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Menin in Cancer
The Roles of Proton-Sensing G-Protein-Coupled Receptors in Inflammation and Cancer
Developing a Machine-Learning ‘Smart’ PCR Thermocycler, Part 1: Construction of a Theoretical Framework
Recent Progress of Antisense Oligonucleotide Therapy for Superoxide-Dismutase-1-Mutated Amyotrophic Lateral Sclerosis: Focus on Tofersen
Cell-Free DNA Hydroxymethylation in Cancer: Current and Emerging Detection Methods and Clinical Applications

Journal Description

Genes

Genes is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Spanish Society for Biochemistry and Molecular Biology (SEBBM) is affiliated with Genes and their members receive discounts on the article processing charges.

Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
Journal Rank: JCR - Q2 (Genetics and Heredity) / CiteScore - Q2 (Genetics (clinical))
Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.3 days after submission; acceptance to publication is undertaken in 2.6 days (median values for papers published in this journal in the first half of 2024).
Recognition of Reviewers: Reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.

Impact Factor: 2.8 (2023); 5-Year Impact Factor: 3.3 (2023)

Imprint Information Journal Flyer Open Access ISSN: 2073-4425

Latest Articles

11 pages, 547 KiB

Open AccessCase 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 (registering DOI) - 5 Dec 2024

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)

15 pages, 2792 KiB

Open AccessArticle

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

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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23 pages, 4761 KiB

Open AccessArticle

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

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

Open AccessOpinion

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

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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20 pages, 10153 KiB

Open AccessArticle

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

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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16 pages, 7730 KiB

Open AccessArticle

Exploration of Key Regulatory Factors in Mesenchymal Stem Cell Continuous Osteogenic Differentiation via Transcriptomic Analysis

by Yu Pan, Tao Liu, Linfeng Li, Liang He, Shu Pan and Yuwei Liu

Genes 2024, 15(12), 1568; https://doi.org/10.3390/genes15121568 - 4 Dec 2024

Background/Objectives: Mesenchymal stem cells (MSCs) possess the remarkable ability to differentiate into various cell types, including osteoblasts. Understanding the molecular mechanisms governing MSC osteogenic differentiation is crucial for advancing clinical applications and our comprehension of complex disease processes. However, the key biological molecules [...] Read more.

Background/Objectives: Mesenchymal stem cells (MSCs) possess the remarkable ability to differentiate into various cell types, including osteoblasts. Understanding the molecular mechanisms governing MSC osteogenic differentiation is crucial for advancing clinical applications and our comprehension of complex disease processes. However, the key biological molecules regulating this process remain incompletely understood. Methods: In this study, we conducted systematic re-analyses of published high-throughput transcriptomic datasets to identify and validate key biological molecules that dynamically regulate MSC osteogenic differentiation. Our approach involved a comprehensive analysis of gene expression patterns across human tissues, followed by the rigorous experimental validation of the identified candidates. Results: Through integrated analytical and experimental approaches, we utilized high-throughput transcriptomics to identify four critical regulators of MSC osteogenic differentiation: PTBP1, H2AFZ, BCL6, and TTPAL (C20ORF121). Among these, PTBP1 and H2AFZ functioned as positive regulators, while BCL6 and TTPAL acted as negative regulators in osteogenesis. The regulatory roles of these genes in osteogenesis were further validated via overexpression experiments. Conclusions: Our findings advance our understanding of MSC differentiation fate determination and open new therapeutic possibilities for bone-related disorders. The identification of these regulators provides a foundation for developing targeted interventions in regenerative medicine. Full article

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

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12 pages, 4934 KiB

Open AccessArticle

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

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 K_A/K_S 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

Open AccessArticle

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

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, 1650 KiB

Open AccessArticle

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

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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21 pages, 1683 KiB

Open AccessArticle

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

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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9 pages, 2121 KiB

Open AccessArticle

A New Bivalve Species Glauconome huangheensis of the Genus Glauconome J. E. Gray, 1828 (Bivalvia, Venerida, Cyrenoidea, Glauconomidae), from Shandong, China

by Lingtong Kong, Yuxi Zhang, Cui Li, Zeyu Tang and Haiyan Wang

Genes 2024, 15(12), 1563; https://doi.org/10.3390/genes15121563 - 1 Dec 2024

The family Glauconomidae has few species, limited molecular data description, and insufficient research attention. The biodiversity of Glauconomidae within China deserves further exploration. In recent years, the taxonomic status of Glauconomidae has undergone changes, and some studies have found a close relationship between [...] Read more.

