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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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26 pages, 362 KiB  
Review
Immune Repertoires in Various Dermatologic and Autoimmune Diseases
by Hanna Terhaar, Victoria Jiminez, Emily Grant, Camden Collins, Mohamed Khass and Nabiha Yusuf
Genes 2024, 15(12), 1591; https://doi.org/10.3390/genes15121591 - 11 Dec 2024
Viewed by 2224
Abstract
The immune repertoire (IR) is a term that defines the combined unique genetic rearrangements of antigen receptors expressed by B and T lymphocytes. The IR determines the ability of the immune system to identify and respond to foreign antigens while preserving tolerance to [...] Read more.
The immune repertoire (IR) is a term that defines the combined unique genetic rearrangements of antigen receptors expressed by B and T lymphocytes. The IR determines the ability of the immune system to identify and respond to foreign antigens while preserving tolerance to host antigens. When immune tolerance is disrupted, development of autoimmune diseases can occur due to the attack of self-antigens. Recent technical advances in immune profiling allowed identification of common patterns and shared antigen-binding sequences unique to diverse array of diseases. However, there is no current literature to date evaluates IR findings in autoimmune and skin inflammatory conditions. In this review, we provide an overview of the past and current research findings of IR in various autoimmune and dermatologic conditions. Enriching our understanding of IRs in these conditions is critical for understanding the pathophysiology behind autoimmune skin disease onset and progression. Furthermore, understanding B-cell and T-cell IR will help devise therapeutic treatments in the hopes of restoring immune tolerance and preventing disease onset and progression. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
16 pages, 3901 KiB  
Article
Comparative Genomic Analysis of Bacillus velezensis BRI3 Reveals Genes Potentially Associated with Efficient Antagonism of Sclerotinia sclerotiorum (Lib.) de Bary
by Yaoyao Liu, Changyan Yin, Min Zhu, Yuhua Zhan, Min Lin and Yongliang Yan
Genes 2024, 15(12), 1588; https://doi.org/10.3390/genes15121588 - 11 Dec 2024
Viewed by 1651
Abstract
Background/Objectives: Bacillus velezensis has recently received increased attention as a potential biological agent because of its broad-spectrum antagonistic capacity against harmful bacteria and fungi. This study aims to thoroughly analyze the genomic characteristics of B. velezensis BRI3, thereby providing theoretical groundwork for the [...] Read more.
Background/Objectives: Bacillus velezensis has recently received increased attention as a potential biological agent because of its broad-spectrum antagonistic capacity against harmful bacteria and fungi. This study aims to thoroughly analyze the genomic characteristics of B. velezensis BRI3, thereby providing theoretical groundwork for the agronomic utilization of this strain. Methods: In this work, we evaluated the beneficial traits of the newly isolated strain B. velezensis BRI3 via in vitro experiments, whole-genome sequencing, functional annotation, and comparative genomic analysis. Results: B. velezensis BRI3 exhibits broad-spectrum antifungal activity against various soilborne pathogens, displays inhibitory effects comparable to those of the type strain FZB42, and exhibits particularly effective antagonism against Sclerotinia sclerotiorum (Lib.) de Bary. Whole-genome sequencing and assembly revealed that the genome of BRI3 contains one chromosome and two plasmids, which carry a large amount of genetic information. Moreover, 13 biosynthetic gene clusters (BGCs) involved in the biosynthesis of secondary metabolites were predicted within the BRI3 genome. Among these, two unique BGCs (cluster 11 and cluster 13), which were not previously reported in the genomes of other strains and could potentially encode novel metabolic products, were identified. The results of the comparative genomic analysis demonstrated the genomic structural conservation and genetic homogeneity of BRI3. Conclusions: The unique characteristics and genomic data provide insights into the potential application of BRI3 as a biocontrol and probiotic agent. Full article
(This article belongs to the Section Microbial Genetics and Genomics)
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20 pages, 3102 KiB  
Article
Identification and Evolution Analysis of the Genes Involved in the 20-Hydroxyecdysone Metabolism in the Mud Crab, Scylla paramamosain: A Preliminary Study
by Xin Jin, Lingbo Ma, Fengying Zhang, Linzi Zhang, Jinju Yin, Wei Wang and Ming Zhao
Genes 2024, 15(12), 1586; https://doi.org/10.3390/genes15121586 - 10 Dec 2024
Cited by 1 | Viewed by 1200
Abstract
Background: 20-Hydroxyecdysone (20E) is the most ubiquitous ecdysteroid (Ecd) and plays critical roles during the life cycle of arthropods. To elucidate the metabolism pathway of 20E in the economically important species, Scylla paramamosain, we conducted a comprehensive exploration of the genes involved [...] Read more.
Background: 20-Hydroxyecdysone (20E) is the most ubiquitous ecdysteroid (Ecd) and plays critical roles during the life cycle of arthropods. To elucidate the metabolism pathway of 20E in the economically important species, Scylla paramamosain, we conducted a comprehensive exploration of the genes involved in the 20E metabolism pathway. Methods: A comprehensive exploration of genes involved in the 20E metabolism pathway was conducted, including gene annotation, local blast using the Drosophila ortholog as query, and TreeFam ortholog genes identification. Bioinformatics and expression profiling of the identified genes were performed to assess their roles in the 20E metabolism of green mud crabs. Results: This experiment indicated that, except for CYP306a1 and CYP314a1, all other ortholog genes involved in the Drosophila 20E metabolism can be found in the mud crab, suggesting that the function of these two genes might be replaced by other CYP genes or the “active” Ecd in mud crabs was not the 20E. All genes had the typical features of each gene family, clustered with the specific clade in the phylogenetic trees. In addition, all the identified genes had the highest expression level in the Y-organ, and sex-biased gene expression was observed in these genes. Conclusions: This study provided some valuable insights into the metabolism and diversity of ecdysteroids in crustaceans. Full article
(This article belongs to the Section Bioinformatics)
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26 pages, 12976 KiB  
Article
HROB Is Implicated in DNA Replication
by Julia Kutz, Hannes Schmietendorf, Sheikh Anika Rahman, Franz Opel and Helmut Pospiech
Genes 2024, 15(12), 1587; https://doi.org/10.3390/genes15121587 - 10 Dec 2024
Viewed by 1375
Abstract
DNA replication represents a series of precisely regulated events performed by a complex protein machinery that guarantees accurate duplication of the genetic information. Since DNA replication is permanently faced by a variety of exogenous and endogenous stressors, DNA damage response, repair and replication [...] Read more.
DNA replication represents a series of precisely regulated events performed by a complex protein machinery that guarantees accurate duplication of the genetic information. Since DNA replication is permanently faced by a variety of exogenous and endogenous stressors, DNA damage response, repair and replication must be closely coordinated to maintain genomic integrity. HROB has been identified recently as a binding partner and activator of the Mcm8/9 helicase involved in DNA interstrand crosslink (ICL) repair. We identified HROB independently as a nuclear protein whose expression is co-regulated with various DNA replication factors. Accordingly, the HROB protein level showed a maximum in S phase and a downregulation in quiescence. Structural prediction and homology searches revealed that HROB is a largely intrinsically disordered protein bearing a helix-rich region and a canonical oligonucleotide/oligosaccharide-binding-fold motif that originated early in eukaryotic evolution. Employing a flow cytometry Förster resonance energy transfer (FRET) assay, we detected associations between HROB and proteins of the DNA replication machinery. Moreover, ectopic expression of HROB protein led to an almost complete shutdown of DNA replication. The available data imply a function for HROB during DNA replication across barriers such as ICLs. Full article
(This article belongs to the Special Issue Mechanisms and Regulation of Human DNA Replication)
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13 pages, 659 KiB  
Review
Polygenic Risk Score Implementation into Clinical Practice for Primary Prevention of Cardiometabolic Disease
by Julia Hughes, Mikayla Shymka, Trevor Ng, Jobanjit S. Phulka, Sina Safabakhsh and Zachary Laksman
Genes 2024, 15(12), 1581; https://doi.org/10.3390/genes15121581 - 9 Dec 2024
Cited by 2 | Viewed by 2532
Abstract
Background: Cardiovascular disease is a leading cause of mortality globally and a major contributor to disability. Traditional risk factors, as initially established in the FRAMINGHAM study, have helped to stratify populations and identify patients for early intervention. Incorporating genetic factors enhances risk [...] Read more.
Background: Cardiovascular disease is a leading cause of mortality globally and a major contributor to disability. Traditional risk factors, as initially established in the FRAMINGHAM study, have helped to stratify populations and identify patients for early intervention. Incorporating genetic factors enhances risk stratification tools, enabling the earlier identification of individuals at increased risk and facilitating more targeted and effective risk factor modifications. While monogenic risk variants are present in a minority of the population, polygenic risk scores (PRS) are collections of multiple single-nucleotide variants that collectively provide summative risk and capture a more accurate risk score for a greater number of people. PRS have demonstrated clear utility in cardiometabolic diseases by predicting onset, progression, and therapeutic response. Methods: A structured and exploratory hybrid search strategy was employed, combining keyword-based database searches and supplementary techniques to comprehensively synthesize the literature on PRS implementation in clinical practice. Discussion: A comprehensive overview of PRS in cardiometabolic diseases and their potential avenues for integration into primary care is discussed. First, we examine the implementation of genetic screening, risk communication, and intervention strategies through the lens of the American Heart Association’s implementation criteria, focusing on their efficacy, minimization of harm, and logistical considerations. Then, we explores how the varied perceptions of patients and practitioners towards PRS can influence both adoption and utilization. Lastly, we addresses the need for the development of clear guidelines and regulations to support this process, ensuring PRS integration is both scientifically sound and ethically responsible. Future directions: Initiatives aimed at advancing personalized approaches to disease prevention will enhance health outcomes. Developing guidelines for the responsible use of PRS by establishing benefits, while mitigating risk, will a key factor in implementation for clinical utility. Conclusions: For integration into clinical practice, we must address both patient and provider concerns and experience. Standardized guidelines and training will help to effectively implement PRS into clinical practice. Developing these resources will be essential for PRS to fulfill its potential in personalized, patient-centered care. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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14 pages, 15679 KiB  
Article
Transcriptome Analysis Reveals Sertoli Cells Adapting Through Redox and Metabolic Pathways Under Heat Stress in Goats
by Guang Yang, Yiwei Wang, Pengyun Ji, Bingyuan Wang and Guoshi Liu
Genes 2024, 15(12), 1582; https://doi.org/10.3390/genes15121582 - 9 Dec 2024
Viewed by 1250
Abstract
Background/Objectives: Climate change-induced temperature elevations pose significant challenges to livestock reproduction, particularly affecting testicular function in small ruminants. This study investigates the acute heat-stress response in goat Sertoli cells (SCs), aiming to elucidate the molecular mechanisms underlying heat-induced damage to male reproductive tissues. [...] Read more.
Background/Objectives: Climate change-induced temperature elevations pose significant challenges to livestock reproduction, particularly affecting testicular function in small ruminants. This study investigates the acute heat-stress response in goat Sertoli cells (SCs), aiming to elucidate the molecular mechanisms underlying heat-induced damage to male reproductive tissues. Methods: SCs were isolated from testes of 4-month-old black goats and exposed to heat stress (44 °C for 2.5 h). We employed transcriptome sequencing, CCK-8 assay, electron microscopy, ROS measurement, autophagy detection, Western blot analysis, and lactate concentration measurement. Bioinformatics analyses including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein–protein interaction network analyses were performed on the transcriptome data. Results: Heat stress significantly reduced SC viability, induced oxidative stress and autophagy, and altered gene expression profiles. We identified 1231 significantly differentially expressed genes, with significant enrichment in membrane-related processes and metabolic pathways. Metabolism-related genes, including PKLR, ACOT11, and LPCT12, were significantly downregulated. Protein–protein interaction network analysis revealed ten hub genes potentially crucial in the heat-stress response: HSP90AA1, HSPA5, BAG3, IGF1, HSPH1, IL1A, CCL2, CXCL10, ALB, and CALML4. Conclusions: This study provides comprehensive insights into the molecular mechanisms underlying goat SC response to heat stress. The identified genes and pathways, particularly those related to metabolism and stress response, offer potential targets for developing strategies to mitigate heat-stress effects on livestock reproduction. These findings contribute to our understanding of climate change impacts on animal husbandry and may inform the development of heat-stress resistant livestock lines. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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10 pages, 2264 KiB  
Case Report
Expanding the Clinical Spectrum of CEP290 Variants: A Case Report on Non-Syndromic Retinal Dystrophy with a Mild Phenotype
by Anna Esteve-Garcia, Cristina Sau, Ariadna Padró-Miquel, Jaume Català-Mora, Cinthia Aguilera and Estefania Cobos
Genes 2024, 15(12), 1584; https://doi.org/10.3390/genes15121584 - 9 Dec 2024
Viewed by 1483
Abstract
Background/Objectives: Biallelic pathogenic variants in the CEP290 gene are typically associated with severe, early-onset inherited retinal dystrophies (IRDs) in both syndromic and non-syndromic forms. This study explores the phenotypic variability of non-syndromic IRDs associated with CEP290 variants, focusing on two siblings with [...] Read more.
