Genes

Article

10 pages, 2029 KiB

Open AccessEditor’s ChoiceArticle

Genetic Variations of MSTN and Callipyge in Tibetan Sheep: Implications for Early Growth Traits

by Kai Zhao, Xue Li, Dehui Liu, Lei Wang, Quanbang Pei, Buying Han, Zian Zhang, Dehong Tian, Song Wang, Jincai Zhao, Bin Huang and Fuqiang Zhang

Genes 2024, 15(7), 921; https://doi.org/10.3390/genes15070921 - 15 Jul 2024

Cited by 1 | Viewed by 1340

Abstract

Tibetan sheep are vital to the ecosystem and livelihood of the Tibetan Plateau; however, traditional breeding methods limit their production and growth. Modern molecular breeding techniques are required to improve these traits. This study identified a single nucleotide polymorphism (SNP) in myostatin ( [...] Read more.

Tibetan sheep are vital to the ecosystem and livelihood of the Tibetan Plateau; however, traditional breeding methods limit their production and growth. Modern molecular breeding techniques are required to improve these traits. This study identified a single nucleotide polymorphism (SNP) in myostatin (MSTN) and Callipyge in Tibetan sheep. The findings indicated notable associations between MSTN genotypes and growth traits including birth weight (BW), body length (BL), chest width (ChW), and chest circumference (ChC), as well as a particularly strong association with cannon circumference (CaC) at 2 months of age. Conversely, Callipyge polymorphisms did not have a significant impact on Tibetan sheep. Moreover, the analyses revealed a significant association between sex and BW or hip width (HW) at 2 months of age and ChW, ChC, and CaC at 4 months of age. Furthermore, the study’s results suggested that the genotype of MSTN as a GA was associated with a notable sex effect on BW, while the genotype of Callipyge (CC) showed a significant impact of sex on CaC at 2 months of age. These results indicated that the SNP of MSTN could potentially serve as a molecular marker for early growth traits in Tibetan sheep. Full article

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

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11 pages, 1117 KiB

Open AccessEditor’s ChoiceArticle

Intellectual Disabilities and Neurocognitive Impairment in Adult Patients with Inherited Metabolic Diseases: A UK Single Centre Experience

by John Warner-Levy, Adrian H. Heald, Daniel Hand, Reena Sharma, Rachel Thomasson and Karolina M. Stepien

Genes 2024, 15(7), 923; https://doi.org/10.3390/genes15070923 - 15 Jul 2024

Viewed by 2101

Abstract

Inherited metabolic diseases (IMDs) are a group of heterogeneous genetic disorders resulting in substrate accumulation, energy deficiency, or complex molecular defects due to the failure of specific molecules to act as enzymes, cofactors, transporters, or receptors in specific metabolic pathways. The pathophysiological changes [...] Read more.

Inherited metabolic diseases (IMDs) are a group of heterogeneous genetic disorders resulting in substrate accumulation, energy deficiency, or complex molecular defects due to the failure of specific molecules to act as enzymes, cofactors, transporters, or receptors in specific metabolic pathways. The pathophysiological changes seen in IMDs are sometimes associated with intellectual disability (ID) or neurocognitive decline, necessitating multidisciplinary input. We here describe our experience at one tertiary metabolic centre in the UK. We reviewed the case prevalence and existing service provision in one adult IMD service covering a multi-ethnic population of 10 million in North England. In our cohort of 2268 IMD patients, 1598 patients had general metabolic conditions (70.5%), and 670 had lysosomal storage disease/disorders (LSD)s (29.5%). The overall prevalence of ID and neurocognitive decline was found to be 15.7% (n = 357), with patients with LSDs accounting for 23.5% (n = 84) of affected patients. Given the prevalence of ID in adults with IMDs, access to multidisciplinary input from neuropsychology and neuropsychiatry services is important. Education of healthcare professionals to diagnose IMDs in patients with ID, in addition to neurocognitive and neuropsychiatric presentations, will avoid missed diagnoses of IMD and will have a positive effect on patient outcomes. Full article

(This article belongs to the Special Issue Molecular Genetics of Neurodevelopmental Disorders)

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18 pages, 2362 KiB

Open AccessEditor’s ChoiceArticle

T-Allele Carriers of Mono Carboxylate Transporter One Gene Polymorphism rs1049434 Demonstrate Altered Substrate Metabolization during Exhaustive Exercise

by Benedikt Gasser, Alain Dössegger, Marie-Noëlle Giraud and Martin Flück

Genes 2024, 15(7), 918; https://doi.org/10.3390/genes15070918 - 14 Jul 2024

Cited by 5 | Viewed by 1601

Abstract

Background: Polymorphism rs1049434 characterizes the nonsynonymous exchange of adenosine (A) by thymidine (T) in the gene for monocarboxylate transporter 1 (MCT1). We tested whether T-allele carriers of rs1049434 demonstrate increased accumulation of markers of metabolic strain. Methods: Physically active, healthy, young [...] Read more.

