; https://doi.org/10.3390/genes16010004 - 24 Dec 2024
Cited by 2 | Viewed by 1350
Abstract
Background/Objectives: Previous studies suggest that there is a genetically determined component of fat oxidation at rest and during exercise. To date, the FTO gene has been proposed as a candidate gene to affect fat oxidation during exercise because of the association of [...] Read more.
Background/Objectives: Previous studies suggest that there is a genetically determined component of fat oxidation at rest and during exercise. To date, the FTO gene has been proposed as a candidate gene to affect fat oxidation during exercise because of the association of the “at-risk” A allele with different obesity-related factors such as increased body fat, higher appetite and elevated insulin and triglyceride levels. The A allele of the FTO gene may also be linked to obesity through a reduced capacity for fat oxidation during exercise, a topic that remains largely underexplored in the current literature. The aim of this study was to analyze the association between the FTO rs9939609 polymorphism with the rate of fat oxidation during exercise and metabolic syndrome criteria in healthy participants. Methods: A total of 80 healthy participants (41 men and 39 women) underwent comprehensive assessments, including measurements of anthropometric variables, blood pressure and blood measures of fasting glucose, triglycerides, low- and high-density lipoprotein cholesterol (LDL-c and HDL-c), insulin, interleukin-6 (IL-6) and C-reactive protein (CRP) concentrations. Additionally, the Homeostatic Model Assessment (HOMA-IR) was used to evaluate insulin resistance. Peak oxygen uptake (VO2peak) and maximal fat oxidation rate (MFO) were also measured during an incremental cycling test. FTO rs9939609 genotyping (TT, AT, AA) was performed using genomic DNA samples obtained from a buccal swab and measured with PCR. Results: There were 32 participants (40.0%) with the TT genotype; 31 (38.8%) with the AT genotype; and 17 (21.2%) with the AA genotype. Age, body characteristics, VO2peak, blood pressure and blood variables were similar across all three genotypes. However, serum insulin concentration and HOMA-IR were associated with the FTO rs9939609 genotype with higher values in AA with respect to AT and TT participants (p < 0.050). Still, MFO was similar in TT, AT and AA participants (0.35 ± 0.13, 0.37 ± 0.11, 0.33 ± 0.11 g/min, p = 0.702). In the dominant model, there was no statistical difference between TT and A allele carriers. However, the recessive model revealed that AA participants had higher values of body mass, body mass index, blood insulin concentration and HOMA-IR than T allele carriers (p < 0.050), with no differences in MFO. Conclusions: In our sample of healthy individuals, the FTO rs9939609 polymorphism was associated with several phenotypes associated with obesity and insulin resistance, particularly under the AA vs. T allele/recessive model. However, the FTO rs9939609 polymorphism was not associated with MFO during exercise as fat oxidation was similar across genotypes. This suggests that reduced fat oxidation during exercise is unlikely to be a cause of the obesogenic influence of the FTO AA genotype. Clinically, these findings suggest that the obesogenic effects of the FTO AA genotype are unlikely driven by impaired fat oxidation during exercise. Instead, attention should focus on mechanisms like appetite regulation and energy intake. Moreover, exercise interventions may still effectively mitigate obesity risk, as AA individuals retain normal fat oxidation capacity during exercise. Full article
(This article belongs to the Special Issue Molecular Genetics in Obesity and Metabolic Syndrome)
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5 pages, 141 KiB  
Editorial
Genetic and Epigenetic Insights into Pregnancy-Related Complications
by Nihar R. Nayak, Akhilesh Srivastava, Manoj Kumar Jena, Anthony Odibo and Gary Sutkin
Genes 2025, 16(1), 1; https://doi.org/10.3390/genes16010001 - 24 Dec 2024
Cited by 1 | Viewed by 1357
Abstract
Placental dysfunction is a leading cause of numerous pregnancy complications, including preeclampsia, preterm birth, fetal growth restrictions, placental abruption, and late spontaneous abortion [...] Full article
(This article belongs to the Special Issue Genetic and Epigenetic Regulation of Placental Development and Disease)
12 pages, 1476 KiB  
Article
Genetic Association Study of Acetylcholinesterase (ACHE) and Butyrylcholinesterase (BCHE) Variants in Sudden Infant Death Syndrome (SIDS)
by Dong Qu, Peter Schürmann, Thomas Rothämel, Thilo Dörk and Michael Klintschar
Genes 2024, 15(12), 1656; https://doi.org/10.3390/genes15121656 - 23 Dec 2024
Viewed by 1045
Abstract
Background: Sudden infant death syndrome (SIDS) is the leading cause of death among infants aged between one month and one year. Altered enzyme activities or expression of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) have been observed in SIDS patients that might lead to disturbed [...] Read more.