Background/Objectives: Biallelic pathogenic variants in the CEP290 gene are typically associated with severe, early-onset inherited retinal dystrophies (IRDs) in both syndromic and non-syndromic forms. This study explores the phenotypic variability of non-syndromic IRDs associated with CEP290 variants, focusing on two siblings with biallelic variants, one of whom exhibits a remarkably mild phenotype, thereby expanding the clinical spectrum. Methods: Whole-exome sequencing (WES) and mRNA analysis were performed to identify and characterize CEP290 variants in the siblings. Comprehensive ophthalmologic evaluations assessed retinal function and disease progression. Results: Two CEP290 variants, a frameshift (c.955del, p.(Ser319LeufsTer16)) and a missense (c.5777G>C, p.(Arg1926Pro)), were identified in trans in both siblings. Despite sharing the same genetic variants, the sister exhibited significantly preserved retinal function, while the brother presented with a more severe, progressive retinal dystrophy. Conclusions: This study broadens the phenotypic spectrum of non-syndromic CEP290-related IRDs, demonstrating variability in disease severity ranging from mild to severe. These findings highlight the importance of personalized monitoring and tailored management strategies based on individual clinical presentations of CEP290-related IRDs. Full article
(This article belongs to the Section Genetic Diagnosis)
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20 pages, 10024 KiB  
Article
Kir4.1 and Aqp4 Contribution to Schisis Cystic Water Accumulation and Clearance in the Rs1 Exon-1 Del XLRS Rat Model
by Zeljka Smit-McBride, Ning Sun, Serafina Thomas, In Hwan Cho, Robin G. Stricklin and Paul A. Sieving
Genes 2024, 15(12), 1583; https://doi.org/10.3390/genes15121583 - 9 Dec 2024
Cited by 2 | Viewed by 1231
Abstract
Background/Objective: The Rs1 exon-1-del rat (Rs1KO) XLRS model shows normal retinal development until postnatal day 12 (P12) when small cystic spaces start to form in the inner nuclear layer. These spaces enlarge rapidly, peak at P15, and then collapse by P19. Methods: We [...] Read more.
Background/Objective: The Rs1 exon-1-del rat (Rs1KO) XLRS model shows normal retinal development until postnatal day 12 (P12) when small cystic spaces start to form in the inner nuclear layer. These spaces enlarge rapidly, peak at P15, and then collapse by P19. Methods: We explored the possible involvement of Kir4.1 and Aqp4, the principal retina channels for water movement and homeostasis, along with Muller glia cells (MGCs), using semi-quantitative fluorescent immunohistochemistry at P7, P9, P12, and P30, in Rs1KO and WT littermates. Results: Kir4.1 expression was reduced in Rs1KO retinas at all the early time points—P7, P9, and P12—as the schisis cavities began to form; downregulation would reduce water egress from the retina. Aqp4 was upregulated at P30 in Rs1KO retinas during schisis cavity closure but not as cavities formed at P12. When examined by GFAP expression, MGCs were not activated at the preschisis P12 age but showed considerable GFAP expression at P30 following retinal cystic structural damage at P15, indicating that MGCs were activated during the period of retina water removal and cavity closure. Conclusions: The study results implicate the downregulation of Kir4.1 in schisis formation and a role for both Kir4.1 and Aqp4 upregulation in subsequent schisis closure. Full article
(This article belongs to the Special Issue Study of Inherited Retinal Diseases—Volume II)
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14 pages, 3290 KiB  
Article
Characterization of the Mitochondrial Genome of Cambaroides schrenckii (Astacidea: Cambaridae) and Its Phylogenetic Implications
by Xuewei Liu, Ben Li, Yan Yang, Jun Zhang, Chunbo Hu, Yuxi Zhang, Jiawang Zhou, Yinlong Liu, Hongyu Qiu, Chunren Wang and Junfeng Gao
Genes 2024, 15(12), 1578; https://doi.org/10.3390/genes15121578 - 8 Dec 2024
Viewed by 1026
Abstract
Background: Cambaroides schrenckii is an endangered freshwater crayfish in China, belonging to the genus Cambaroides, that can act as a complementary host for paragonimus. The objective of this study was to examine the complete mitochondrial genome characteristics and their evolutionary relationships within the [...] Read more.
Background: Cambaroides schrenckii is an endangered freshwater crayfish in China, belonging to the genus Cambaroides, that can act as a complementary host for paragonimus. The objective of this study was to examine the complete mitochondrial genome characteristics and their evolutionary relationships within the Astacidea. Methods: The analysis of gene rearrangements and evolutionary relationships was conducted through the sequencing of the mitochondrial genome of C. schrenckii. Results: C. schrenckii mitochondrial genome length was 15,572, comprising thirteen PCGs, two rRNAs, 22 tRNAs, and one d-loop region of C. schrenckii. The mitochondrial genome of C. schrenckii exhibits an A + T content of 69.61% and a G + C content of 30.39%. Among the thirteen PCGs, cytb, nad3, and nad6 have a start codon of ATT, while the other ten PCGs have ATC, ATA, and ATG start codons. All 22 tRNA genes displayed a typical cloverleaf secondary structure. Gene rearrangement analysis showed that seven gene arrangements were identified based on PCGs in the infraorder Astacidea, with type I being the most common. Conclusions: The relationship between the American Cambaridae is closer to Astacidae than the Asian Cambaridae. The present study provides a theoretical basis for further discussions of developmental relationships in the infraorder Astacidea. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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12 pages, 870 KiB  
Review
The Roles of Phytohormones in Plant Defense Mechanisms Against the Brown Planthopper
by Huiying Wang, Wenjun Zha, An Huang, Yan Wu, Shaojie Shi, Lei Zhou and Aiqing You
Genes 2024, 15(12), 1579; https://doi.org/10.3390/genes15121579 - 8 Dec 2024
Cited by 1 | Viewed by 1955
Abstract
The brown planthopper (BPH; Nilaparvata lugens Stål) is the most significant insect pest compromising rice production globally. Phytohormones, which are small organic compounds produced by plants, play a crucial role in regulating plant growth and development. Nevertheless, extensive research has established that phytohormones [...] Read more.
The brown planthopper (BPH; Nilaparvata lugens Stål) is the most significant insect pest compromising rice production globally. Phytohormones, which are small organic compounds produced by plants, play a crucial role in regulating plant growth and development. Nevertheless, extensive research has established that phytohormones are essential in modulating plant defense against BPH. Plants can achieve equilibrium between growth and defense by utilizing the intricate network of phytohormone signaling pathways to initiate optimal and efficient defensive responses to insects. In this review, we primarily address the roles of phytohormones in conferring resistance against BPH, with a focus on hormone cross-talk. We also discuss the potential value of integrating hormones with other agricultural practices to enhance plant defense and agricultural yield, which highlights the significance of novel approaches for environment-friendly insect pest management. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Responses)
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10 pages, 219 KiB  
Case Report
A Novel Pathogenic Sense Variant in Exon 7 of the HK1 Gene in a Patient with Hexokinase Deficiency and Gilbert Syndrome
by Magdalena Bartnik, Weronika Pawlik, Beata Burzyńska, Konrad Wasilewski, Elżbieta Kamieńska and Tomasz Urasiński
Genes 2024, 15(12), 1576; https://doi.org/10.3390/genes15121576 - 7 Dec 2024
Viewed by 1477
Abstract
Background: Hexokinase (HK) deficiency is a rare autosomal recessively inherited disease manifested by chronic nonspherocytic hemolytic anemia. Most patients present with a mild to severe course of the disease (fetal hydrocephalus, neonatal hyperbilirubinemia, severe anemia). We reviewed 37 cases of patients with hexokinase [...] Read more.
Background: Hexokinase (HK) deficiency is a rare autosomal recessively inherited disease manifested by chronic nonspherocytic hemolytic anemia. Most patients present with a mild to severe course of the disease (fetal hydrocephalus, neonatal hyperbilirubinemia, severe anemia). We reviewed 37 cases of patients with hexokinase deficiency described so far, focusing on the severity of the disease, clinical presentation, treatment applied, and genetic test results. Methods: We present a 10-year-old girl who initially presented with symptoms of weakness, excessive fatigue, and yellowing of the skin and sclerae. Genetic testing detected the (TA)7 variant in both alleles of the UGT1A1 gene and diagnosed Gilbert’s disease. In the follow-up, red cell hemolysis was observed. The diagnosis was extended, and tests for red cell enzymopathy were performed and a reduced level of hexokinase—0.65 IU/gHb (normal 0.78–1.57) was found. Next-generation sequencing revealed a new sense-change variant in exon 7 in the hexokinase gene not previously reported in databases. Results: Up to this date, only around 37 cases of hexokinase deficiency associated with hereditary nonspherocytic hemolytic anemia have been documented around the world. Diagnosing hexokinase deficiency involves clinical evaluation, laboratory testing, and genetic analysis. Management focuses on treating symptoms and preventing complications; there is no cure for the underlying enzyme deficiency. In patients with severe anemia, the treatment is multiple blood transfusions followed by iron chelation therapy. Conclusions: Understanding and diagnosing hexokinase deficiency is critical for providing appropriate care and improving the quality of life for affected individuals. Full article
(This article belongs to the Special Issue Variations of Rare Genetic Diseases)
18 pages, 5572 KiB  
Article
Genetic Analysis of the Peach SnRK1β3 Subunit and Its Function in Transgenic Tomato Plants
by Shilong Zhao, Xuelian Wu, Jiahui Liang, Zhe Wang, Shihao Fan, Hao Du, Haixiang Yu, Yuansong Xiao and Futian Peng
Genes 2024, 15(12), 1574; https://doi.org/10.3390/genes15121574 - 6 Dec 2024
Viewed by 1165
Abstract
Background/Objectives: The sucrose non-fermentation-related kinase 1 (SnRK1) protein complex in plants plays an important role in energy metabolism, anabolism, growth, and stress resistance. SnRK1 is a heterotrimeric complex. The SnRK1 complex is mainly composed of α, β, βγ, and γ subunits. Studies on [...] Read more.
Background/Objectives: The sucrose non-fermentation-related kinase 1 (SnRK1) protein complex in plants plays an important role in energy metabolism, anabolism, growth, and stress resistance. SnRK1 is a heterotrimeric complex. The SnRK1 complex is mainly composed of α, β, βγ, and γ subunits. Studies on plant SnRK1 have primarily focused on the functional α subunit, with the β regulatory subunit remaining relatively unexplored. The present study aimed to elucidate the evolutionary relationship, structural prediction, and interaction with the core α subunit of peach SnRK1β3 (PpSnRK1) subunit. Methods: Bioinformatics analysis of PpSnRK1 was performed through software and website. We produced transgenic tomato plants overexpressing PpSnRK1 (OEPpSnRK1). Transcriptome analysis was performed on OEPpSnRK1 tomatoes. We mainly tested the growth index and drought resistance of transgenic tomato plants. Results: The results showed that PpSnRK1 has a 354 bp encoded protein sequence (cds), which is mainly located in the nucleus and cell membrane. Phylogenetic tree analysis showed that PpSnRK1β3 has similar domains to other woody plants. Transcriptome analysis of OEPpSnRK1β3 showed that PpSnRK1β3 is widely involved in biosynthetic and metabolic processes. Functional analyses of these transgenic plants revealed prolonged growth periods, enhanced growth potential, improved photosynthetic activity, and superior drought stress tolerance. Conclusions: The study findings provide insight into the function of the PpSnRK1 subunit and its potential role in regulating plant growth and drought responses. This comprehensive analysis of PpSnRK1 will contribute to further enhancing our understanding of the plant SnRK1 protein complex. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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23 pages, 4761 KiB  
Article
Physiological and Transcriptomic Dynamics in Mulberry: Insights into Species-Specific Responses to Midday Depression
by Yong Li, Jin Huang, Fangyuan Song, Zhiyue Guo and Wen Deng
Genes 2024, 15(12), 1571; https://doi.org/10.3390/genes15121571 - 5 Dec 2024
Viewed by 954
Abstract
Background/Objective: The midday depression of photosynthesis, a physiological phenomenon driven by environmental stress, impacts plant productivity. This study aims to elucidate the molecular and physiological responses underlying midday depression in two mulberry species, Ewu No. 1 (Ew1) and Husan No. 32 (H32), to [...] Read more.
Background/Objective: The midday depression of photosynthesis, a physiological phenomenon driven by environmental stress, impacts plant productivity. This study aims to elucidate the molecular and physiological responses underlying midday depression in two mulberry species, Ewu No. 1 (Ew1) and Husan No. 32 (H32), to better understand their species-specific stress adaptation mechanisms. Methods: RNA-seq analysis was conducted on leaf samples collected at three time points (10:00 a.m., 12:00 p.m., and 4:00 p.m.), identifying 22,630 differentially expressed genes (DEGs). A comparative Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed to reveal the involvement of key metabolic and signaling pathways in stress responses. Results: Ew1 displayed enhanced stress tolerance by upregulating genes involved in energy management, water conservation, and photosynthetic processes, maintaining higher photosynthetic rates under midday stress. In contrast, H32 adopted a more conservative response, downregulating genes related to photosynthesis and metabolism, favoring survival at the expense of productivity. The KEGG analysis highlighted starch and sucrose metabolism and plant hormone signaling as critical pathways contributing to these species-specific responses. Conclusions: Ew1’s adaptive molecular strategies make it more suitable for environments with variable light and temperature conditions, while H32’s conservative approach may limit its productivity. These findings provide valuable insights for breeding programs aimed at improving stress tolerance and photosynthetic efficiency in mulberry and other crops, particularly under fluctuating environmental conditions. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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11 pages, 564 KiB  
Opinion
The Newborn Screening Programme Revisited: An Expert Opinion on the Challenges of Rett Syndrome
by Jatinder Singh and Paramala Santosh
Genes 2024, 15(12), 1570; https://doi.org/10.3390/genes15121570 - 5 Dec 2024
Cited by 1 | Viewed by 1423
Abstract
Genomic sequencing has the potential to revolutionise newborn screening (NBS) programmes. In 2024, Genomics England began to recruit for the Generation Study (GS), which uses whole genome sequencing (WGS) to detect genetic changes in 500 genes in more than 200 rare conditions. Ultimately, [...] Read more.