The family Glauconomidae has few species, limited molecular data description, and insufficient research attention. The biodiversity of Glauconomidae within China deserves further exploration. In recent years, the taxonomic status of Glauconomidae has undergone changes, and some studies have found a close relationship between Glauconomidae and the family Cyrenidae based on molecular data, suggesting that Glauconomidae should be classified under the superfamily Cyrenoidea. However, both domestic and international research has mainly focused on only four species of Glauconomidae, indicating an urgent need for more species data support. Recently, 46 specimens of Glauconomidae were collected in the Yellow River Estuary in Dongying City of Shandong Province in China. Through a comparative analysis of shell morphology and molecular phylogenetic analysis of COI and 16S rRNA, two species of Glauconomidae was discovered. One is Glauconome angulata Reeve, 1844, and the other is a new species of Glauconomidae found in the Yellow River, named Glauconome huangheensis sp. nov. The G. huangheensis sp. nov. exhibits distinct differences in shell shape and shell color compared to other species of Glauconomidae, resembling G. angulata. There are also significant differences in shell color, shell sculpture, ligament size, and shell thickness. Furthermore, the molecular phylogenetic analysis based on COI and 16S rRNA genes supports the validity of G. huangheensis sp. nov. as a species. It indicates a close phylogenetic relationship with G. angulata, making them sister species. This study provides a redescription of the morphological characteristics of G. angulata and G. huangheensis sp. nov., laying the foundation for the morphological classification, biodiversity research, and conservation of Glauconomidae species. Full article

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

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16 pages, 5425 KiB

Open AccessArticle

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

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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13 pages, 2792 KiB

Open AccessArticle

Biliverdinuria Caused by Exonic BLVRA Deletions in Two Dogs with Green Urine

by Eva Furrow, Jade A. Peralta, A Russell Moore, Katie M. Minor, Candace Guerrero, Charlotte R. Hemmila, Victoria DiCiccio, Jonah N. Cullen, Steven G. Friedenberg and Urs Giger

Genes 2024, 15(12), 1561; https://doi.org/10.3390/genes15121561 - 30 Nov 2024

Background/Objectives: In heme degradation, biliverdin reductase catalyzes the conversion of biliverdin to bilirubin. Defects in the biliverdin reductase A gene (BLVRA) causing biliverdinuria are extraordinarily rare in humans, and this inborn error of metabolism has not been reported in other mammals. [...] Read more.

Background/Objectives: In heme degradation, biliverdin reductase catalyzes the conversion of biliverdin to bilirubin. Defects in the biliverdin reductase A gene (BLVRA) causing biliverdinuria are extraordinarily rare in humans, and this inborn error of metabolism has not been reported in other mammals. The objective of this study was to diagnose biliverdinuria and identify the causal BLVRA variants in two adult mixed-breed dogs with life-long green urine. One of the dogs also had an unexplained regenerative anemia and mild hepatopathy. Methods: Clinicopathological evaluations, urinary mass spectroscopy, and molecular genetic studies were performed. Urine metabolic screening identified increased biliverdin concentrations in both cases relative to control dogs. Results: Whole genome and Sanger sequencing revealed that each case was homozygous for large deletions in BLVRA: UU_Cfam_GSD_1.0/canFam4 chr18:6,532,022–6,551,313 (19,292 bp) in Case 1 and chr18:6,543,863–6,545,908 (2046 bp) in Case 2. These variants were predicted to result in major BLVRA truncations (ENSCAFT00805017018.1 p.[Lys117-Lys296del] and p.[Ala154fs], respectively) and loss of enzyme function. In a genomic variant database, 671 dogs from 63 breeds had coverage over these regions, ruling out homozygosity for the BLVRA deletions. A gene defect for the regenerative anemia in Case 1 was not discovered. Conclusions: While expected to be rare, genotyping for the BLVRA deletions can be used to identify other affected and carrier dogs. This study illustrates the use of targeted metabolic and genomic screening as key diagnostic tools to diagnose a rare metabolic disorder. These are the first confirmed cases of biliverdinuria caused by BLVRA defects in non-human mammals. Full article

(This article belongs to the Special Issue Advances in Canine Genetics)

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13 pages, 5282 KiB

Open AccessArticle

The ebony Gene in Silkworm Black Pupae Significantly Affects 30 K Proteins During the Pupal Stage

by Runhuan Yang, Huiduo Guo, Juan Sun, Tao Gui, Xinyu Li, Heying Qian and Anli Chen

Genes 2024, 15(12), 1560; https://doi.org/10.3390/genes15121560 - 29 Nov 2024

Background/Objectives: The body color and patterns of insects play important roles in foraging, evading predators, mating, thermoregulation, and environmental adaptation. During the rearing of the QiufengN silkworm strain, a mutant with black pupal cuticle (QiufengNBP) was discovered. Preliminary map-based cloning and sequence [...] Read more.