Background: Polymorphism rs1049434 characterizes the nonsynonymous exchange of adenosine (A) by thymidine (T) in the gene for monocarboxylate transporter 1 (MCT1). We tested whether T-allele carriers of rs1049434 demonstrate increased accumulation of markers of metabolic strain. Methods: Physically active, healthy, young male subjects (n = 22) conducted a power-matched one-legged cycling exercise to exhaustion. Metabolic substrates in capillary blood, selected metabolic compounds, and indices for the slow oxidative phenotype of vastus lateralis muscle were quantified in samples collected before and after exercise. The genotypes of the rs1049434 polymorphism were determined with polymerase chain reactions. Results: One-legged exercise affected the concentration of muscle metabolites entering the tricarboxylic acid cycle, such as acetyl-co-enzyme A (+448%) and acetyl-L-carnitine (+548%), muscle glycogen (−59%), and adenosine monophosphate (−39%), 30 min post-exercise. Exercise-related variability in the muscular concentration of glycogen, long-chain acyl co-enzyme As and a triglyceride, nicotinamide adenine dinucleotide (NADH), and adenosine monophosphate (AMP) interacted with rs1049434. T-allele carriers demonstrated a 39% lesser reduction in glycogen after exercise than non-carriers when NADH increased only in the non-carriers. Muscle lactate concentration was 150% higher, blood triacyl-glyceride concentration was 53% lower, and slow fiber percentage was 20% lower in T-allele carriers. Discussion: The observations suggest a higher anaerobic glycolytic strain during exhaustive exercise and a lowered lipid handling in T-allele non-carriers. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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21 pages, 3433 KiB

Open AccessEditor’s ChoiceArticle

Genetic Ancestry and Self-Reported “Skin Color/Race” in the Urban Admixed Population of São Paulo City, Brazil

by Jaqueline L. Pereira, Camila A. de Souza, Jennyfer E. M. Neyra, Jean M. R. S. Leite, Andressa Cerqueira, Regina C. Mingroni-Netto, Julia M. P. Soler, Marcelo M. Rogero, Flavia M. Sarti and Regina M. Fisberg

Genes 2024, 15(7), 917; https://doi.org/10.3390/genes15070917 - 13 Jul 2024

Cited by 1 | Viewed by 3553

Abstract

Epidemiological studies frequently classify groups based on phenotypes like self-reported skin color/race, which inaccurately represent genetic ancestry and may lead to misclassification, particularly among individuals of multiracial backgrounds. This study aimed to characterize both global and local genome-wide genetic ancestries and to assess [...] Read more.

Epidemiological studies frequently classify groups based on phenotypes like self-reported skin color/race, which inaccurately represent genetic ancestry and may lead to misclassification, particularly among individuals of multiracial backgrounds. This study aimed to characterize both global and local genome-wide genetic ancestries and to assess their relationship with self-reported skin color/race in an admixed population of Sao Paulo city. We analyzed 226,346 single-nucleotide polymorphisms from 841 individuals participating in the population-based ISA-Nutrition study. Our findings confirmed the admixed nature of the population, demonstrating substantial European, significant Sub-Saharan African, and minor Native American ancestries, irrespective of skin color. A correlation was observed between global genetic ancestry and self-reported color-race, which was more evident in the extreme proportions of African and European ancestries. Individuals with higher African ancestry tended to identify as Black, those with higher European ancestry tended to identify as White, and individuals with higher Native American ancestry were more likely to self-identify as Mixed, a group with diverse ancestral compositions. However, at the individual level, this correlation was notably weak, and no deviations were observed for specific regions throughout the individual’s genome. Our findings emphasize the significance of accurately defining and thoroughly analyzing race and ancestry, especially within admixed populations. Full article

(This article belongs to the Special Issue Human Genome Diversity: History and Health)