Genomic sequencing has the potential to revolutionise newborn screening (NBS) programmes. In 2024, Genomics England began to recruit for the Generation Study (GS), which uses whole genome sequencing (WGS) to detect genetic changes in 500 genes in more than 200 rare conditions. Ultimately, its purpose is to facilitate the earlier identification of rare conditions and thereby improve health-related outcomes for individuals. The adoption of rare conditions into the GS was guided by four criteria: (1) the gene causing the condition can be reliably detected; (2) if undiagnosed, the rare condition would have a serious impact; (3) early or presymptomatic testing would substantially improve outcomes; and (4) interventions for conditions screened are accessible to all. Rett syndrome (RTT, OMIM 312750), a paediatric neurodevelopment disorder, was not included in the list of rare conditions in the GS. In this opinion article, we revisit the GS and discuss RTT from the perspective of these four criteria. We begin with an introduction to the GS and then summarise key points about the four principles, presenting challenges and opportunities for individuals with RTT. We provide insight into how data could be collected during the presymptomatic phase, which could facilitate early diagnosis and improve our understanding of the prodromal stage of RTT. Although many features of RTT present a departure from criteria adopted by the GS, advances in RTT research, combined with advocacy from parent-based organisations, could facilitate its entry into future newborn screening programmes. Full article
(This article belongs to the Special Issue Genetics and Therapy of Neurodevelopmental Disorders)
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11 pages, 2019 KiB  
Case Report
Two Novel Biallelic Variants in the FARSA Gene: The First Italian Case and a Literature Review
by Sonia Lomuscio, Dario Cocciadiferro, Francesco Petrizzelli, Niccolò Liorni, Tommaso Mazza, Annalisa Allegorico, Nicola Ullmann, Giuseppe Novelli, Renato Cutrera and Antonio Novelli
Genes 2024, 15(12), 1573; https://doi.org/10.3390/genes15121573 - 5 Dec 2024
Viewed by 1355
Abstract
Background/Objectives: The FARSA gene encodes for the catalytic α subunit of Cytoplasmic phenylalanine-tRNA synthetase (FARS1), an essential enzyme for protein biosynthesis in transferring its amino acid component to tRNAs. Biallelic pathogenic variants have been associated with a multisystemic condition, characterized by variable [...] Read more.
Background/Objectives: The FARSA gene encodes for the catalytic α subunit of Cytoplasmic phenylalanine-tRNA synthetase (FARS1), an essential enzyme for protein biosynthesis in transferring its amino acid component to tRNAs. Biallelic pathogenic variants have been associated with a multisystemic condition, characterized by variable expressivity and incomplete penetrance. Here, we report the case of an 11 year-old girl presenting interstitial lung disease, supratentorial leukoencephalopathy with brain cysts, hepatic dysfunction, hypoalbuminemia, skin and joint hyperlaxity, growth retardation, and dysmorphic features. In addition, our patient also developed two clinical features never reported before: hypergammaglobulinemia and myopic chorioretinitis. Methods: NGS analysis of the patient’s skin-derived DNA revealed two novel biallelic variants in FARSA gene (NM_004461.3) never described before: the maternal nonsense variant, c.799C>T [p.(Gln267Ter)], and the paternal missense variant, c.737T>C [p.(Met246Thr)], both predicted as deleterious. Results: From a therapeutic perspective, this young girl has been enrolled in a clinical trial with Nintedanib, in order to treat the severe pulmonary fibrosis, with interesting initial results. Conclusions: Our findings expand the clinical and molecular spectrum of the FARSA-related phenotype and introduce new cues on lung fibrosis treatment in pediatric age. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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15 pages, 2792 KiB  
Article
Evidence for the Transcription of a Satellite DNA Widely Found in Frogs
by Jennifer Nunes Pompeo, Kaleb Pretto Gatto, Diego Baldo and Luciana Bolsoni Lourenço
Genes 2024, 15(12), 1572; https://doi.org/10.3390/genes15121572 - 5 Dec 2024
Viewed by 1124
Abstract
Background: The satellite DNA (satDNA) PcP190 has been identified in multiple frog species from seven phylogenetically distant families within Hyloidea, indicating its broad distribution. This satDNA consists of repeats of approximately 190 bp and exhibits a highly conserved region (CR) of 120 bp, [...] Read more.
Background: The satellite DNA (satDNA) PcP190 has been identified in multiple frog species from seven phylogenetically distant families within Hyloidea, indicating its broad distribution. This satDNA consists of repeats of approximately 190 bp and exhibits a highly conserved region (CR) of 120 bp, which is similar to the transcribed region of 5S ribosomal DNA (rDNA), and a hypervariable region (HR) that varies in size and nucleotide composition among and within species. Here, to improve our understanding of PcP190 satDNA, we searched for evidence of its transcription in the available transcriptomes of Rhinella marina (Bufonidae) and Engystomops pustulosus (Leptodactylidae), two phylogenetically distantly related species. Methods: We first characterized the 5S rDNA and PcP190 sequences in these species by searching for them in available genome assemblies. Next, we used the PcP190 (CR and HR) and 5S rDNA sequences of each species as queries to search for these sequences in RNA-seq libraries. Results: We identified two types of 5S rDNA in each analyzed species, with a new type found in E. pustulosus. Our results also revealed a novel type of PcP190 sequence in R. marina and a new subtype of PcP-1 in E. pustulosus. Transcriptome analyses confirmed the expected transcription of the 5S rRNA gene and showed transcription of both the CR and HR of the PcP190 satDNA in both species and in different tissues. Conclusions: As the entire repeat of this satDNA is susceptible to transcription, the high variability observed in the HR cannot be attributed to transcriptional activity confined to the CR. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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20 pages, 10153 KiB  
Article
Characterization of the Complete Mitogenome of the Ring-Necked Pheasant Phasianus colchicus (Galliformes: Phasianidae) and Systematic Implications for Phasianinae Phylogenetics
by Qinggang Mei, Yiming Deng, Dongmei Zhao, Daoyu Jiang, Yaqing Liao, Xiangmei Yu, Peng Liu and Lichun Jiang
Genes 2024, 15(12), 1569; https://doi.org/10.3390/genes15121569 - 4 Dec 2024
Cited by 1 | Viewed by 1118
Abstract
Background: Phasianidae mitogenomes exhibit significant structural variations critical for understanding evolution and subspecies divergence. However, annotations of these features in some pheasant species remain limited. This study aimed to enhance understanding of Phasianidae mitogenomes and their evolutionary patterns. Methods: A comparative analysis of [...] Read more.
Background: Phasianidae mitogenomes exhibit significant structural variations critical for understanding evolution and subspecies divergence. However, annotations of these features in some pheasant species remain limited. This study aimed to enhance understanding of Phasianidae mitogenomes and their evolutionary patterns. Methods: A comparative analysis of complete mitogenomes from Phasianus colchicus, Phasianus versicolor, and 22 other accipitrids was conducted, examining codon usage, rRNA structures, selective pressures, phylogenetics, and structural variations. Results: The mitogenome of P. colchicus is 16,696 bp, comprising 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, with a base composition of A: 30.61%, T: 25.26%, C: 30.85%, and G: 13.28%. Phylogenetic analysis revealed P. colchicus and P. versicolor are closely related, with the following relationship: ((Phasianus + Chrysolophus) + (Crossoptilon + Lophura)). Divergence timing aligns with the Tibetan Plateau uplift during the Tertiary Pliocene. Ka/Ks analysis suggests the CO I, CO II, CO III, ND1, ND4L, and ND6 genes in Phasianus underwent strong selective pressure for plateau adaptation. Conclusions: The study confirms Phasianus monophyly and its close relationship with Chrysolophus. Adaptation-related selective pressures on the CO I, CO II, CO III, ND1, ND4L, and ND6 genes highlight its role in plateau environments, offering valuable insights into pheasant phylogeny. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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12 pages, 4934 KiB  
Article
Comparative and Adaptive Analyses of the Complete Chloroplast Genome Diversity in Sium serra
by SeongJun Park and SeonJoo Park
Genes 2024, 15(12), 1567; https://doi.org/10.3390/genes15121567 - 3 Dec 2024
Viewed by 1062
Abstract
Background/Objectives: Sium serra is distributed in Korea, China, and Japan. It was first identified as the genus Pimpinella and then reclassified as Sium by Kitagawa. Some Sium species are used as herbal medicine and are often confused with the similar form Ligusticum sinense [...] Read more.
Background/Objectives: Sium serra is distributed in Korea, China, and Japan. It was first identified as the genus Pimpinella and then reclassified as Sium by Kitagawa. Some Sium species are used as herbal medicine and are often confused with the similar form Ligusticum sinense. In this study, we analyzed the cp genome of S. serra and conducted comparative analyses with the cp genomes of related taxa. Methods: We extracted gDNA from fresh leaves and sequenced it using Illumina HiSeq2500. For the chloroplast genome assembly, de novo assembly was performed using Velvet v1.2.07. For the annotation, GeSeq and NCBI BLASTN were used. Afterwards, related taxa were analyzed using programs such as DnaSP and MISA. Results: S. serra was excluded from the study on the chloroplast (cp) genome in Sium because it was classified as Pimpinella in China. Therefore, this study aimed to analyze the cp genome of S. serra for the first time and its location within the genus Sium. The complete cp genome of S. serra was 154,755 bp in length, including a pair of inverted repeats, each 26,255 bp, a large single-copy region of 84,581 bp, and a small single-copy region of 17,664 bp. The cp genome comprised 79 protein-coding, 30 tRNA, and 4 rRNA genes. Furthermore, six regions of high nucleotide diversity were identified in the genus Sium. In the genus Sium, 1630 repeats that can serve as markers were also identified. Eight protein-coding genes with high KA/KS values were under positive selection in the Sium. Our phylogenetic analyses suggest that S. serra was positioned with high bootstrap support within the Sium of the tribe Oenantheae, specifically in the southern Palearctic subclade. Conclusions: In this study, the S. serra chloroplast genome was sequenced and assembled. The genus Sium formed a monophyletic group; however, as not all the Sium species were included in this study, further research is necessary. This study can serve as foundational data not only for Sium but also for the tribe Oenantheae. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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6 pages, 461 KiB  
Article
Exploring the Role of CCNF Variants in Italian ALS Patients
by Giulia Bisogni, Amelia Conte, Umberto Costantino, Serena Lattante, Daniela Bernardo, Gabriele Lucioli, Agata Katia Patanella, Paola Cimbolli, Elda Del Giudice, Federica Vettor, Giuseppe Marangi, Paolo Niccolò Doronzio, Marcella Zollino and Mario Sabatelli
Genes 2024, 15(12), 1566; https://doi.org/10.3390/genes15121566 - 3 Dec 2024
Viewed by 958
Abstract
Objectives: Variants in Cyclin F (CCNF) have been associated to amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD) in a group of cases. The objectives of this study were to determine the contribution of CCNF in a large cohort of Italian [...] Read more.
Objectives: Variants in Cyclin F (CCNF) have been associated to amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD) in a group of cases. The objectives of this study were to determine the contribution of CCNF in a large cohort of Italian ALS patients, to look for genotype-phenotype correlation of the mutations and to evaluate the CCNF-associated clinical features. Methods: We applied next-generation sequencing technologies on 971 unrelated Italian ALS patients and we filtered results to look for variants in CCNF gene. Results: We identified 13 rare missense variants in 16 index cases (2 familial and 14 sporadic), with a cumulative mutational frequency of 1.6%. The most prevalent variant was p.Phe197Leu, found in three patients. The clinical presentation was heterogeneous, with a classic phenotype in eight patients, upper motor neuron dominant (UMN-D) phenotype in four patients, and flail arm in four patients. Clinical evaluation for cognitive impairment was performed in 13 patients using the Edinburgh Cognitive and Behavioural ALS Screen (ECAS) test, demonstrating that almost half of the patients (n = 6) had variable degrees of frontal dysfunction. Discussion: In our cohort, we observed CCNF variants in 1.6% of patients (16/971), a percentage similar to that found in other series. Clinical presentation is heterogeneous, but CCNF variants are significantly associated to cognitive impairment. Conclusions: Our study expands the CCNF genetic variant spectrum in a large cohort of Italian ALS patients. Further studies are needed to assess genotype-phenotype associations of CCNF variants and to specify the role of each variant, which are quite common, especially in sALS patients. Full article
(This article belongs to the Special Issue Research Strategies to Unveil the Genetic and Molecular Basis of ALS)
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21 pages, 1683 KiB  
Article
Screening and Genomic Profiling of Antimicrobial Bacteria Sourced from Poultry Slaughterhouse Effluents: Bacteriocin Production and Safety Evaluation
by Nuria Peña, Irene Lafuente, Ester Sevillano, Javier Feito, Diogo Contente, Estefanía Muñoz-Atienza, Luis M. Cintas, Pablo E. Hernández and Juan Borrero
Genes 2024, 15(12), 1564; https://doi.org/10.3390/genes15121564 - 2 Dec 2024
Viewed by 1462
Abstract
Background/Objectives: Antimicrobial-resistant (AMR) pathogens represent a serious threat to public health, particularly in food production systems where antibiotic use remains widespread. As a result, alternative antimicrobial treatments to antibiotics are essential for effectively managing bacterial infections. This study aimed to identify and characterize [...] Read more.