Background: Sudden infant death syndrome (SIDS) is the leading cause of death among infants aged between one month and one year. Altered enzyme activities or expression of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) have been observed in SIDS patients that might lead to disturbed autonomic function and, together with other risk factors, might trigger SIDS. To explore the contribution of AChE and BChE from a genomic viewpoint, we sought to investigate the association between SIDS and selected single nucleotide polymorphisms (SNPs) in the ACHE and BCHE genes. Methods: In this case-control study, 13 potentially regulatory SNPs were selected from ACHE and BCHE and were genotyped in 201 SIDS cases and 338 controls. The association of SIDS with the 11 successfully genotyped candidate variants was examined using statistical analyses of overall or stratified cases and haplotype analyses. Results: No significant overall associations were observed between SIDS and ACHE and BCHE variants in allele, genotype, and haplotype analyses. In subgroup analyses, eight variants were found to be nominally associated with SIDS, though these associations did not remain statistically significant after correction for multiple comparisons. One haplotype (T-C-G-C-C in rs3495-rs1803274-rs1355538-rs2048493-rs1126680) of BCHE was associated with the female SIDS subgroup (57.3% in controls vs. 46.3% in female SIDS cases, p = 0.010). Conclusions: The selected variants in ACHE and BCHE were not overall associated with SIDS in this study, and thus cannot generally explain the previously reported dysregulation of enzyme activities in SIDS. However, some evidence of association in subgroups and a possible contribution of variants other than those tested here would need to be explored in larger studies. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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17 pages, 2616 KiB  
Article
Exploring the Role of FICD, a New Potential Gene Involved in Borderline Intellectual Functioning, Psychological and Metabolic Disorders
by Mirella Vinci, Donatella Greco, Maria Grazia Figura, Simone Treccarichi, Antonino Musumeci, Vittoria Greco, Rossella Pettinato, Angelo Gloria, Carla Papa, Salvatore Saccone, Concetta Federico and Francesco Calì
Genes 2024, 15(12), 1655; https://doi.org/10.3390/genes15121655 - 23 Dec 2024
Cited by 1 | Viewed by 1070
Abstract
Background/Objectives: AMPylation is a post-translational modification involving the transfer of adenosine monophosphate (AMP) from adenosine triphosphate (ATP) to target proteins, serving as a critical regulatory mechanism in cellular functions. This study aimed to expand the phenotypic spectrum associated with mutations in the FICD [...] Read more.