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16 pages, 5650 KiB

Open AccessEditor’s ChoiceArticle

Illuminating Genetic Diversity and Selection Signatures in Matou Goats through Whole-Genome Sequencing Analysis

by Ruiyao HuangFu, Haobang Li, Yang Luo, Fang He, Cheng Huan, Zulfiqar Ahmed, Baizhong Zhang, Chuzhao Lei and Kangle Yi

Genes 2024, 15(7), 909; https://doi.org/10.3390/genes15070909 - 12 Jul 2024

Cited by 1 | Viewed by 1604

Abstract

(1) Background: Matou goats, native to Hunan and Hubei provinces in China, are renowned for their exceptional meat and skin quality. However, a comprehensive whole-genome-based exploration of the genetic architecture of this breed is scant in the literature. (2) Methods: To address this [...] Read more.

(1) Background: Matou goats, native to Hunan and Hubei provinces in China, are renowned for their exceptional meat and skin quality. However, a comprehensive whole-genome-based exploration of the genetic architecture of this breed is scant in the literature. (2) Methods: To address this substantial gap, we used whole-genome sequences of 20 Matou goats and compared them with published genomic data of 133 goats of different breeds across China. This comprehensive investigation sought to assess genetic diversity, population structure, and the presence of genomic selection signals. (3) Results: The whole genome of Matou goat populations yielded a substantial catalog of over 19 million single nucleotide polymorphisms (SNPs), primarily distributed within intergenic and intron regions. The phylogenetic tree analysis revealed distinct clades corresponding to each goat population within the dataset. Notably, this analysis positioned Matou goats in a closer genetic affinity with Guizhou White goats, compared to other recognized goat breeds. This observation was corroborated by principal component analysis (PCA) and admixture analysis. Remarkably, Matou goats exhibited diminished genetic diversity and a notable degree of inbreeding, signifying a reduced effective population size. Moreover, the study employed five selective sweep detection methods (including PI, CLR, PI-Ratio, Fst, and XP-EHH) to screen top signal genes associated with critical biological functions, encompassing cardiomyocytes, immunity, coat color, and meat quality. (4) Conclusions: In conclusion, this study significantly advances our understanding of the current genetic landscape and evolutionary dynamics of Matou goats. These findings underscore the importance of concerted efforts in resource conservation and genetic enhancement for this invaluable breed. Full article

(This article belongs to the Special Issue Advances in Cattle, Sheep, and Goats Molecular Genetics and Breeding)

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12 pages, 2224 KiB

Open AccessEditor’s ChoiceArticle

invdup(8)(8q24.13q24.3)—A Complex Alteration and Its Clinical Consequences

by Rafaella Mergener, Marcela Rodrigues Nunes, Ana Kalise Böttcher, Monique Banik Siqueira, Helena Froener Peruzzo, Milene Carvalho Merola, Mariluce Riegel and Paulo Ricardo Gazzola Zen

Genes 2024, 15(7), 910; https://doi.org/10.3390/genes15070910 - 12 Jul 2024

Cited by 1 | Viewed by 1616

Abstract

Structural variation is a source of genetic variation that, in some cases, may trigger pathogenicity. Here, we describe two cases, a mother and son, with the same partial inverted duplication of the long arm of chromosome 8 [invdup(8)(q24.21q24.21)] of 17.18 Mb, showing different [...] Read more.

Structural variation is a source of genetic variation that, in some cases, may trigger pathogenicity. Here, we describe two cases, a mother and son, with the same partial inverted duplication of the long arm of chromosome 8 [invdup(8)(q24.21q24.21)] of 17.18 Mb, showing different clinical manifestations: microcephaly, dorsal hypertrichosis, seizures and neuropsychomotor development delay in the child, and a cleft lip/palate, down-slanted palpebral fissures and learning disabilities in the mother. The deleterious outcome, in general, is reflected by the gain or loss of genetic material. However, discrepancies among the clinical manifestations raise some concerns about the genomic configuration within the chromosome and other genetic modifiers. With that in mind, we also performed a literature review of research published in the last 20 years about the duplication of the same, or close, chromosome region, seeking the elucidation of at least some relevant clinical features. Full article

(This article belongs to the Special Issue Molecular Basis of Rare Genetic Diseases)

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21 pages, 6208 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Identification of APX Gene Family in Citrus maxima and Expression Analysis at Different Postharvest Preservation Times

by Yu Zhang, Yujiao Peng, Huixin Zhang, Qiuyu Gao, Fangfei Song, Xueyu Cui and Fulei Mo

Genes 2024, 15(7), 911; https://doi.org/10.3390/genes15070911 - 12 Jul 2024

Cited by 2 | Viewed by 1603

Abstract

Ascorbate peroxidase (APX) is a crucial enzyme involved in cellular antioxidant defense and plays a pivotal role in modulating reactive oxygen species (ROS) levels under various environmental stresses in plants. This study utilized bioinformatics methods to identify and analyze the APX gene family [...] Read more.