Background/Objectives: Antimicrobial-resistant (AMR) pathogens represent a serious threat to public health, particularly in food production systems where antibiotic use remains widespread. As a result, alternative antimicrobial treatments to antibiotics are essential for effectively managing bacterial infections. This study aimed to identify and characterize novel antimicrobial peptides produced by bacteria, known as bacteriocins, as well as to recognize safe bacteriocin-producing strains, sourced from poultry slaughterhouse effluents. Methods: A total of 864 bacterial isolates were collected across eight stages of a poultry slaughter line and screened for antimicrobial activity against Gram-positive and Gram-negative indicator strains. Whole-genome sequencing (WGS) was performed on 12 selected strains, including Enterococcus faecium (6 isolates), Lactococcus lactis (1 isolate), Lactococcus garvieae (1 isolate) and Escherichia coli (4 isolates). The presence of bacteriocin gene clusters (BGC), antibiotic resistance genes (ARG), and virulence factors (VF) was analyzed. The antimicrobial activity of a novel bacteriocin was further evaluated using in vitro cell-free protein synthesis (IV-CFPS). Results: WGS revealed multiple BGCs, including a novel class IId bacteriocin, lactococcin P1A (LcnP1A), in L. lactis SWD9. LcnP1A showed antimicrobial activity against various indicator strains, including Listeria monocytogenes. While most bacteriocin-encoding strains harbored ARGs and VFs, E. faecium SWG6 was notable for its absence of ARGs and minimal VFs, highlighting its potential as a probiotic. Conclusions: These findings underscore the importance of discovering novel bacteriocins and safer bacteriocin producing strains to address antimicrobial resistance in the food chain. Further research would validate the efficacy of both the novel lactococcin P1A bacteriocin and the E. faecium SWG6 isolate for application in processed food and animal production systems. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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21 pages, 1650 KiB  
Article
Genetic Identity and Diversity of Loggerhead Sea Turtles in the Central Mediterranean Sea
by Adriana Vella and Noel Vella
Genes 2024, 15(12), 1565; https://doi.org/10.3390/genes15121565 - 2 Dec 2024
Viewed by 1314
Abstract
Background: The conservation of loggerhead sea turtles (Caretta caretta) in the central Mediterranean benefits from an in-depth understanding of its population genetic structure and diversity. Methods: This study, therefore, investigates C. caretta in Maltese waters by genetically analysing 63 specimens collected [...] Read more.
Background: The conservation of loggerhead sea turtles (Caretta caretta) in the central Mediterranean benefits from an in-depth understanding of its population genetic structure and diversity. Methods: This study, therefore, investigates C. caretta in Maltese waters by genetically analysing 63 specimens collected through strandings and in-water sampling, using mitochondrial DNA control region and microsatellites. Additionally, the two nests detected in Malta in 2023 were analysed for the same markers. Results: Mitochondrial data identified 10 haplotypes, with mixed stock analyses tracing 87.5% of the specimens to Mediterranean origins, primarily from Libyan rookeries, with contributions from Lebanon, Israel and Turkey. Three Atlantic haplotypes were identified in six specimens, with CC-A17.1 linking central Mediterranean foraging individuals to rookeries in Cape Verde. Five of these six Atlantic haplotype records were from recently sampled individuals (2022–2023), possibly indicating a recent eastward expansion of Atlantic haplotypes into the Mediterranean. Bayesian clustering (K = 2) of microsatellite data using haplotypes as priori revealed similar proportions for clusters across most specimens, except for three specimens with Atlantic haplotypes CC-A1.1 and CC-A1.3, which exhibited distinct patterns. The two nests examined here displayed Mediterranean haplotypes, with nuclear DNA matching the predominant Mediterranean profiles found in foraging individuals, suggesting that local clutches originated from Mediterranean parents. Conclusions: Increasing nesting activity on Maltese beaches and this archipelago’s geographical position highlight the need for ongoing genetic monitoring to track changes in genetic diversity and develop conservation strategies that support the effective protection of this species and its habitats. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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16 pages, 5425 KiB  
Article
Integrative Transcriptomics and Proteomics Analysis Reveals THRSP’s Role in Lipid Metabolism
by Yujie Li, Ke Xu, Ao Zhou, Zhong Xu, Junjing Wu, Xianwen Peng, Shuqi Mei and Hongbo Chen
Genes 2024, 15(12), 1562; https://doi.org/10.3390/genes15121562 - 30 Nov 2024
Viewed by 1846
Abstract
Background/Objectives: Abnormalities in lipid metabolism and endoplasmic reticulum (ER) stress are strongly associated with the development of a multitude of pathological conditions, including nonalcoholic fatty liver disease (NAFLD), diabetes mellitus, and obesity. Previous studies have indicated a potential connection between thyroid hormone responsive [...] Read more.
Background/Objectives: Abnormalities in lipid metabolism and endoplasmic reticulum (ER) stress are strongly associated with the development of a multitude of pathological conditions, including nonalcoholic fatty liver disease (NAFLD), diabetes mellitus, and obesity. Previous studies have indicated a potential connection between thyroid hormone responsive (THRSP) and lipid metabolism and that ER stress may participate in the synthesis of key regulators of adipogenesis. However, the specific mechanisms remain to be investigated. Methods: In this study, we explored the roles of THRSP in lipid metabolism by interfering with THRSP gene expression in mouse mesenchymal stem cells, comparing the effects on adipogenesis between control and interfered groups, and by combining transcriptomic and proteomic analysis. Results: Our results showed that the number of lipid droplets was significantly reduced after interfering with THRSP, and the expression levels of key regulators of adipogenesis, such as LPL, FABP4, PLIN1, and CIDEC, were significantly downregulated. Both transcriptomic and proteomic results showed that the differential genes (proteins) were enriched in the processes of lipolytic regulation, ER stress, cholesterol metabolism, sphingolipid metabolism, PPAR signaling pathway, and glycerophospholipid metabolism. The ER stress marker gene, ATF6, was the most significantly downregulated transcription factor. In addition, RT-qPCR validation indicated that the expression levels of PPAR signaling pathway gene SCD1; key genes of lipid droplet generation including LIPE, DGAT1, and AGPAT2; and ER stress marker gene ATF6 were significantly downregulated. Conclusions: These suggest that THRSP is involved in regulating ER stress and the PPAR signaling pathway, which is closely related to lipid synthesis and metabolism. Interfering with the expression of THRSP may be helpful in ameliorating the occurrence of diseases related to abnormalities in lipid metabolism. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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15 pages, 2651 KiB  
Article
TrAnnoScope: A Modular Snakemake Pipeline for Full-Length Transcriptome Analysis and Functional Annotation
by Aysevil Pektas, Frank Panitz and Bo Thomsen
Genes 2024, 15(12), 1547; https://doi.org/10.3390/genes15121547 - 29 Nov 2024
Viewed by 1575
Abstract
Background/Objectives: Transcriptome assembly and functional annotation are essential in understanding gene expression and biological function. Nevertheless, many existing pipelines lack the flexibility to integrate both short- and long-read sequencing data or fail to provide a complete, customizable workflow for transcriptome analysis, particularly [...] Read more.
Background/Objectives: Transcriptome assembly and functional annotation are essential in understanding gene expression and biological function. Nevertheless, many existing pipelines lack the flexibility to integrate both short- and long-read sequencing data or fail to provide a complete, customizable workflow for transcriptome analysis, particularly for non-model organisms. Methods: We present TrAnnoScope, a transcriptome analysis pipeline designed to process Illumina short-read and PacBio long-read data. The pipeline provides a complete, customizable workflow to generate high-quality, full-length (FL) transcripts with broad functional annotation. Its modular design allows users to adapt specific analysis steps for other sequencing platforms or data types. The pipeline encompasses steps from quality control to functional annotation, employing tools and established databases such as SwissProt, Pfam, Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and Eukaryotic Orthologous Groups (KOG). As a case study, TrAnnoScope was applied to RNA-Seq and Iso-Seq data from zebra finch brain, ovary, and testis tissue. Results: The zebra finch transcriptome generated by TrAnnoScope from the brain, ovary, and testis tissue demonstrated strong alignment with the reference genome (99.63%), and it was found that 93.95% of the matched protein sequences in the zebra finch proteome were captured as nearly complete. Functional annotation provided matches to known protein databases and assigned relevant functional terms to the majority of the transcripts. Conclusions: TrAnnoScope successfully integrates short and long sequencing technologies to generate transcriptomes with minimal user input. Its modularity and ease of use make it a valuable tool for researchers analyzing complex datasets, particularly for non-model organisms. Full article
(This article belongs to the Section Bioinformatics)
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12 pages, 2210 KiB  
Article
Clinical and Cytogenetic Impact of Maternal Balanced Double Translocation: A Familial Case of 15q11.2 Microduplication and Microdeletion Syndromes with Genetic Counselling Implications
by Daniela Koeller R. Vieira, Ingrid Bendas Feres Lima, Carla Rosenberg, Carlos Roberto da Fonseca, Leonardo Henrique Ferreira Gomes, Letícia da Cunha Guida, Patrícia Camacho Mazzonetto, Juan Llerena, Jr. and Elenice Ferreira Bastos
Genes 2024, 15(12), 1546; https://doi.org/10.3390/genes15121546 - 29 Nov 2024
Viewed by 1635
Abstract
Background: Balanced chromosomal translocations occur in approximately 0.16 to 0.20% of live births. While most carriers are phenotypically normal, they are at risk of generating unbalanced gametes during meiosis, leading to genetic anomalies such as aneuploidies, deletions, duplications, and gene disruptions. These anomalies [...] Read more.
Background: Balanced chromosomal translocations occur in approximately 0.16 to 0.20% of live births. While most carriers are phenotypically normal, they are at risk of generating unbalanced gametes during meiosis, leading to genetic anomalies such as aneuploidies, deletions, duplications, and gene disruptions. These anomalies can result in spontaneous abortions or congenital anomalies, including neurodevelopmental disorders. Complex chromosomal rearrangements (CCRs) involving more than two chromosomes are rare but further increase the probability of producing unbalanced gametes. Neurodevelopmental disorders such as Angelman syndrome (AS) and duplication 15q11q13 syndrome (Dup15q) are associated with such chromosomal abnormalities. Methods: This study describes a family with a de novo maternal balanced double translocation involving chromosomes 13, 19, and 15, resulting in two offspring with unbalanced chromosomal abnormalities. Cytogenetic evaluations were performed using GTG banding, fluorescence in situ hybridization (FISH), and low-pass whole-genome sequencing (LP-WGS). Methylation analysis was conducted using methylation-sensitive high-resolution melting (MS-HRM) to diagnose Angelman syndrome. Results: The cytogenetic and molecular analyses identified an 8.9 Mb duplication in 15q11.2q13.3 in one child, and an 8.9 Mb deletion in the same region in the second child. Both abnormalities affected critical neurodevelopmental genes, such as SNRPN. FISH and MS-HRM confirmed the chromosomal imbalances and the diagnosis of Angelman syndrome in the second child. The maternal balanced translocation was found to be cryptic, contributing to the complex inheritance pattern. Conclusion: This case highlights the importance of using multiple genetic platforms to uncover complex chromosomal rearrangements and their impact on neurodevelopmental disorders. The findings underscore the need for thorough genetic counseling, especially in families with such rare chromosomal alterations, to manage reproductive outcomes and neurodevelopmental risks. Full article
(This article belongs to the Section Genetic Diagnosis)
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15 pages, 3556 KiB  
Article
The Characteristics and Expression Analysis of the Tomato KWL Gene Family Under Biotic Stress
by Mei Su, Xuejuan Ru, Yang Chen, Hongjuan Wang, Jia Luo and Hong Wu
Genes 2024, 15(12), 1555; https://doi.org/10.3390/genes15121555 - 29 Nov 2024
Viewed by 1096
Abstract
Background: Tomatoes are renowned for their popularity and nutritional value across the globe, yet their production and quality face significant challenges from various biotic stresses in their growing environments. Kiwellin (KWL) has been implicated in plant disease resistance. However, our comprehension of this [...] Read more.
Background: Tomatoes are renowned for their popularity and nutritional value across the globe, yet their production and quality face significant challenges from various biotic stresses in their growing environments. Kiwellin (KWL) has been implicated in plant disease resistance. However, our comprehension of this gene family in plants is still remarkably insufficient. Methods: We conducted a comprehensive genomic analysis of the KWL gene family in tomatoes. The tertiary structures of SlKWLs were predicted by AlphaFold2. EMBOSS was used for codon analysis. RNA-seq and RT-qPCR analysis were performed to explore the expression profile of SlKWLs. Results: Our findings identified 12 distinct SlKWL members distributed across four chromosomes within the tomato genome. By examining their gene structure, conserved motifs, functional domains, and phylogenetic relationships, we elucidated the complex evolutionary relationships and potential functions of these genes. Notably, we identified numerous cis-regulatory elements within the promoter regions of the SlKWL genes which are associated with responses to both abiotic and biotic stresses, as well as hormone signaling pathways. This finding strongly implies that SlKWLs are integral to plant growth and adaptation to diverse stress conditions. Furthermore, RNA-seq and RT-qPCR analysis revealed an upregulation of five SlKWLs expressed subsequent to Phytophthora infestans infection. Particularly, SlKWL2 and SlKWL3 exhibited substantially elevated expression levels, underscoring their active involvement in biotic stress responses. Conclusions: Collectively, these findings advance our comprehension of the SlKWL gene family and provide a robust foundation for future investigations into the roles of SlKWL genes in tomato stress responses. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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17 pages, 2703 KiB  
Article
Identification of Candidate Genes for Sebum Deposition in Pekin Ducks Using Genome-Wide Association Studies
by Xueze Lv, Bozhi Shi, Haiyuan Ren, Weifang Yang, Lujiang Qu, Uchechukwu Edna Obianwuna and Xueqi Lyu
Genes 2024, 15(12), 1553; https://doi.org/10.3390/genes15121553 - 29 Nov 2024
Viewed by 1128
Abstract
Background: Sebum deposition is a vital trait influencing meat quality and production efficiency in Pekin ducks. Providing insights into the genetic basis of fat deposition could help improve breeding strategies aimed at producing high-quality meat ducks. This study aimed to identify the genetic [...] Read more.