Background/Objectives: AMPylation is a post-translational modification involving the transfer of adenosine monophosphate (AMP) from adenosine triphosphate (ATP) to target proteins, serving as a critical regulatory mechanism in cellular functions. This study aimed to expand the phenotypic spectrum associated with mutations in the FICD gene, which encodes an adenyltransferase enzyme involved in both AMPylation and deAMPylation. Methods: A clinical evaluation was conducted on a patient presenting with a complex clinical profile. Whole-exome sequencing (WES) was performed to identify potential genetic variants contributing to the observed phenotype. Results: The patient exhibited borderline intellectual functioning (BIF), acanthosis, abdominal muscle hypotonia, anxiety, depression, obesity, and optic nerve subatrophy. WES revealed a de novo missense variant, c.1295C>T p.Ala432Val, in the FICD gene. This variant, classified as of uncertain significance, is located in the highly conserved region TLLFATTEY (aa 428–436), suggesting a potential impact on protein function. Conclusions: These findings highlight the importance of the FICD gene in diverse clinical manifestations and emphasize the need for further studies to elucidate the genetic mechanisms underlying these phenotypes. Continued research is essential to improve our understanding of FICD-related conditions. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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33 pages, 4545 KiB  
Review
Chemical and Biological Investigations of Antiviral Agents Against Plant Viruses Conducted in China in the 21st Century
by Yuanyou Yang, Lei Hu, Tongtong Chen, Libo Zhang, Delu Wang and Zhuo Chen
Genes 2024, 15(12), 1654; https://doi.org/10.3390/genes15121654 - 23 Dec 2024
Viewed by 1656
Abstract
Research into the biology of plant viruses, their mechanisms of pathogenicity, and the induction of host resistance has laid a solid foundation for the discovery of antiviral agents and their targets and the development of effective control technologies. Additionally, recent advancements in fields [...] Read more.
Research into the biology of plant viruses, their mechanisms of pathogenicity, and the induction of host resistance has laid a solid foundation for the discovery of antiviral agents and their targets and the development of effective control technologies. Additionally, recent advancements in fields such as chemical biology, cheminformatics, bioinformatics, and synthetic biology have provided valuable methods and tools for the design of antiviral drugs, the synthesis of drug molecules, assessment of their activity, and investigation of their modes of action. Compared with drug development for human viral diseases, the control of plant viral diseases presents greater challenges, including the cost-benefit of agents, simplification of control technologies, and the effectiveness of treatments. Therefore, in the current context of complex outbreaks and severe damage caused by plant viral diseases, it is crucial to delve deeper into the research and development of antiviral agents. This review provides a detailed overview of the biological characteristics of current targets for antiviral agents, the mode of interaction between plant virus targets and antivirals, and insights for future drug development. We believe this review will not only facilitate the in-depth analysis of the development of antivirals for crops but also offer valuable perspectives for the development of antiviral agents for use in human and veterinary medicine. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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25 pages, 779 KiB  
Review
Epigenetic Regulation and Neurodevelopmental Disorders: From MeCP2 to the TCF20/PHF14 Complex
by Gaea Dominguez, Yongji Wu and Jian Zhou
Genes 2024, 15(12), 1653; https://doi.org/10.3390/genes15121653 - 23 Dec 2024
Cited by 1 | Viewed by 2439
Abstract
Background: Neurodevelopmental disorders (NDDs) affect approximately 15% of children and adolescents worldwide. This group of disorders is often polygenic with varying risk factors, with many associated genes converging on shared molecular pathways, including chromatin regulation and transcriptional control. Understanding how NDD-associated chromatin regulators [...] Read more.