Ascorbate peroxidase (APX) is a crucial enzyme involved in cellular antioxidant defense and plays a pivotal role in modulating reactive oxygen species (ROS) levels under various environmental stresses in plants. This study utilized bioinformatics methods to identify and analyze the APX gene family of pomelo, while quantitative real-time PCR (qRT-PCR) was employed to validate and analyze the expression of CmAPXs at different stages of fruit postharvest. This study identified 96 members of the CmAPX family in the entire pomelo genome, with uneven distribution across nine chromosomes and occurrences of gene fragment replication. The subcellular localization includes peroxisome, cytoplasm, chloroplasts, and mitochondria. The CmAPX family exhibits a similar gene structure, predominantly consisting of two exons. An analysis of the upstream promoter regions revealed a significant presence of cis-acting elements associated with light (Box 4, G-Box), hormones (ABRE, TCA-element), and stress-related (MBS, LTR, ARE) responses. Phylogenetic and collinearity analyses revealed that the CmAPX gene family can be classified into three subclasses, with seven collinear gene pairs. Furthermore, CmAPXs are closely related to citrus, pomelo, and lemon, followed by Arabidopsis, and exhibit low homology with rice. Additionally, the transcriptomic heat map and qPCR results revealed that the expression levels of CmAPX57, CmAPX34, CmAPX50, CmAPX4, CmAPX5, and CmAPX81 were positively correlated with granulation degree, indicating the activation of the endogenous stress resistance system in pomelo cells by these genes, thereby conferring resistance to ROS. This finding is consistent with the results of GO enrichment analysis. Furthermore, 38 miRNAs were identified as potential regulators targeting the CmAPX family for post-transcriptional regulation. Thus, this study has preliminarily characterized members of the APX gene family in pomelo and provided valuable insights for further research on their antioxidant function and molecular mechanism. Full article

(This article belongs to the Collection Feature Papers: 'Plant Genetics and Genomics' Section)

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15 pages, 2306 KiB

Open AccessEditor’s ChoiceArticle

Exploring the Influence of Fok1/Apa1 Polymorphic Variants on Adolescent Mental Health and Response to Vitamin D Supplementation in Embryonic Hippocampal Cell Lines

by Giulia Gizzi, Federico Fiorani, Samuela Cataldi, Martina Mandarano, Elisa Delvecchio, Claudia Mazzeschi and Elisabetta Albi

Genes 2024, 15(7), 913; https://doi.org/10.3390/genes15070913 - 12 Jul 2024

Viewed by 1324

Abstract

Several single nucleotide polymorphisms (SNPs) of the vitamin D receptor (VDR) have been observed in association with susceptibility to various pathologies, including autism, major depression, age-related changes in cognitive functioning, and Parkinson’s and Alzheimer’s diseases. This study aimed to establish the association between [...] Read more.

Several single nucleotide polymorphisms (SNPs) of the vitamin D receptor (VDR) have been observed in association with susceptibility to various pathologies, including autism, major depression, age-related changes in cognitive functioning, and Parkinson’s and Alzheimer’s diseases. This study aimed to establish the association between Fok1/Apa1 polymorphic variants and anxious/depressive symptoms in nonclinical adolescents from central Italy, with the goal of identifying the risk of developing both symptoms. We found no significant difference in genotype distribution or dominant/recessive models of Fok1/Apa1 VDR polymorphic variants between subjects with anxious/depressive symptoms and controls. HN9.10e cell lines carrying the AA genotype for Fok1 and the CC genotype for Apa1 responded better to treatment with vitamin D3 than cell lines carrying the AG genotype for Fok1 and CA genotype for Apa1. Cell lines carrying the GG genotype for Fok1 and the AA genotype for Apa1 did not respond at all, suggesting avenues for future studies in both the general population and individuals with mental and/or neuropsychiatric disorders. These studies suggest that the level of response to vitamin D3 administered to prevent and/or treat mental or neurological disorders could depend on the polymorphic variants of the vitamin D receptor. Full article