Background/Objectives: The body color and patterns of insects play important roles in foraging, evading predators, mating, thermoregulation, and environmental adaptation. During the rearing of the QiufengN silkworm strain, a mutant with black pupal cuticle (QiufengNBP) was discovered. Preliminary map-based cloning and sequence analysis indicated that the ebony gene might significantly influence the formation of the black pupa mutant and the expression of 30K proteins. This study aims to determine the function of the ebony gene and its effect on the expression of the 30K protein during the pupal stage; Methods and Results: We employed CRISPR/Cas9 gene-editing technology to knock out the ebony gene in the Nistari strain, resulting in individuals with black pupae, named Nistari Black Pupa (NisBP). This confirmed that the ebony gene plays a crucial role in black pupa formation. Two-dimensional electrophoresis (2-DE) analysis of the pupal cuticle of NisBP and its wild-type Nistari found that the ebony gene has a significant impact on the expression of 30K proteins, which are vital for embryonic development and serve as key storage proteins; Conclusions: This study is the first to demonstrate that the ebony gene affects the expression of 30K proteins, laying the foundation for further research on their functions and providing insights into the developmental mechanisms of silkworms. Full article

(This article belongs to the Special Issue Genomics, Transcriptomics, and Proteomics of Insects)

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18 pages, 356 KiB

Open AccessReview

Insights on the Genetic and Phenotypic Complexities of Optic Neuropathies

by Fabiana D’Esposito, Marco Zeppieri, Maria Francesca Cordeiro, Matteo Capobianco, Alessandro Avitabile, Giuseppe Gagliano, Mutali Musa, Piero Barboni and Caterina Gagliano

Genes 2024, 15(12), 1559; https://doi.org/10.3390/genes15121559 - 29 Nov 2024

Background/Objectives: Optic neuropathies are a category of illnesses that ultimately cause damage to the optic nerve, leading to vision impairment and possible blindness. Disorders such as dominant optic atrophy (DOA), Leber hereditary optic neuropathy (LHON), and glaucoma demonstrate intricate genetic [...] Read more.

Background/Objectives: Optic neuropathies are a category of illnesses that ultimately cause damage to the optic nerve, leading to vision impairment and possible blindness. Disorders such as dominant optic atrophy (DOA), Leber hereditary optic neuropathy (LHON), and glaucoma demonstrate intricate genetic foundations and varied phenotypic manifestations. This narrative review study seeks to consolidate existing knowledge on the genetic and molecular mechanisms underlying ocular neuropathies, examine genotype-phenotype correlations, and assess novel therapeutic options to improve diagnostic and treatment methodologies. Methods: A systematic literature review was performed in October 2024, utilizing PubMed, Medline, the Cochrane Library, and ClinicalTrials.gov. Search terms encompassed “optic neuropathy”, “genetic variants”, “LHON”, “DOA”, “glaucoma”, and “molecular therapies”. Studies were chosen according to established inclusion criteria, concentrating on the genetic and molecular dimensions of optic neuropathies and their therapeutic ramifications. Results: The results indicate that DOA and LHON are mostly associated with the mitochondrial dysfunction resulting from pathogenic variants in nuclear genes, mainly OPA1, and mitochondrial DNA (mtDNA) genes, respectively. Glaucoma, especially its intricate variants, is linked to variants in genes like MYOC, OPTN, and TBK1. Molecular mechanisms, such as oxidative stress and inflammatory modulation, are pivotal in disease progression. Innovative therapeutics, including gene therapy, RNA-based treatments, and antioxidants such as idebenone, exhibit promise for alleviating optic nerve damage and safeguarding vision. Conclusions: Genetic and molecular investigations have markedly enhanced our comprehension of ocular neuropathies. The amalgamation of genetic and phenotypic data is essential for customized medical strategies. Additional research is required to enhance therapeutic strategies and fill the gaps in our understanding of the underlying pathophysiology. This interdisciplinary approach shows potential for enhancing patient outcomes in ocular neuropathies. Full article

(This article belongs to the Special Issue Study on Genotypes and Phenotypes of Neurodegenerative Diseases—2nd Edition)

25 pages, 5418 KiB

Open AccessArticle

Transcriptomic Characterization of Genes Harboring Markers Linked to Maize Yield

by Agnieszka Tomkowiak, Tomasz Jamruszka, Jan Bocianowski, Aleksandra Sobiech, Karolina Jarzyniak, Maciej Lenort, Sylwia Mikołajczyk and Monika Żurek

Genes 2024, 15(12), 1558; https://doi.org/10.3390/genes15121558 - 29 Nov 2024

Background: It is currently believed that breeding priorities, including maize breeding, should focus on introducing varieties with greater utility value, specifically higher yields, into production. Global modern maize breeding relies on various molecular genetics techniques. Using the above mentioned technologies, we can identify [...] Read more.