Background: Neurodevelopmental disorders (NDDs) affect approximately 15% of children and adolescents worldwide. This group of disorders is often polygenic with varying risk factors, with many associated genes converging on shared molecular pathways, including chromatin regulation and transcriptional control. Understanding how NDD-associated chromatin regulators and protein complexes orchestrate these regulatory pathways is crucial for elucidating NDD pathogenesis and developing targeted therapeutic strategies. Recently, the TCF20/PHF14 chromatin complex was identified in the mammalian brain, expanding the list of chromatin regulatory remodelers implicated in NDDs. This complex—which includes MeCP2, RAI1, TCF20, PHF14, and HMG20A—plays a vital role in epigenetic and transcriptional regulation. Methods: We review and summarize current research and clinical reports pertaining to the different components of the MeCP2-interacting TCF20/PHF14 complex. We examine the NDDs associated with the TCF20/PHF14 complex, explore the molecular and neuronal functions of its components, and discuss emerging therapeutic strategies targeting this complex to mitigate symptoms, with broader applicability to other NDDs. Results: Mutations in the genes encoding the components of the MeCP2-interacting TCF20/PHF14 complex have been linked to various NDDs, underscoring its critical contribution to brain development and NDD pathogenesis. Conclusions: The MeCP2-interacting TCF20/PHF14 complex and its associated NDDs could serve as a model system to provide insight into the interplay between epigenetic regulation and NDD pathogenesis. Full article
(This article belongs to the Special Issue The Genetic and Epigenetic Basis of Neurodevelopmental Disorders)
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14 pages, 4479 KiB  
Article
Genetic Mapping by 55K Single-Nucleotide Polymorphism Array Reveals Candidate Genes for Tillering Trait in Wheat Mutant dmc
by Kemeng Jiao, Guojun Xia, Yuan Zhou, Chenyu Zhao, Huiyuan Yan, Menglei Qi, Pingfan Xie, Yongjing Ni, Jingxue Zhao, Jishan Niu, Zhaofei Chao, Jiangping Ren and Lei Li
Genes 2024, 15(12), 1652; https://doi.org/10.3390/genes15121652 - 22 Dec 2024
Cited by 1 | Viewed by 1237
Abstract
Background: The tiller number is a key agronomic trait for increasing the yield potential of wheat (Triticum aestivum L.). A number of quantitative trait loci (QTLs) and key genes controlling tillering have been identified, but the regulatory mechanisms remain unclear. Methods: In [...] Read more.
Background: The tiller number is a key agronomic trait for increasing the yield potential of wheat (Triticum aestivum L.). A number of quantitative trait loci (QTLs) and key genes controlling tillering have been identified, but the regulatory mechanisms remain unclear. Methods: In this study, we utilized the dwarf-monoculm mutant (dmc) obtained from the ethyl methane sulfonate (EMS)-treated wheat cultivar Guomai 301. The F2 populations were constructed using the dmc mutant crossed to multiple tiller parents. The F2 populations were surveyed for tillering traits at the critical fertility stage for genetic analyses. The extreme-tillering-phenotype plants from the F2 population were used to construct mixing pools that were analyzed by a wheat 55K SNP array. The tillering genes of dmc were mapped using the wheat 55K SNP array combined with transcriptomic data. Results: The results showed that the genetic phenotype of dmc is controlled by two dominant genes. The tillering genes of dmc were mapped on the 60–100 Mb region of chromosome 5B and the 135–160 Mb region of chromosome 7A. A total of sixteen candidate genes associated with the tillering trait of dmc were identified. Two candidate genes, TraesCS5B02G058800 and TraesCS7A02G184200, were predicted to be involved in indole acetic acid (IAA) response and transport, which were considered as potential regulatory genes. Conclusions: This study elucidated the genetic basis of the dmc mutant and provided two valuable reference genes for studying the development and regulatory mechanisms of wheat tillering. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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15 pages, 687 KiB  
Review
Federated Learning: Breaking Down Barriers in Global Genomic Research
by Giulia Calvino, Cristina Peconi, Claudia Strafella, Giulia Trastulli, Domenica Megalizzi, Sarah Andreucci, Raffaella Cascella, Carlo Caltagirone, Stefania Zampatti and Emiliano Giardina
Genes 2024, 15(12), 1650; https://doi.org/10.3390/genes15121650 - 22 Dec 2024
Cited by 5 | Viewed by 2258
Abstract
Recent advancements in Next-Generation Sequencing (NGS) technologies have revolutionized genomic research, presenting unprecedented opportunities for personalized medicine and population genetics. However, issues such as data silos, privacy concerns, and regulatory challenges hinder large-scale data integration and collaboration. Federated Learning (FL) has emerged as [...] Read more.