Background: Sebum deposition is a vital trait influencing meat quality and production efficiency in Pekin ducks. Providing insights into the genetic basis of fat deposition could help improve breeding strategies aimed at producing high-quality meat ducks. This study aimed to identify the genetic mechanisms and lipid metabolism pathways regulating subcutaneous and intramuscular fat deposition in two Pekin duck strains: Nankou No. 1 and Jingdian. Methods: A total of 72 male ducks, Nankou No. 1 (n = 36) and Jingdian (n = 36), were raised under controlled conditions for 42 days. On days 28, 35, and 42, ducks from each group were selected and slaughtered, and their subcutaneous and liver tissues were collected to analyze lipid enzyme activities. On day 42, additional ducks from each strain were slaughtered and evaluated for carcass performance, as well as intramuscular and sebum yield. Genome-wide association analysis (GWAS) was conducted in the Nankou No. 1 strain. Conclusion: Our results showed statistically significant differences in intramuscular and subcutaneous fat yield between the two strains, with Nankou No. 1 exhibiting a higher yield than Jingdian (p < 0.05). The GWAS results identified 96 significant single nucleotide polymorphisms (SNPs), associated with sebum deposition. Functional annotation identified ALDH7A1 as a key candidate gene involved in lipid metabolism and fat storage regulation in Pekin ducks, Nankou No. 1 strain. Enzyme activity assays in liver and subcutaneous tissues revealed breed-specific differences in lipid metabolism, aligning with genetic findings. The activities of the lipid enzymes changed over time, suggesting changes in the developmental stages. The results on fat yield and enzymatic activities further align with molecular findings from the GWAS, which identified variations in lipid metabolism pathways. These results highlight genetic markers and biochemical pathways related to fat deposition in Pekin ducks, offering new insights for selective breeding programs aimed at optimizing fat content in meat production. Further research is needed to clarify the specific role of ALDH7A1 in lipid metabolism and its potential to enhance fat deposition traits in poultry. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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17 pages, 2127 KiB  
Article
Quantitative Trait Loci Mappings for the Sulfur Utilization Efficiency-Related Traits at the Seedling Stage of Wheat
by Longteng Ma, Jiali Li, Hui Wang, Yunhui Zhai, Qing Xu, Hongling Yang, Yizheng Li, Ying Guo, Fanmei Kong, Sishen Li and Yan Zhao
Genes 2024, 15(12), 1550; https://doi.org/10.3390/genes15121550 - 29 Nov 2024
Cited by 1 | Viewed by 795
Abstract
Background: Sulfur (S) is a vital element for the normal growth and development of plants, performing crucial biological functions in various life processes. Methods: This study investigated thirteen S utilization efficiency (SUE)-related traits at the seedling stage of wheat using a recombinant inbred [...] Read more.
Background: Sulfur (S) is a vital element for the normal growth and development of plants, performing crucial biological functions in various life processes. Methods: This study investigated thirteen S utilization efficiency (SUE)-related traits at the seedling stage of wheat using a recombinant inbred line (RIL) population. The quantitative trait loci (QTLs) were mapped by genetic mapping. Thirteen S utilization efficiency-related traits were investigated under two hydroponic culture trials with low S (0.1S, T1), moderate S (0.5S, T2), and high S (1.5S, T3) levels, using the wheat RILs. Results: A total of 170 QTLs for the thirteen traits in different treatment environments were identified. Among them, 89, 103, and 101 QTLs were found in T1, T2, and T3, respectively. A total of 63 QTLs were found in the multiple treatment environments, the other 107 QTLs only being detected in a single treatment environment. Among them, thirteen relatively high-frequency QTLs (RHF-QTLs) and eleven QTL clusters were found. Five (QSh-1D, QRn-1D, QSdw-1D, QTdw-1D, and QTsc-1D) and six (QRdw-6A, QSdw-6A, QTdw-6A, QRsc-6A, QSsc-6A, and QTsc-6A) RHF-QTLs were identified in QTL clusters C3 and C10, respectively. Conclusion: These thirteen RHF-QTLs and eleven QTL clusters are expected to apply to the molecular marker-assisted selection (MAS) of wheat. Full article
(This article belongs to the Special Issue Genomic Studies of Plant Breeding)
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21 pages, 4375 KiB  
Review
Haplotype-Based Approach Represents Locus Specificity in the Genomic Diversification Process in Humans (Homo sapiens)
by Makoto K. Shimada and Tsunetoshi Nishida
Genes 2024, 15(12), 1554; https://doi.org/10.3390/genes15121554 - 29 Nov 2024
Viewed by 855
Abstract
Background/Objectives: Recent progress in evolutionary genomics on human (Homo sapiens) populations has revealed complex demographic events and genomic changes. These include population expansion with complicated migration, substantial population structure, and ancient introgression from other hominins, as well as human characteristics selections. [...] Read more.
Background/Objectives: Recent progress in evolutionary genomics on human (Homo sapiens) populations has revealed complex demographic events and genomic changes. These include population expansion with complicated migration, substantial population structure, and ancient introgression from other hominins, as well as human characteristics selections. Nevertheless, the genomic regions in which such evolutionary events took place have remained unclear. Methods: Here, we focused on eight loci containing the haplotypes that were previously presented as atypical for the mutation pattern in sequence and/or geographic distribution pattern with the model of recent African origin, which constitute two major clusters: African only, and global. This was the consensus model before information regarding introgression from Neanderthal (Homo neanderthalensis) was available. We compared diversity in identical datasets of the modern human population genome, with the 1000 Genomes project among them. Results/Conclusions: This study identified representative genomic regions that show traces of various demographic events and genomic changes that modern humans have undergone by categorizing the relationships in sequence similarity and in worldwide geographic distribution among haplotypes. Full article
(This article belongs to the Special Issue The Genetic Diversification of Human Populations)
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17 pages, 8879 KiB  
Article
Identification and Expression Analysis of Lipoxygenase Gene in Bitter Gourd (Momordica charantia)
by Haicui Ge, Shuang Liu, Hongzhe Zheng, Pengyan Chang, Weiqun Huang, Shanshan Lin, Jingyuan Zheng, Honglong Li, Zedong Huang, Qi Jia and Fenglin Zhong
Genes 2024, 15(12), 1557; https://doi.org/10.3390/genes15121557 - 29 Nov 2024
Cited by 1 | Viewed by 907
Abstract
Background: Lipoxygenases (LOXs) are key enzymes in the unsaturated fatty acid oxidation reaction pathway and play an important regulatory role in the synthesis of fruit aroma volatiles. Methods: LOX gene family members were identified in the whole genome database of bitter gourd and [...] Read more.
Background: Lipoxygenases (LOXs) are key enzymes in the unsaturated fatty acid oxidation reaction pathway and play an important regulatory role in the synthesis of fruit aroma volatiles. Methods: LOX gene family members were identified in the whole genome database of bitter gourd and analyzed bioinformatically. An RT-qPCR was used to analyze the expression differences in different tissues. Monoterpenes were determined by gas chromatography-mass spectrometry (GC-MS) technique. Results: A total of 12 LOX gene family members were identified in the genome. The expression of LOX genes varied significantly among the tissues of roots, stems, leaves, flowers, fruits, seeds and tendrils. A total of 29 monoterpenes were detected in the fruits of five different fruit colors of bitter gourd, mainly containing six types of alcohols, aldehydes, terpenes, ketones, esters and alkynes, with the highest relative content of alcohols. Conclusions: The present study provides a reference for further elucidation of the biological functions of the LOX gene in the synthesis pathway of aroma volatiles in bitter gourd. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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26 pages, 1476 KiB  
Review
From Omics to Multi-Omics: A Review of Advantages and Tradeoffs
by C. Nelson Hayes, Hikaru Nakahara, Atsushi Ono, Masataka Tsuge and Shiro Oka
Genes 2024, 15(12), 1551; https://doi.org/10.3390/genes15121551 - 29 Nov 2024
Cited by 14 | Viewed by 5889
Abstract
Bioinformatics is a rapidly evolving field charged with cataloging, disseminating, and analyzing biological data. Bioinformatics started with genomics, but while genomics focuses more narrowly on the genes comprising a genome, bioinformatics now encompasses a much broader range of omics technologies. Overcoming barriers of [...] Read more.
Bioinformatics is a rapidly evolving field charged with cataloging, disseminating, and analyzing biological data. Bioinformatics started with genomics, but while genomics focuses more narrowly on the genes comprising a genome, bioinformatics now encompasses a much broader range of omics technologies. Overcoming barriers of scale and effort that plagued earlier sequencing methods, bioinformatics adopted an ambitious strategy involving high-throughput and highly automated assays. However, as the list of omics technologies continues to grow, the field of bioinformatics has changed in two fundamental ways. Despite enormous success in expanding our understanding of the biological world, the failure of bulk methods to account for biologically important variability among cells of the same or different type has led to a major shift toward single-cell and spatially resolved omics methods, which attempt to disentangle the conflicting signals contained in heterogeneous samples by examining individual cells or cell clusters. The second major shift has been the attempt to integrate two or more different classes of omics data in a single multimodal analysis to identify patterns that bridge biological layers. For example, unraveling the cause of disease may reveal a metabolite deficiency caused by the failure of an enzyme to be phosphorylated because a gene is not expressed due to aberrant methylation as a result of a rare germline variant. Conclusions: There is a fine line between superficial understanding and analysis paralysis, but like a detective novel, multi-omics increasingly provides the clues we need, if only we are able to see them. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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16 pages, 6728 KiB  
Article
Exploring Immune Cell Infiltration and Small Molecule Compounds for Ulcerative Colitis Treatment
by Yi Lu, Dongqing Lu, Chujie Li and Luping Chen
Genes 2024, 15(12), 1548; https://doi.org/10.3390/genes15121548 - 29 Nov 2024
Viewed by 2067
Abstract
Background/Objectives: Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) with a relapsing nature and complex etiology. Bioinformatics analysis has been widely applied to investigate various diseases. This study aimed to identify crucial differentially expressed genes (DEGs) and explore potential therapeutic agents [...] Read more.
Background/Objectives: Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) with a relapsing nature and complex etiology. Bioinformatics analysis has been widely applied to investigate various diseases. This study aimed to identify crucial differentially expressed genes (DEGs) and explore potential therapeutic agents for UC. Methods: The GSE47908 and GSE55306 colon tissue transcriptome gene datasets were downloaded from the Gene Expression Omnibus-NCBI (GEO) database. GEO2R and Gene Set Enrichment Analysis (GSEA) were used to screen for DEGs in patients with UC compared to the normal population based on weighted gene co-expression network analysis (WGCNA). GO-BP analysis and KEGG enrichment analysis were performed on the intersecting differential genes via the Metascape website, while hub genes were analyzed by STRING11.0 and Cytoscape3.7.1. The expression of hub genes was verified in the dataset GSE38713 colon tissue specimens. Finally, the gene expression profiles of the validation set were analyzed by immuno-infiltration through the ImmuCellAI online tool, and the CMap database was used to screen for negatively correlated small molecule compounds. Results: A total of 595 and 926 genes were screened by analysis of GSE47908 and GSE55306 datasets, respectively. Combined WGCNA hub module intersection yielded 12 hub genes (CXCL8, IL1β, CXCL1, CCL20, CXCL2, CXCR2, LCN2, SELL, AGT, LILRB3, MMP3, IDO1) associated with the pathogenesis of UC. GSEA analysis yielded intersecting pathways for both datasets (colorectal cancer pathway, base excision repair, cell cycle, apoptosis). GO-BP and KEGG enrichment analyses were performed to obtain key biological processes (inflammatory response, response to bacteria, leukocyte activation involved in the immune response, leukocyte–cell adhesion, apoptosis, positive regulation of immune effector processes) and key signaling pathways (cytokine–cytokine receptor interactions, IBD, NOD-like receptor signaling pathways). The immune cell infiltration analysis suggested that the incidence of UC was mainly related to the increase in CD4+T cells, depletion of T cells, T follicular helper cells, natural killer cells, γδ T cells and the decrease in CD8 naive T cells, helper T cells 17 and effector T cells. The CMap database results showed that small molecule compounds such as vorinostat, roxarsone, and wortmannin may be therapeutic candidates for UC. Conclusions: This study not only aids in early prediction and prevention but also provides novel insights into the pathogenesis and treatment of UC. Full article
(This article belongs to the Topic Advances in Genetics and Precision Medicine in Human Diseases)
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22 pages, 4197 KiB  
Article
Deeply Saddening Life Events Play a Carcinogenic Role by Inducing Mutations in ALOX12 and FKBP5 Genes
by Ahmet Kutluhan, Osman Z. Topak, Hakan Akca, Elvan Tokgun, Osman I. Ozdel, Sevda Yilmaz, Ugur Sungurtekin, Ergun Erdem and Arzu Yaren
Genes 2024, 15(12), 1531; https://doi.org/10.3390/genes15121531 - 28 Nov 2024
Viewed by 1254
Abstract
Background/Objectives: In the past few decades, many studies have been conducted to find out that psychological stress and cancer are closely linked. Moreover, it was reported that stress can induce mutations in gene level. Therefore, in this study we want to examine a [...] Read more.
Background/Objectives: In the past few decades, many studies have been conducted to find out that psychological stress and cancer are closely linked. Moreover, it was reported that stress can induce mutations in gene level. Therefore, in this study we want to examine a relationship between stressful life events, gene mutation and cancer. Methods: Stressful Life Experiences Screening (SLES), Hospital Anxiety and Depression Scale (HADS) and the Coping with Stress Style Scale (CSS) were applied to the participants to examine relationship between stress and cancer. Results: NGS results showed higher level of mutations accumulated on FKBP5 and ALOX12 genes in cancer patients who were exposed to stressful life events. The expression status of ALOX12 and FKBP5 genes on patients with or without cancer and several cancer cell lines demonstrated that both ALOX12 and FKBP5 mRNA levels were downregulated only in cancer patients and cancer cell lines but not in cancer free control groups. Re-created overexpression of the WT-ALOX12 and WT-FKBP5 extremely inhibited cellular growth, cellular invasion in cancer cell lines, tumor growth in xenograft model too. Conclusions: Our results indicate that Stressful Life Experiences may induce cancer development by increased somatic mutations in ALOX12 and FKBP5 genes. Full article
(This article belongs to the Section Genes & Environments)
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29 pages, 4490 KiB  
Article
Genotypic Influences on Actuators of Aerobic Performance in Tactical Athletes
by Martin Flück, Christian Protte, Marie-Noëlle Giraud, Thomas Gsponer and Alain Dössegger
Genes 2024, 15(12), 1535; https://doi.org/10.3390/genes15121535 - 28 Nov 2024
Viewed by 2070
Abstract
Background: This study examines genetic variations in the systemic oxygen transport cascade during exhaustive exercise in physically trained tactical athletes. Research goal: To update the information on the distribution of influence of eleven polymorphisms in ten genes, namely ACE (rs1799752), AGT (rs699), MCT1 [...] Read more.