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

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16 pages, 6478 KiB

Open AccessEditor’s ChoiceArticle

Comprehensive Identification and Expression Profiling of Epidermal Pattern Factor (EPF) Gene Family in Oilseed Rape (Brassica napus L.) under Salt Stress

by Shanshan Wang, Wei Wang, Jingdong Chen, Heping Wan, Huixia Zhao, Xiaoyun Liu, Xigang Dai, Changli Zeng and Danyun Xu

Genes 2024, 15(7), 912; https://doi.org/10.3390/genes15070912 - 12 Jul 2024

Viewed by 1411

Abstract

Rapeseed is a crucial oil crop globally, and in recent years, abiotic stress has increasingly affected its growth, development, yield, and quality. Salt stress is a significant abiotic factor that restricts crop production. The EPF gene family is vital in managing salt stress [...] Read more.

Rapeseed is a crucial oil crop globally, and in recent years, abiotic stress has increasingly affected its growth, development, yield, and quality. Salt stress is a significant abiotic factor that restricts crop production. The EPF gene family is vital in managing salt stress by controlling stomatal development and opening, which reduces water loss and increases plant salt tolerance. To explore the features of the EPF gene family in Brassica napus and their expression under salt stress, this study utilized Arabidopsis EPF protein sequences as seed sequences, including their PF17181 and PF16851 domains. A total of 27 members of the EPF gene family were detected within the rapeseed genome. The study examined the physicochemical properties, gene structure, phylogenetic relationships, and collinearity of BnEPFs. Through transcriptomes, we employed the qPCR method to determine the relative expression levels of BnEPF genes potentially associated with rapeseed stress resistance under both non-salt and salt stress conditions. Subsequently, we assessed their influence on rapeseed plants subjected to salt stress. During salt stress conditions, all BnEPF genes displayed a downregulation trend, indicating their potential impact on stomatal development and signal transduction pathways, consequently improving rapeseed’s resistance to salt stress. The study findings establish a basis for exploring the roles of BnEPFs and offer candidate genes for breeding stress-resistant varieties and enhancing the yield in rapeseed. Full article

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

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13 pages, 2719 KiB

Open AccessEditor’s ChoiceArticle

Evaluating the Urinary Exosome microRNA Profile of von Hippel Lindau Syndrome Patients with Clear Cell Renal Cell Carcinoma

by Beatriz Walter-Rodriguez, Christopher J. Ricketts, W. Marston Linehan and Maria J. Merino

Genes 2024, 15(7), 905; https://doi.org/10.3390/genes15070905 - 11 Jul 2024

Cited by 5 | Viewed by 1773

Abstract

Introduction: Renal cell carcinoma is one of the ten more common malignant tumors worldwide, with a high incidence and mortality rate. Kidney cancer frequently presents at an advanced stage, and it is almost invariably fatal. Much progress has been made in identifying molecular [...] Read more.

Introduction: Renal cell carcinoma is one of the ten more common malignant tumors worldwide, with a high incidence and mortality rate. Kidney cancer frequently presents at an advanced stage, and it is almost invariably fatal. Much progress has been made in identifying molecular targets for therapy in the hope of improving survival rates, but still, we have no good markers for early detection or progression of the disease. Von Hippel Lindau syndrome (VHL) is an autosomal dominant cancer hereditary syndrome in which affected individuals are at risk of developing bilateral and multifocal renal cell carcinomas (RCC) as well as other tumors. These patients provide an ideal platform to investigate the potential of urinary exosomal miRNA biomarkers in the early development of ccRCC, as these patients are regularly imaged and tumors are actively monitored until the tumor reaches 3 cm before surgical excision. This allows for pre- and post-surgical urine collection and comparison to excised tumor tissues. Studying different biomarkers in urine can provide comprehensive molecular profiling available to patients and physicians and can be a great source of additional tumor genetic information. Methods: Pre- and postoperative urine samples were obtained from a cohort of VHL patients undergoing surveillance and surgical excision of ccRCCs, and exosomes were extracted. MicroRNA-Seq analysis was performed on miRNA extracted from both urine-derived exosomes and FFPE material from excised ccRCCs. Results: MicroRNA-Seq analysis highlighted a significant difference in the urinary exosome-derived miRNA expression profiles between VHL patients and normal control individuals. This included decreased expression of the miR-320 family, such as miR-320a, known to be decreased in sporadic ccRCC and suppressed by the HIF1α transcription factor activated by the loss of the VHL gene. MiR-542-5p represented a potential marker of VHL-associated ccRCC that was lowly expressed in normal control urinary exosomes, significantly increased in the preoperative urinary exosomes of tumor-bearing VHL patients, and subsequently reduced to normal levels of expression after tumor excision. In concordance with this, the expression of miR-542-5p was increased in the VHL-associated ccRCC in comparison to the normal kidney. Conclusions: This study shows the potential for miRNA profiling of exosomes from readily available biofluids to both distinguish VHL patient urine from normal control urine microRNAs and to provide biomarkers for the presence of VHL syndrome-associated ccRCC. Further validation studies are necessary to demonstrate the utility of urinary exosome-derived miRNAs as biomarkers in kidney cancer. Full article