Background: It is currently believed that breeding priorities, including maize breeding, should focus on introducing varieties with greater utility value, specifically higher yields, into production. Global modern maize breeding relies on various molecular genetics techniques. Using the above mentioned technologies, we can identify regions of the genome that are associated with various phenotypic traits, including yield, which is of fundamental importance for understanding and manipulating these regions. Objectives: The aim of the study was to analyze the expression of candidate genes associated with maize yield. To better understand the function of the analyzed genes in increasing maize yield, their expression in different organs and tissues was also assessed using publicly available transcriptome data. Methods: RT-qPCR analyses were performed using iTaq Universal SYBR Green Supermix (Bio-Rad, Hercules, CA, USA) and CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA). Each of the performed RT-qPCR experiments consisted of three biological replicates and three technical replicates, the results of which were averaged. Results: The research results allowed us to select three out of six candidate genes (cinnamoyl-CoA reductase 1—CCR1, aspartate aminotransferase—AAT and sucrose transporter 1—SUT1), which can significantly affect grain yield in maize. Not only our studies but also literature reports clearly indicate the participation of CCR1, AAT and SUT1 in the formation of yield. Identified molecular markers located within these genes can be used in breeding programs to select high yielding maize genotypes. Full article

(This article belongs to the Special Issue Genetic and Genomic Studies of Crop Breeding)

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17 pages, 8879 KiB

Open AccessArticle

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

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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9 pages, 358 KiB

Open AccessArticle

A Novel GBF1 Variant in a Charcot-Marie-Tooth Type 2: Insights from Familial Analysis

by Valentina Ciampana, Lucia Corrado, Luca Magistrelli, Elena Contaldi, Cristoforo Comi, Sandra D’Alfonso and Domizia Vecchio

Genes 2024, 15(12), 1556; https://doi.org/10.3390/genes15121556 - 29 Nov 2024

Background/Objectives: Axonal Charcot–Marie–Tooth disease type 2 (CMT2) accounts for 24% of Hereditary Motor/Sensory Peripheral Neuropathies. CMT2 type GG, due to four distinct heterozygous mutations in the Golgi brefeldin A resistant guanine nucleotide exchange factor 1 (GBF1) gene (OMIM 606483), was described [...] Read more.

Background/Objectives: Axonal Charcot–Marie–Tooth disease type 2 (CMT2) accounts for 24% of Hereditary Motor/Sensory Peripheral Neuropathies. CMT2 type GG, due to four distinct heterozygous mutations in the Golgi brefeldin A resistant guanine nucleotide exchange factor 1 (GBF1) gene (OMIM 606483), was described in seven cases from four unrelated families with autosomal dominant inheritance. It is characterized by slowly progressive distal muscle weakness and atrophy, primarily affecting the lower limbs. Here, we present two siblings sharing a novel GBF1 variant. Methods: Patient II.1 (male, 61 years at onset) presented lower limb hypoesthesia and walking difficulty; the examination revealed a postural tremor, a positive Romberg test, and muscle atrophy in the lower limbs and hands. Patient II.2 (his sister, 59 years at onset) had lower limb dysesthesias, hand paresthesia, and lower-limb stiffness. They underwent clinical evaluations, blood tests, and electroneurography. Their father represents a potentially affected individual, although a genetic analysis was not conducted. Results: All tests for peripheral neuropathies were unremarkable, including metabolic and autoimmune screening. Both showed a mixed demyelinating–axonal sensory–motor neuropathy. Genetic analysis revealed a new heterozygous GBF1 variant of uncertain significance. Conclusions: Based on autosomal dominant inheritance, as well as clinical and physiological features, a possible novel CMT2GG was diagnosed. Further research, including functional assays and in vitro studies, is necessary to confirm this variant’s causal link. Full article

(This article belongs to the Special Issue Molecular Genetics of Neurodegenerative Diseases and Neuromuscular Diseases)

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15 pages, 3556 KiB

Open AccessArticle

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

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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21 pages, 4375 KiB

Open AccessReview

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

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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