Recent advancements in Next-Generation Sequencing (NGS) technologies have revolutionized genomic research, presenting unprecedented opportunities for personalized medicine and population genetics. However, issues such as data silos, privacy concerns, and regulatory challenges hinder large-scale data integration and collaboration. Federated Learning (FL) has emerged as a transformative solution, enabling decentralized data analysis while preserving privacy and complying with regulations such as the General Data Protection Regulation (GDPR). This review explores the potential use of FL in genomics, detailing its methodology, including local model training, secure aggregation, and iterative improvement. Key challenges, such as heterogeneous data integration and cybersecurity risks, are examined alongside regulations like GDPR. In conclusion, successful implementations of FL in global and national initiatives demonstrate its scalability and role in supporting collaborative research. Finally, we discuss future directions, including AI integration and the necessity of education and training, to fully harness the potential of FL in advancing precision medicine and global health initiatives. Full article
(This article belongs to the Special Issue Bioinformatics and Computational Genomics)
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18 pages, 1681 KiB  
Article
Complete Genome Assembly of Amycolatopsis bartoniae DSM 45807T Allows the Characterization of a Novel Glycopeptide Biosynthetic Gene Cluster
by Anastasia Stepanyshyn, Christian Rückert-Reed, Tobias Busche, Bohdan Yaruta, Andres Andreo-Vidal, Flavia Marinelli, Jörn Kalinowski and Oleksandr Yushchuk
Genes 2024, 15(12), 1651; https://doi.org/10.3390/genes15121651 - 22 Dec 2024
Cited by 1 | Viewed by 1085
Abstract
Background: Glycopeptide antibiotics (GPAs) are a very successful class of clinically relevant antibacterials, used to treat severe infections caused by Gram-positive pathogens, e.g., multidrug resistant and methicillin-resistant staphylococci. The biosynthesis of GPAs is coded within large biosynthetic gene clusters (BGCs). In recent years, [...] Read more.
Background: Glycopeptide antibiotics (GPAs) are a very successful class of clinically relevant antibacterials, used to treat severe infections caused by Gram-positive pathogens, e.g., multidrug resistant and methicillin-resistant staphylococci. The biosynthesis of GPAs is coded within large biosynthetic gene clusters (BGCs). In recent years, modern DNA sequencing technologies have allowed the identification and characterization of multiple novel GPA BGCs, leading to the discovery of novel compounds. Our previous research anticipated that the genome of Amycolatopsis bartoniae DSM 45807T carries a novel GPA BGC, although the genomic sequence quality available at that time did not allow us to characterize its organization properly. Objectives: To address this gap, in the current work we aimed to produce a complete genome assembly of A. bartoniae DSM 45807, and to identify and analyze the corresponding GPA BGC. Methods: Bioinformatic and microbiological methods were utilized in this research. Results: We de novo sequenced and completely assembled the genome of A. bartoniae DSM 45807, and fully characterized the BGC of interest, named aba. This BGC has an unusual gene organization and it contains four genes for sulfotransferases, which are considered to be rare in GPA BGCs. Our pathway prediction indicated that aba encodes the biosynthesis of a putatively novel GPA, although we were not able to detect any GPA production under different cultivation conditions, implying that aba pathway is inactive. Conclusions: Our results indicate aba as a promising source for new GPA tailoring enzymes. Full article
(This article belongs to the Section Microbial Genetics and Genomics)
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17 pages, 2764 KiB  
Article
Drought Stress Inhibits the Accumulation of Rotenoids and the Biosynthesis of Drought-Responsive Phytohormones in Mirabilis himalaica (Edgew.) Heim Calli
by Shiyi Zhang, Jiaqi Gao, Xiaozhong Lan, Linfan Zhang, Weipeng Lian, Chenglin Wang, Zhanyun Shen, Xiang Li and Juan Liu
Genes 2024, 15(12), 1644; https://doi.org/10.3390/genes15121644 - 21 Dec 2024
Viewed by 1048
Abstract
Background: Mirabilis himalaica, distributed in the high-altitude, arid, and semi-arid regions of Xizang, exhibits great tolerance to drought, which is rich in rotenoids and other secondary metabolites. It is still unknown, though, how drought stress influences rotenoid synthesis in M. himalaica [...] Read more.