Background: This study examines genetic variations in the systemic oxygen transport cascade during exhaustive exercise in physically trained tactical athletes. Research goal: To update the information on the distribution of influence of eleven polymorphisms in ten genes, namely ACE (rs1799752), AGT (rs699), MCT1 (rs1049434), HIF1A (rs11549465), COMT (rs4680), CKM (rs8111989), TNC (rs2104772), PTK2 (rs7460 and rs7843014), ACTN3 (rs1815739), and MSTN (rs1805086)—on the connected steps of oxygen transport during aerobic muscle work. Methods: 251 young, healthy tactical athletes (including 12 females) with a systematic physical training history underwent exercise tests, including standardized endurance running with a 12.6 kg vest. Key endurance performance metrics were assessed using ergospirometry, blood sampling, and near-infrared spectroscopy of knee and ankle extensor muscles. The influence of gene polymorphisms on the above performance metrics was analyzed using Bayesian analysis of variance. Results: Subjects exhibited good aerobic fitness (maximal oxygen uptake (VO2max): 4.3 ± 0.6 L min−1, peak aerobic power: 3.6 W ± 0.7 W kg−1). Energy supply-related gene polymorphisms rs1799752, rs4680, rs1049434, rs7843014, rs11549465, and rs8111989 did not follow the Hardy–Weinberg equilibrium. Polymorphisms in genes that regulate metabolic and contractile features were strongly associated with variability in oxygen transport and metabolism, such as body mass-related VO2 (rs7843014, rs2104772), cardiac output (rs7460), total muscle hemoglobin content (rs7460, rs4680), oxygen saturation in exercised muscle (rs1049434), and respiration exchange ratio (rs7843014, rs11549465) at first or secondary ventilatory thresholds or VO2max. Moderate influences were found for mass-related power output. Conclusions: The posterior distribution of effects from genetic modulators of aerobic metabolism and muscle contractility mostly confirmed prior opinions in the direction of association. The observed genetic effects of rs4680 and rs1049434 indicate a crucial role of dopamine- and lactate-modulated muscle perfusion and oxygen metabolism during running, suggesting self-selection in Swiss tactical athletes. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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13 pages, 3601 KiB  
Article
Metagenomic Insights into the Enhancement of Bioavailable Nitrogen in Continuous Cropping Soil Through the Application of Traditional Chinese Medicine Residue Following Fumigation
by Xiangqin Xu, Xi Gao, Chen Gui, Hang Wang, Xiaowen Liu and Guoxing Wu
Genes 2024, 15(12), 1532; https://doi.org/10.3390/genes15121532 - 28 Nov 2024
Cited by 2 | Viewed by 858
Abstract
Background/Objectives: Chemical fumigation can effectively inhibit the occurrence of soil-borne diseases; however, this approach can negatively affect the structure of the soil microbial community. The combination of soil fumigant and organic fertilizer application thus represents a widely adopted strategy in agricultural practice. Traditional [...] Read more.
Background/Objectives: Chemical fumigation can effectively inhibit the occurrence of soil-borne diseases; however, this approach can negatively affect the structure of the soil microbial community. The combination of soil fumigant and organic fertilizer application thus represents a widely adopted strategy in agricultural practice. Traditional Chinese medicine residue (TCMR) is a high-quality organic fertilizer; however, the impact of post-fumigation TCMR application on keystone taxa and their functional traits remains uncertain. Methods: This study examined the effects of five fertilization treatments on the diversity, key species, and related functional genes of microbial communities in rhizosphere soil of continuous cropping pepper. Results: Chemical fumigation followed by TCMR application markedly enhanced soil nutrient content in the rhizosphere and significantly influenced microbial community composition as well as functional gene patterns associated with microbial nitrogen cycling. It was also strongly correlated with soil bioavailable nitrogen content. The abundance of keystone bacterial species (Pseudomonadota, Actinomycetota, and Bacillota) substantially increased following TCMR application, alongside a notable rise in Ascomycota abundance within the fungal community. This shift contributed to an increase in beneficial bacterial abundance while reducing that of harmful bacteria. Additionally, TCMR addition affected the abundance of denitrification and DNRA genes involved in nitrogen cycling; specifically, nirB and nirK were strongly associated with soil organic nitrogen content. Conclusions: The combined application of chemical fumigants and TCMR modified the composition of keystone microbial community species by influencing rhizosphere soil TN and other nutrients, and these alterations were linked to multiple nitrogen-cycling functional genes. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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16 pages, 3842 KiB  
Article
Genetic Diversity and Subspecific Races of Upland Cotton (Gossypium hirsutum L.)
by Asiya K. Safiullina, Dilrabo K. Ernazarova, Ozod S. Turaev, Feruza U. Rafieva, Ziraatkhan A. Ernazarova, Sevara K. Arslanova, Abdulqahhor Kh. Toshpulatov, Barno B. Oripova, Mukhlisa K. Kudratova, Kuvandik K. Khalikov, Abdulloh A. Iskandarov, Mukhammad T. Khidirov, John Z. Yu and Fakhriddin N. Kushanov
Genes 2024, 15(12), 1533; https://doi.org/10.3390/genes15121533 - 28 Nov 2024
Cited by 1 | Viewed by 1357
Abstract
Background/Objectives: The classification and phylogenetic relationships of Gossypium hirsutum L. landraces, despite their proximity to southern Mexico, remain unresolved. This study aimed to clarify these relationships using SSR markers and hybridization methods, focusing on subspecies and race differentiation within G. hirsutum L. [...] Read more.
Background/Objectives: The classification and phylogenetic relationships of Gossypium hirsutum L. landraces, despite their proximity to southern Mexico, remain unresolved. This study aimed to clarify these relationships using SSR markers and hybridization methods, focusing on subspecies and race differentiation within G. hirsutum L. Methods: Seventy polymorphic SSR markers (out of 177 tested) were used to analyze 141 alleles and calculate genetic distances among accessions. Phylogenetic relationships were determined using MEGA software (version 11.0.13) and visualized in a phylogenetic tree. ANOVA in NCSS 12 was used for statistical analysis. Over 1000 inter-race crosses were conducted to assess boll-setting rates. Results: Distinct phylogenetic patterns were identified between G. hirsutum subspecies and races, correlating with boll-setting rates. Latifolium, richmondii, and morilli showed no significant increase in boll-setting rates in reciprocal crosses. Cultivars Omad and Bakht, as paternal parents, yielded higher boll-setting rates. Religiosum and yucatanense displayed high boll- and seed-setting rates as maternal parents but low rates as paternal parents. Additionally, phylogenetic analysis revealed a close relationship between cultivars ‘Omad’ and ‘Bakht’ with G. hirsutum race richmondii, indicating their close evolutionary relationship. Conclusions: Reciprocal differentiation characteristics of G. hirsutum subspecies and races, particularly religiosum and yucatanense, should be considered during hybridization for genetic and breeding studies. Understanding the phylogenetic relationships among G. hirsutum taxa is crucial for exploring the genetic diversity of this economically important species. Full article
(This article belongs to the Special Issue Plant Genetic Resources: Genetic Diversity, Conservation, and Utilization)
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13 pages, 2256 KiB  
Article
Identification of Key Genes Involved in Sesquiterpene Synthesis in Nardostachys jatamansi Based on Transcriptome and Component Analysis
by Xiaohui Tang, Tingju Li, Zhiyu Hao, Wenji Zhao, Yanlong Han, Guofu Jia, Zhengjun He, Chaoxiang Ren, Ke Rao, Jin Pei and Jiang Chen
Genes 2024, 15(12), 1539; https://doi.org/10.3390/genes15121539 - 28 Nov 2024
Viewed by 962
Abstract
Background: Nardostachys jatamansi (D. Don) DC. (N. jatamansi.) is an endangered medicinal plant native to the Himalayas that is widely used in traditional medicine due to its terpenoid compounds, especially sesquiterpenes, which are abundant in N. jatamansi. However, the [...] Read more.
Background: Nardostachys jatamansi (D. Don) DC. (N. jatamansi.) is an endangered medicinal plant native to the Himalayas that is widely used in traditional medicine due to its terpenoid compounds, especially sesquiterpenes, which are abundant in N. jatamansi. However, the mechanism of sesquiterpene metabolism remains unclear. Methods: Transcriptome sequencing analyses of different parts (roots and rhizomes, leaves, anthocaulus and flowers) and developmental stages (rejuvenation, budding, flowering, fruiting and withering) of cultivated N. jatamansi were conducted using the Illumina platform. Key genes involved in regulating the sesquiterpene metabolism pathway in N. jatamansi were identified by combining component analyses of various tissues and developmental stages. Furthermore, these key genes were validated through MeJA treatment and a chemical composition analysis. Results: A transcriptome sequencing analysis was performed on 24 samples from four tissues and in five developmental stages, yielding 183.18 Gb of clean data with a Q30 base percentage of 92% or above. A total of 269,136 UniGenes were obtained and annotated. Genes related to sesquiterpene synthesis were screened and validated by RT–qPCR using annotation results from various databases. Twelve candidate genes involved in sesquiterpene synthase were identified. Following MeJA treatment, an RT–qPCR analysis revealed that the expression of the NjTPS-49, NjTPS-54, NjTPS-56, NjTPS-57 and NjTPS-59 genes was positively regulated. Additionally, an HPLC analysis indicated an increase in the nardosinone content after MeJA treatment. This study demonstrates that NjTPS-49, NjTPS-54, NjTPS-56, NjTPS-57 and NjTPS-59 are potential candidate genes for sesquiterpene synthesis. Conclusion: The obtained findings establish the groundwork for elucidating the mechanism of sesquiterpene synthesis in N. jatamansi and contribute to the conservation of N. jatamansi resources. Full article
(This article belongs to the Special Issue Molecular Genetics and Multi-omics in Medicinal Plants)
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40 pages, 4795 KiB  
Article
New Insights into the Molecular Evolution of Tapirus pinchaque (Tapiridae, Perissodactyla) and the Rise and Fall of Tapirus kabomani as a Full Species
by Manuel Ruiz-García, Armando Castellanos, Franz Kaston, Myreya Pinedo-Castro and Joseph Mark Shostell
Genes 2024, 15(12), 1537; https://doi.org/10.3390/genes15121537 - 28 Nov 2024
Viewed by 1732
Abstract
Large wild mammals are extremely important in their respective ecological communities and are frequently considered to be emblematic. This is the case of the different tapir species, the largest terrestrial mammals from the Neotropics. Despite their large size and being objects of interest [...] Read more.
Large wild mammals are extremely important in their respective ecological communities and are frequently considered to be emblematic. This is the case of the different tapir species, the largest terrestrial mammals from the Neotropics. Despite their large size and being objects of interest for many naturalists, the field still lacks critical genetics and systematics information about tapir species. In the current work, we analyzed four molecular datasets (mitogenomes, and three nuclear genes, RAG 1-2, IRBP, and BRCA1) of two South American tapirs: the Andean tapir (Tapirus pinchaque) and the alleged new species of tapir, Tapirus kabomani. We derived four main findings. (1) Our molecular phylogenetic analyses showed T. pinchaque as the youngest tapir branch in Neotropics and a sister species of Tapirus terrestris. This contradicts the traditional morphological observations of renowned zoologists and paleontologists, who considered T. pinchaque as the oldest Neotropical tapir. (2) Our data does not support that the alleged T. kabomani is a full species. Rather, it is a specific group within T. terrestris. (3) T. pinchaque is the Neotropical tapir species which yielded the lowest levels of genetic diversity (both for mitochondrial and nuclear data). (4) The spatial genetic structure for T. pinchaque shows differences depending on the type of molecular marker used. With mitogenomes, the spatial structure is relatively weak, whereas with two nuclear genes (RAG 1-2 and IRBP), the spatial structure is highly significant. Curiously, for the other nuclear gene (BRCA1), the spatial structure is practically nonexistent. In any case, the northernmost population of T. pinchaque we studied (Los Nevados National Park in Colombia) was in a peripatric situation and was the most genetically differentiated. This is important for the adequate conservation of this population. (5) T. pinchaque showed clear evidence of population expansion during the last part of the Pleistocene, a period during which the dryness and glacial cold extinguished many large mammals in the Americas. However, T. pinchaque survived and spread throughout the Northern Andes. Full article
(This article belongs to the Special Issue New Phylogenetic and Phylogeography Insights in Animals Using Genes, Genomics, Chromosomes, and Morphological Traits)
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13 pages, 1929 KiB  
Review
Hotspots for Disease-Causing Mutations in the Mitochondrial TIM23 Import Complex
by Sahil Jain, Eyal Paz and Abdussalam Azem
Genes 2024, 15(12), 1534; https://doi.org/10.3390/genes15121534 - 28 Nov 2024
Viewed by 1441
Abstract
The human mitochondrial proteome comprises approximately 1500 proteins, with only 13 being encoded by mitochondrial DNA. The remainder are encoded by the nuclear genome, translated by cytosolic ribosomes, and subsequently imported into and sorted within mitochondria. The process of mitochondria-destined protein import is [...] Read more.
The human mitochondrial proteome comprises approximately 1500 proteins, with only 13 being encoded by mitochondrial DNA. The remainder are encoded by the nuclear genome, translated by cytosolic ribosomes, and subsequently imported into and sorted within mitochondria. The process of mitochondria-destined protein import is mediated by several intricate protein complexes distributed among the four mitochondrial compartments. The focus of this mini-review is the translocase of the inner membrane 23 (TIM23) complex that assists in the import of ~60% of the mitochondrial proteome, which includes the majority of matrix proteins as well as some inner membrane and intermembrane space proteins. To date, numerous pathogenic mutations have been reported in the genes encoding various components of the TIM23 complex. These diseases exhibit mostly developmental and neurological defects at an early age. Interestingly, accumulating evidence supports the possibility that the gene for Tim50 represents a hotspot for disease-causing mutations among core TIM23 complex components, while genes for the mitochondrial Hsp70 protein (mortalin) and its J domain regulators represent hotspots for mutations affecting presequence translocase-associated motor (PAM) subunits. The potential mechanistic implications of the discovery of disease-causing mutations on the function of the TIM23 complex, in particular Tim50, are discussed. Full article
(This article belongs to the Special Issue Variations of Rare Genetic Diseases)
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13 pages, 5625 KiB  
Article
Chromosome-Level Assembly and Annotation of the Endangered Red-Wing Fish (Distoechodon macrophthalmus)
by Xiangyun Zhu, Yanping Luo, Baoshan Ma, Qi Shen, Xingyu Zheng, Mei Xu, Qiang Sheng and Junjie Wu
Genes 2024, 15(12), 1536; https://doi.org/10.3390/genes15121536 - 28 Nov 2024
Viewed by 982
Abstract
Background/Objectives: The red-wing fish (Distoechodon macrophthalmus), an endangered species native to Yunnan, is endemic to Chenghai Lake. The natural population of this species has suffered a sharp decline due to the invasion of alien fish species. Fortunately, the artificial domestication and [...] Read more.
Background/Objectives: The red-wing fish (Distoechodon macrophthalmus), an endangered species native to Yunnan, is endemic to Chenghai Lake. The natural population of this species has suffered a sharp decline due to the invasion of alien fish species. Fortunately, the artificial domestication and reproduction of D. macrophthalmus have been successful and this species has become an economic species locally. However, there is still little research on D. macrophthalmus. Methods: In this study, a high-quality genome of D. macrophthalmus was assembled and annotated. The genome was sequenced and assembled using the PacBio platform and Hi-C method. Results: The genome size is 1.01 Gb and N50 is 37.99 Mb. The assembled contigs were anchored into 24 chromosomes. BUSCO analysis revealed that the genome assembly has 95.6% gene coverage completeness. A total of 455.62 Mb repeat sequences (48.50% of the assembled genome) and 30,424 protein-coding genes were identified in the genome. Conclusions: This study provides essential genomic data for further research on the evolution and conservation of D. macrophthalmus. Meanwhile, the high-quality genome assembly also provides insights into the genomic evolution of the genus Distoechodon. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science—2nd Edition)
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21 pages, 10653 KiB  
Article
5-Hydroxytryptamine G-Protein-Coupled Receptor Family Genes: Key Players in Cancer Prognosis, Immune Regulation, and Therapeutic Response
by Simeng Liu, Mingang He, Hefen Sun, Yi Wu and Wei Jin
Genes 2024, 15(12), 1541; https://doi.org/10.3390/genes15121541 - 28 Nov 2024
Cited by 2 | Viewed by 1445
Abstract
Background: Firstly, 5-hydroxytryptamine G-protein-coupled receptors (HTGPCRs) are a family of 13 genes associated with cancer progression. Nevertheless, a comprehensive understanding of HTGPCRs in cancer remains largely lacking. Method: We tested the gene expression levels and prognostic values for the HTGPCRs in [...] Read more.
Background: Firstly, 5-hydroxytryptamine G-protein-coupled receptors (HTGPCRs) are a family of 13 genes associated with cancer progression. Nevertheless, a comprehensive understanding of HTGPCRs in cancer remains largely lacking. Method: We tested the gene expression levels and prognostic values for the HTGPCRs in relation to pan-cancer. A subsequent analysis examined the relationships among HTGPCR expression and clinical characteristics, immune subtypes, stemness scores, tumor microenvironments (TMEs), single-cell analyses, and drug sensitivity. Result: A significant difference in HTGPCR expression was found between normal tissues and tumors. HTR1D/2C expressed higher levels in breast invasive carcinoma (BRCA), colon adenocarcinoma, and liver hepatocellular carcinoma. HTGPCR gene expression was correlated with prognosis in many cancers. HTR1D/2C were associated with poorer overall survival for head and neck squamous cell carcinoma. In addition, HTGPCR expression correlated significantly with the stemness scores of RNA and DNA, TMB, and MSI, as well as stromal and immune scores of pan-cancer patients. Additionally, the expression of HTR2A/2B/7 was correlated significantly with immune cells and immune checkpoint genes in a variety of cancers, such as BRCA, brain lower-grade glioma, and lung adenocarcinoma. Immune regulation and TME were both regulated by HTGPCRs. Using single-cell analysis, we found that the gene set of HTGPCRs correlated with many cancer-related functional states in retinoblastoma. Moreover, drug sensitivity and HTR4 were significantly correlated. Furthermore, we validated results in breast cancer and found knockdown of HTR1D inhibited breast cancer cell growth and metastasis. Conclusion: As prognostic indicators, HTGPCRs hold considerable promise and offer insights into the therapeutic targets for malignancy. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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16 pages, 4546 KiB  
Article
Potential Utility of Bacillus amyloliquefaciens SFB-1 as a Biocontrol Agent for Sweetpotato Black Rot Caused by Ceratocystis fimbriata
by Fangyuan Gao, Xiaosi Zhou, Dongjing Yang, Jingwei Chen, Veronica Tshegofatso Kgosi, Chengling Zhang, Jukui Ma, Wei Tang, Zhao Liang and Houjun Sun
Genes 2024, 15(12), 1540; https://doi.org/10.3390/genes15121540 - 28 Nov 2024
Cited by 2 | Viewed by 980
Abstract
Background/Objectives: Sweetpotato black rot, caused by Ceratocystis fimbriata, is a severe fungal disease in sweetpotato production. Biological control strategies represent a promising, environmentally sustainable approach to managing this disease. This study investigates the biocontrol potential of Bacillus amyloliquefaciens SFB-1 against C. [...] Read more.
Background/Objectives: Sweetpotato black rot, caused by Ceratocystis fimbriata, is a severe fungal disease in sweetpotato production. Biological control strategies represent a promising, environmentally sustainable approach to managing this disease. This study investigates the biocontrol potential of Bacillus amyloliquefaciens SFB-1 against C. fimbriata. Methods: The antagonistic activities of strain SFB-1 on C. fimbriata were assessed through in vitro assays, including evaluations of mycelial inhibition, spore germination, and mycelial morphology. Pathogenicity assays on harvested sweetpotato roots assessed lesion diameter and depth. A transcriptomic analysis of C. fimbriata exposed to strain SFB-1 was performed to explore the underlying antifungal mechanism of SFB-1 on C. fimbriata. The qRT-PCR was employed to validate the RNA-seq results. Results: In vitro assays demonstrated that strain SFB-1 inhibited C. fimbriata mycelial growth by up to 81.01%, caused mycelial swelling, and completely suppressed spore germination at 108 CFU/mL. The cell-free supernatant of strain SFB-1 also suppressed C. fimbriata growth. Pathogenicity assays revealed that strain SFB-1 treatments reduced lesion diameter and depth on harvested sweetpotato roots by over 50% compared to untreated controls. Transcriptomic analysis of C. fimbriata treated with strain SFB-1 identified 1164 differentially expressed genes, with significant alterations in genes associated with cell wall integrity, cell membrane stability, spore germination, detoxification, and antioxidant responses. The qRT-PCR validation of 16 genes confirmed the consistency with the RNA-seq results. Conclusions: B. amyloliquefaciens SFB-1 demonstrates significant biocontrol efficacy against C. fimbriata through multiple mechanisms, positioning it as a promising solution for the sustainable management of sweetpotato black rot. Full article
(This article belongs to the Special Issue Advances in Genetic Breeding of Sweetpotato)
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12 pages, 3585 KiB  
Article
Melatonin Improves H2O2-Induced Oxidative Stress in Sertoli Cells Through Nrf2-Keap1 Signaling Pathway
by Ying Tang, Ziming Wang, Yanru Chen, Junying Wang, Hongzhan Wang, Bo Li, Bojing Liu and Peng Zheng
Genes 2024, 15(12), 1544; https://doi.org/10.3390/genes15121544 - 28 Nov 2024
Viewed by 1142
Abstract
Background: Oxidative stress in the testicles of male livestock can cause reduced fertility. Melatonin is a natural product with antioxidant effects, but its specific antioxidant mechanism is still unclear. This study used calf testicular Sertoli cells as materials to explore the mechanism [...] Read more.
Background: Oxidative stress in the testicles of male livestock can cause reduced fertility. Melatonin is a natural product with antioxidant effects, but its specific antioxidant mechanism is still unclear. This study used calf testicular Sertoli cells as materials to explore the mechanism by which melatonin alleviates the oxidative stress of Sertoli cells, laying a foundation for improving the fertility of bulls. Methods: The optimal treatment concentrations of H2O2 and melatonin (MLT) were screened out using a CCK8 kit and MDA kit. Then, the cells were divided into four groups for treatment: control group, H2O2 treatment group, MLT treatment group, and H2O2 and MLT co-treatment group, then the MDA, ROS, GSH, and SOD contents were detected. Real-time quantitative PCR analysis and Western blot analysis were used to detect genes and proteins related to the Nrf2-Keap1 pathway. Immunofluorescence staining was used to analyze changes in Nrf2. Results: Research results show that the MDA content of cells in the group treated with H2O2 and MLT combined was significantly lower than that in the group treated with H2O2 alone, but there was no difference from the control group. Compared with the control group, the ROS level of cells in the H2O2-treated group significantly increased, and the content of GSH and SOD significantly decreased. Compared with the H2O2-treated group, the ROS level of cells in the H2O2 and MLT co-treated group significantly decreased, and the content of GSH and SOD increased significantly, but no difference from the control group. Similarly, MTL can alleviate the changes in cellular Nrf2, Keap1, HO-1, and NQO1 expression caused by H2O2. Conclusions: Melatonin activates the Nrf2-Keap1 signaling pathway in Sertoli cells, elevating the expression of HO-1 and NQO1, and thereby exerting its antioxidant capabilities. Full article
(This article belongs to the Special Issue Genetic Regulation Mechanisms of Animal Reproduction)
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15 pages, 1428 KiB  
Article
Upregulation of ABLIM1 Differentiates Intrahepatic Cholangiocarcinoma from Hepatocellular Carcinoma and Both Colorectal and Pancreatic Adenocarcinoma Liver Metastases
by Tina Draškovič, Branislava Ranković, Nina Zidar and Nina Hauptman
Genes 2024, 15(12), 1545; https://doi.org/10.3390/genes15121545 - 28 Nov 2024
Cited by 1 | Viewed by 1332
Abstract
Background: Altered gene expression in cancers holds great potential to improve the diagnostics and differentiation of primary and metastatic liver cancers. In this study, the expression of the protein-coding genes ring finger protein 135 (RNF135), ephrin-B2 (EFNB2), ring finger [...] Read more.
Background: Altered gene expression in cancers holds great potential to improve the diagnostics and differentiation of primary and metastatic liver cancers. In this study, the expression of the protein-coding genes ring finger protein 135 (RNF135), ephrin-B2 (EFNB2), ring finger protein 125 (RNF125), homeobox-C 4 (HOXC4), actin-binding LIM protein 1 (ABLIM1) and oncostatin M receptor (OSMR) and the long non-coding RNAs (lncRNA) prospero homeobox 1 antisense RNA 1 (PROX1-AS1) and leukemia inhibitory factor receptor antisense RNA 1 (LIFR-AS1) was investigated in hepatocellular carcinoma, cholangiocarcinoma, colorectal liver metastases and pancreatic ductal adenocarcinoma liver metastases. Methods: This study included 149 formalin-fixed, paraffin-embedded samples from 80 patients. After RNA isolation, quantification, reverse transcription and preamplification, real-time qPCR was performed. The gene expression between different groups was calculated relative to the expression of the reference genes using the ∆∆Cq method and statistically analyzed. The expression of the genes was additionally analyzed using the AmiCA and UCSC Xena platforms. Results: In primary cancers, our results showed differential expression between primary tumors and healthy tissues for all the genes and lncRNA examined. Moreover, we found downregulation of RNF135 in hepatocellular carcinoma, downregulation of OSMR in colorectal liver metastases and upregulation of HOXC4 in cholangiocarcinoma compared to primary liver cancers and metastatic cancers. The major finding is the upregulation of ABLIM1 in cholangiocarcinoma compared to hepatocellular carcinoma, colorectal liver metastases, pancreatic ductal adenocarcinoma liver metastases and healthy liver tissue. We propose ABLIM1 as a potential biomarker that differentiates cholangiocarcinoma from other cancers and healthy liver tissue. Conclusions: This study emphasizes the importance of understanding the differences in gene expression between healthy tissues and primary and metastatic cancers and highlights the potential use of altered gene expression as a diagnostic biomarker in these malignancies. Full article
(This article belongs to the Special Issue Genomic Diagnosis of Human Cancers)
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13 pages, 1986 KiB  
Review
Loss of Heterozygosity (LOH) Affecting HLA Genes in Breast Cancer: Clinical Relevance and Therapeutic Opportunities
by María Antonia Garrido, Alba Navarro-Ocón, Víctor Ronco-Díaz, Nicolás Olea and Natalia Aptsiauri
Genes 2024, 15(12), 1542; https://doi.org/10.3390/genes15121542 - 28 Nov 2024
Cited by 2 | Viewed by 2575
Abstract
Major histocompatibility complex (MHC) class-I molecules (or Human Leucocyte Antigen class-I) play a key role in adaptive immunity against cancer. They present specific tumor neoantigens to cytotoxic T cells and provoke an antitumor cytotoxic response. The total or partial loss of HLA molecules [...] Read more.