Background: Mirabilis himalaica, distributed in the high-altitude, arid, and semi-arid regions of Xizang, exhibits great tolerance to drought, which is rich in rotenoids and other secondary metabolites. It is still unknown, though, how drought stress influences rotenoid synthesis in M. himalaica. Methods: In this study, the calli of M. himalaica were subjected to 5% PEG6000 for 0, 20, and 40 h and divided into control group (CK), mild-drought-treated group (M), and high-drought-treated group (H), respectively. We then analyzed the relative content of three main rotenoids in M. himalaica using high-performance liquid chromatography–electrospray ionization–tandem mass spectrometry (HPLC-ESI-MS/MS). Results: Our findings demonstrated that the content of rotenoids was significantly reduced under drought stress. Transcriptome analysis subsequently revealed 14,525 differentially expressed genes (DEGs) between the different treatments. Furthermore, these DEGs exhibited enrichment in pathways associated with isoflavone biosynthesis and hormone signaling pathways. Key genes with decreased expression patterns during drought stress were also found to be involved in rotenoid accumulation and drought-responsive phytohormone signaling, including abscisic acid (ABA), auxin (IAA), and jasmonic acid (JA). Conclusions: These findings elucidate the molecular processes of drought resistance in M. himalaica and shed light on the relationship between rotenoid production and drought stress in M. himalaica. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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17 pages, 7574 KiB  
Article
Identification of Retrocopies in Lepidoptera and Impact on Domestication of Silkworm
by Lingzi Bie, Jiahe Sun, Yi Wang and Chunfang Wang
Genes 2024, 15(12), 1641; https://doi.org/10.3390/genes15121641 - 21 Dec 2024
Viewed by 627
Abstract
Background: During the domestication of silkworm, an economic insect, its physiological characteristics have changed greatly. RNA-based gene duplication, known as retrocopy, plays an important role in the formation of new genes and genome evolution, but the retrocopies of lepidopteran insects have not been [...] Read more.
Background: During the domestication of silkworm, an economic insect, its physiological characteristics have changed greatly. RNA-based gene duplication, known as retrocopy, plays an important role in the formation of new genes and genome evolution, but the retrocopies of lepidopteran insects have not been fully identified and analyzed, which not only severely limits researchers from exploring the effects of retrocopies on lepidopteran insects but also affects the studies on the domestication of silkworm. Methods: We compared the genomes and proteomes of eight lepidopteran insects and used a series of screening criteria for auxiliary screening to obtain the retrocopies in lepidopteran insects and explored their characteristics. In addition, based on the silkworm transcriptome data from the SilkDB3.0 website, we explored the functions of the retrocopies on the domestication of the silkworm. Results: A total of 1993 retrocopies and 1208 parental genes in lepidopteran insects were obtained. We revealed that the retrocopies in Lepidoptera do not conform to the “out of X” hypothesis but fit the “out of testis” hypothesis. These retrocopies were subject to strong functional constraints and performed important functions in growth and development. Transcriptome analysis revealed that the expression pattern of the retrocopies and their parental genes were irrelevant. Through the analysis of the retrocopies in silkworm generated after domestication and located in the candidate domestication regions, the possible universal connection between the retrocopies and the domestication of silkworm were found. Conclusions: Our study pioneered the exploration of retrocopies in multiple Lepidoptera species and found the potential association between the retrocopies and the domestication of silkworm. Full article
(This article belongs to the Special Issue Genomics, Transcriptomics, and Proteomics of Insects)
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22 pages, 4014 KiB  
Article
Genomic Analysis of Talaromyces verruculosus SJ9: An Efficient Tetracycline-, Enrofloxacin-, and Tylosin-Degrading Fungus
by Jing Fu, Xiaoqing Wu, Chi Zhang, Yuhan Tang, Fangyuan Zhou, Xinjian Zhang and Susu Fan
Genes 2024, 15(12), 1643; https://doi.org/10.3390/genes15121643 - 21 Dec 2024
Viewed by 896
Abstract
Background/Objectives: Many fungi related to Talaromyces verruculosus can degrade a wide range of pollutants and are widely distributed globally. T. verruculosus SJ9 was enriched from fresh strawberry inter-root soil to yield fungi capable of degrading tetracycline, enrofloxacin, and tylosin. Methods: T. verruculosus SJ9 [...] Read more.
Background/Objectives: Many fungi related to Talaromyces verruculosus can degrade a wide range of pollutants and are widely distributed globally. T. verruculosus SJ9 was enriched from fresh strawberry inter-root soil to yield fungi capable of degrading tetracycline, enrofloxacin, and tylosin. Methods: T. verruculosus SJ9 genome was sequenced, assembled, and annotated in this study utilizing bioinformatics software, PacBio, and the Illumina NovaSeq PE150 technology. Results: The genome size is 40.6 Mb, the N50 scaffold size is 4,534,389 bp, and the predicted number of coding genes is 8171. The T. verruculosus TS63-9 genome has the highest resemblance to the T. verruculosus SJ9 genome, according to a comparative genomic analysis of seven species. In addition, we annotated many genes encoding antibiotic-degrading enzymes in T. verruculosus SJ9 through genomic databases, which also provided strong evidence for its ability to degrade antibiotics. Conclusions: Through the correlation analysis of the whole-genome data of T. verruculosus SJ9, we identified a number of genes capable of encoding antibiotic-degrading enzymes in its gene function annotation database. These antibiotic-related enzymes provide some evidence that T. verruculosus SJ9 can degrade fluoroquinolone antibiotics, tetracycline antibiotics, and macrolide antibiotics. In summary, the complete genome sequence of T. verruculosus SJ9 has now been published, and this resource constitutes a significant dataset that will inform forthcoming transcriptomic, proteomic, and metabolic investigations of this fungal species. In addition, genomic studies of other filamentous fungi can utilize it as a reference. Thanks to the discoveries made in this study, the future application of this fungus in industrial production will be more rapid. Full article
(This article belongs to the Section Microbial Genetics and Genomics)
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13 pages, 2314 KiB  
Article
Complete Mitochondrial Genomes of Pluvialis fulva and Charadrius dubius with Phylogenetic Analysis of Charadriiformes
by Kuo Sun, Qingxiong Wang, Kun Bian, Feiran Li, Jie Tang, Lijuan Suo, Xiang Hou and Chao Yang
Genes 2024, 15(12), 1642; https://doi.org/10.3390/genes15121642 - 21 Dec 2024
Viewed by 746
Abstract
Background: Plovers (Charadriidae), within the order of Charadriiformes, a group of modern birds distributed worldwide, are a frequent subject of molecular phylogenetic studies. While research on mitochondrial genome (mitogenome) variation within the family Charadriidae, especially intraspecific variation, is limited. Additionally, the monophyly of [...] Read more.
Background: Plovers (Charadriidae), within the order of Charadriiformes, a group of modern birds distributed worldwide, are a frequent subject of molecular phylogenetic studies. While research on mitochondrial genome (mitogenome) variation within the family Charadriidae, especially intraspecific variation, is limited. Additionally, the monophyly of Charadrius and the phylogenetic placement of Pluvialis remain contentious. Nevertheless, recent studies utilizing complete mitogenomes from available databases to construct phylogenetic trees for Charadriidae and Charadriiformes remain scarce. Methods: This study aims to explore mitogenome variation within Charadrius dubius and clarify the phylogenetic placement of Pluvialis fulva. We sequenced the complete mitogenome of six C. dubius and one P. fulva, and all additional available mitogenomes were integrated within Charadriiformes. The average complete mitogenome length of C. dubius is 16,889 bp, and P. fulva is 16,859 bp. Results: Our results support the suggestion that the monophyly of Charadrius and P. fulva is nested within Charadriidae. The phylogenetic analysis of Charadriiformes based on mitogenomes strongly supports the recognition of three major shorebird clades: Charadrii, Lari and Scolopaci, with Lari and Scolopaci identified as sister clades. Conclusions: Our study reinforces the credibility of the inferred evolutionary relationships within Charadriidae and Charadriiformes. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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