Major histocompatibility complex (MHC) class-I molecules (or Human Leucocyte Antigen class-I) play a key role in adaptive immunity against cancer. They present specific tumor neoantigens to cytotoxic T cells and provoke an antitumor cytotoxic response. The total or partial loss of HLA molecules can inhibit the immune system’s ability to detect and destroy cancer cells. Loss of heterozygosity (LOH) is a common irreversible genetic alteration that occurs in the great majority of human tumors, including breast cancer. LOH at chromosome 6, which involves HLA genes (LOH-HLA), leads to the loss of an HLA haplotype and is linked to cancer progression and a weak response to cancer immunotherapy. Therefore, the loss of genes or an entire chromosomal region which are critical for antigen presentation is of particular importance in the search for novel prognostic and clinical biomarkers in breast cancer. Here, we review the role of LOH-HLA in breast cancer, its contribution to an understanding of cancer immune escape and tumor progression, and discuss how it can be targeted in cancer therapy. Full article
(This article belongs to the Special Issue Genetic and Genomic Abnormalities in Cancer)
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12 pages, 1834 KiB  
Article
Comparative Evolutionary Genomics Reveals Genetic Diversity and Differentiation in Bacteroides fragilis
by Yoshinori Muto and Kaori Tanaka
Genes 2024, 15(12), 1519; https://doi.org/10.3390/genes15121519 - 27 Nov 2024
Viewed by 1310
Abstract
Background/Objectives: Bacteroides fragilis is the pathogenic anaerobe most commonly isolated from intra-abdominal infections, abscesses, and blood. Despite its clinical importance, research on its pan-genome-scale evolution is still limited. Methods: Herein, we analyzed the pan-genome architecture of 374 B. fragilis strains to explore their [...] Read more.
Background/Objectives: Bacteroides fragilis is the pathogenic anaerobe most commonly isolated from intra-abdominal infections, abscesses, and blood. Despite its clinical importance, research on its pan-genome-scale evolution is still limited. Methods: Herein, we analyzed the pan-genome architecture of 374 B. fragilis strains to explore their intra-species genomic diversity and evolutionary patterns. Results: Our analysis revealed an open pan-genome with a high proportion of accessory genomes, indicating high genetic variability. Accessory genome genes were substantially enriched in the functions of “Replication, Recombination, and Repair” suggesting their roles in gene transfer and divergence. Phylogenomic analysis divided B. fragilis into two distinct clades: divisions I and II, differing in gene content, antimicrobial resistance genes, and mobile genetic elements. Division II revealed higher Tajima’s D values, suggesting that it separated after B. fragilis’s recent species diversification. The extreme shift in the distribution of gene-wise Hudson’s fixation index (Fst) values for each division suggested that several genes are highly differentiated or evolved between the two clades. Average nucleotide identity and 16S rRNA analyses showed that B. fragilis division II represents a distinct species, Bacteroides hominis. Additionally, a considerable depletion of recombination in genes with Fst values > 0.99 was noted, suggesting that the highest Fst genes with little recombination are the basis for differentiation between divisions. Conclusions: Overall, this study enhances the understanding of B. fragilis’s genomic diversity, evolutionary dynamics, and potential role in pathogenesis, shedding light on its adaptation and diversification. Full article
(This article belongs to the Section Microbial Genetics and Genomics)
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13 pages, 2311 KiB  
Article
Assessment of a Novel Stress and Immune Gene Panel on the Development of Australasian Snapper (Chrysophrys auratus) Larvae
by Kerry L. Bentley-Hewitt and Duncan I. Hedderley
Genes 2024, 15(12), 1520; https://doi.org/10.3390/genes15121520 - 27 Nov 2024
Viewed by 707
Abstract
Background: Larvae development is a critical step in aquaculture, yet the development of immune and stress responses during this early phase of life is not well understood. Snapper is a species that has been selected as a candidate for aquaculture in New Zealand. [...] Read more.
Background: Larvae development is a critical step in aquaculture, yet the development of immune and stress responses during this early phase of life is not well understood. Snapper is a species that has been selected as a candidate for aquaculture in New Zealand. Methods: In this study we explore a set of 18 genes identified as potentially being involved in the stress and immune responses of snapper larvae during the first 30 days of development. Larvae were collected between 11:45 a.m. and 16:10 p.m. each day. Results: Most genes did not deviate from baseline expression throughout the 30 days, with some exceptions between Days 0 and 6 with glyceraldehyde-3-phosphate dehydrogenase and superoxide dismutase, mitochondrial uncoupling protein 2-like, peroxiredoxin-5 mitochondrial, and hepcidin, which predominantly increased and then stabilized by Day 6 until Day 30. Some genes were affected by the time of day, such as actin cytoplasmic 1 and catalase isoform X2. Conclusions: This exploratory study is the first to look at a panel of stress- and immune-related marker gene expression during early snapper development. It sets methods in place to explore the expression of these markers and determine the impact of different potential stressors, such as alternative food sources and other environmental changes. It also highlights the importance of same time of day collections for gene expression studies. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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17 pages, 4486 KiB  
Article
Genome-Wide Association Study of Body Weight Traits in Texel and Kazakh Crossbred Sheep
by Sheng Wang, Mingjun Liu, Huiguo Zhang, Sangang He, Wenrong Li and Long Liang
Genes 2024, 15(12), 1521; https://doi.org/10.3390/genes15121521 - 27 Nov 2024
Cited by 2 | Viewed by 1623
Abstract
Background: Originating from the cold and arid regions of northwestern China, Kazakh sheep are dual-purpose breeds optimized for both meat and fat production. In contrast, Texel sheep are internationally recognized for their high-quality meat and exceptional flavor. Previous studies have indicated that the [...] Read more.
Background: Originating from the cold and arid regions of northwestern China, Kazakh sheep are dual-purpose breeds optimized for both meat and fat production. In contrast, Texel sheep are internationally recognized for their high-quality meat and exceptional flavor. Previous studies have indicated that the hybrids of Texel and Kazakh sheep exhibit significant quality advantages. Additionally, body weight is a crucial indicator of sheep production performance, directly correlating with meat yield and economic returns. Objective: This study aims to identify genetic variations and related genes associated with the body weight traits of hybrid lambs, thereby revealing their genetic mechanisms. Methods: This study genotyped hybrid lambs using a 50K chip and performed rigorous quality control on both genotypic and phenotypic data. The traits examined include body weight traits of lambs at various stages such as birth, pre-weaning, and post-weaning. Various genome-wide association study (GWAS) models were utilized to analyze the association between lamb body weight traits and genetic markers. The study then employed an Ensemble-like GWAS (E-GWAS) strategy to integrate these models, achieving a stable list of SNPs, rather than a mere aggregation. Multiple annotation databases were consulted to further investigate the mechanisms by which genetic markers affect body weight traits. All study results were validated through an extensive literature review. Results: Analyses with multiple statistical models revealed that 48 SNPs were significantly associated with body weight traits. The annotation process identified 24 related genes (including 4 unknown genes) and 9 quantitative trait loci (QTLs). Additionally, 6 Gene Ontology (GO) terms and 22 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined. Conclusions: This study identified key genes and pathways in the body weight traits of hybrids between Texel and Kazakh sheep, enhancing our understanding of their genetic mechanisms. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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18 pages, 4639 KiB  
Article
Genomic Landscape of Chromosome X Factor VIII: From Hemophilia A in Males to Risk Variants in Females
by Olivia Morris, Michele Morris, Shawn Jobe, Disha Bhargava, Jena M. Krueger, Sanjana Arora, Jeremy W. Prokop and Cynthia Stenger
Genes 2024, 15(12), 1522; https://doi.org/10.3390/genes15121522 - 27 Nov 2024
Viewed by 1843
Abstract
Background: Variants within factor VIII (F8) are associated with sex-linked hemophilia A and thrombosis, with gene therapy approaches being available for pathogenic variants. Many variants within F8 remain variants of uncertain significance (VUS) or are under-explored as to their connections to phenotypic outcomes. [...] Read more.
Background: Variants within factor VIII (F8) are associated with sex-linked hemophilia A and thrombosis, with gene therapy approaches being available for pathogenic variants. Many variants within F8 remain variants of uncertain significance (VUS) or are under-explored as to their connections to phenotypic outcomes. Methods: We assessed data on F8 expression while screening the UniProt, ClinVar, Geno2MP, and gnomAD databases for F8 missense variants; these collectively represent the sequencing of more than a million individuals. Results: For the two F8 isoforms coding for different protein lengths (2351 and 216 amino acids), we observed noncoding variants influencing expression which are also associated with thrombosis risk, with uncertainty as to differences in females and males. Variant analysis identified a severe stratification of potential annotation issues for missense variants in subjects of non-European ancestry, suggesting a need for further defining the genetics of diverse populations. Additionally, few heterozygous female carriers of known pathogenic variants have sufficiently confident phenotyping data, leaving researchers unable to determine subtle, less defined phenotypes. Using structure movement correlations to known pathogenic variants for the VUS, we determined seven clusters of likely pathogenic variants based on screening work. Conclusions: This work highlights the need to define missense variants, especially those for VUS and from subjects of non-European ancestry, as well as the roles of these variants in women’s physiology. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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17 pages, 3072 KiB  
Article
Association of Variants in IL-1RN (rs2234663) and IL-1β (rs1143627, rs16944) and Interleukin-1β Levels with Colorectal Cancer: Experimental Study and In Silico Analysis
by Martha Patricia Gallegos-Arreola, Asbiel Felipe Garibaldi-Ríos, Itzae Adonaí Gutiérrez-Hurtado, Guillermo Moisés Zúñiga-González, Luis E. Figuera, Belinda Claudia Gómez-Meda, Ana María Puebla-Pérez, José Elías García-Ortiz, Jorge I. Delgado-Saucedo, Paola Beatriz Castro-García, María de Jesús Rentería-Ramírez and Blanca Miriam Torres-Mendoza
Genes 2024, 15(12), 1528; https://doi.org/10.3390/genes15121528 - 27 Nov 2024
Viewed by 918
Abstract
Background/Objectives. Colorectal cancer (CRC) is a multifactorial disease where the inflammatory state is crucial. This study analyzes the association of the IL-1RN (rs2234663) and IL-1β (rs1143627, rs16944) variants and IL-1β levels with CRC. Methods. This study included 230 CRC patients and 256 controls. [...] Read more.
Background/Objectives. Colorectal cancer (CRC) is a multifactorial disease where the inflammatory state is crucial. This study analyzes the association of the IL-1RN (rs2234663) and IL-1β (rs1143627, rs16944) variants and IL-1β levels with CRC. Methods. This study included 230 CRC patients and 256 controls. Genotypes were determined by PCR and plasma IL-1β levels by ELISA. RegulomeDB analyzed the variants’ functional impacts, while OncoDB assessed IL-1β and IL-1RN expression’s influence on CRC. Results. The A1A1 genotype and dominant pattern of the rs2234663 variant were risk factors for CRC, whereas the A1A2 genotype showed a protective effect. The TC genotype of the rs1143627 variant and the T allele of rs16944 were associated with increased risk, whereas the C allele had a protective effect. The A1A1 genotype was associated with stage I–II CRC diagnosis, while the A2A2 genotype was associated with stage III–IV and ethanol consumption. The CC genotype of rs1143627 was associated with people younger than 50 years and tobacco use, and the TCCC genotype was related to stage III–IV stages and metastasis and hemorrhoids (p < 0.05). IL-1β levels were not associated with CRC. In silico analysis revealed that the variants are in located in important regions regulatory of genes. Elevated IL-1B and IL-1RN mRNA levels were found in CRC, linked to clinicopathological features of the disease. Conclusions. The analyzed variants are associated with CRC and may influence gene regulation by being located at critical sites of key genetic regulators. Full article
(This article belongs to the Special Issue Genetic and Genomic Research on Colorectal Cancer)
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14 pages, 11945 KiB  
Article
Mitochondrial Genome Assembly and Comparative Analysis of Chionanthus Retusus (Oleaceae)
by Shasha Zhai, Furong Lin, Xiuge Shu, Hongyun Niu, Qi Jing, Lei Gao, Xiangbin Gao and Dan Liu
Genes 2024, 15(12), 1523; https://doi.org/10.3390/genes15121523 - 27 Nov 2024
Viewed by 1010
Abstract
Background/Objectives: Chionanthus retusus Lindl. & Paxton is an ornamental tree species native to North China. Research on the mitochondrial genome can elucidate the evolution and biological characteristics of C. retusus and better protect this important species. Methods and Results: This work aimed to [...] Read more.
Background/Objectives: Chionanthus retusus Lindl. & Paxton is an ornamental tree species native to North China. Research on the mitochondrial genome can elucidate the evolution and biological characteristics of C. retusus and better protect this important species. Methods and Results: This work aimed to clarify the evolutionary and phylogenetic links by sequencing, assembling, annotating, and analyzing the entire mitochondrial genome of C. retusus. The single-loop structure that made up the mitochondrial genome had a total length of 657,640 bp and a GC content of 44.52%. In total, 37 unique protein-coding genes, 20 tRNA genes, and 3 rRNA genes were identified. Numerous repeat sequences and migrating fragments of chloroplast sequences were found. Using the mitochondrial protein-coding genes to construct evolutionary trees, it was found that the closest relative of C. retusus is C. rupicola (Lingelsh.) Kiew. Conclusions: This research represents the first comprehensive set of data on the mitochondrial genome of an ancient (>500 yr) C. retusus specimen. In addition to elucidating the biological characteristics of C. retusus. The findings contribute to the Oleaceae mitochondrial genome database and offer valuable insights for future studies in molecular breeding, evolutionary biology, and genetic diversity conservation. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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