(This article belongs to the Special Issue Genetic Markers and Liquid Biopsy for Kidney Diseases)

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10 pages, 567 KiB

Open AccessEditor’s ChoiceArticle

Genetic Variants of the Receptor Activator Nuclear of κB Ligand Gene Increase the Risk of Rheumatoid Arthritis in a Mexican Mestizo Population: A Case–Control Study

by Nava-Valdivia Cesar Arturo, Gamez-Nava Jorge Ivan, Contreras-Haro Betsabe, Perez-Guerrero Edsaul Emilio, Esparza-Guerrero Yussef, Rodriguez-Jimenez Norma Alejandra, Gonzalez-Heredia Tonatiuh, Villagomez-Vega Alejandra, Nuño-Arana Ismael, Totsuka-Sutto Sylvia Elena, Ponce-Guarneros Juan Manuel, Jacobo-Cuevas Heriberto, Alvarez-Ayala Efren Gerardo, Gonzalez-Lopez Laura and Saldaña-Cruz Ana Miriam

Genes 2024, 15(7), 907; https://doi.org/10.3390/genes15070907 - 11 Jul 2024

Cited by 1 | Viewed by 1330

Abstract

The Receptor Activator Nuclear of κB Ligand (RANKL) plays an important function in immune responses, activating osteoclast cells and unchanged bone resorption, which in turn leads to bone erosion and inflammation. Genetic variants in the promoter region of the RANKL gene could lead [...] Read more.

The Receptor Activator Nuclear of κB Ligand (RANKL) plays an important function in immune responses, activating osteoclast cells and unchanged bone resorption, which in turn leads to bone erosion and inflammation. Genetic variants in the promoter region of the RANKL gene could lead to a higher risk of rheumatoid arthritis (RA). Objective: To assess the association of rs9533155 (-693C>G) and rs9533156 (-643T>C) genetic variants with RA risk. Methods: A case–control study was carried out. A total of 94 patients with RA (RA group) and 134 subjects without any rheumatologic disease (control group) were included. Genetic DNA was extracted from peripheral white blood cells (leukocytes). Genetic variant rs9533155 (-693C>G) was screened by an approach based on Polymerase Chain Reaction–Restriction Fragment Length Polymorphism (PCR-RFLP), while rs9533156 (-643T>C) was screened using quantitative polymerase chain reaction (qPCR) with TaqMan probes. RANKL serum levels were measured by ELISA. Results: For rs9533155 (-693C>G), the polymorphic homozygous genotype frequencies (CC) were higher in the RA group (p = 0.006). Individuals carrying the risk genotype presented higher levels of serum RANKL. Carriers of the polymorphic homozygous genotype in the dominant model (CC vs. CG + GG) had an increased risk of developing RA (OR: 1.8, 95% CI 1.04 to 3.1). No association between rs9533156 (-643T>C) and the haplotypes with RA risk was observed. Conclusion: The rs9533155 (-693C>G) genetic variant exhibits a potential role in RA risk. The studied population had no association with the rs9533156 (-643T>C) genetic variant. Full article

(This article belongs to the Special Issue Autoimmune Disease Genetics Volume II)

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12 pages, 5214 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Identification and Bioinformatics Analysis of the FK506 Binding Protein Family in Rice

by Fanhao Nie, Minghao Wang, Linlin Liu, Xuefei Ma and Juan Zhao

Genes 2024, 15(7), 902; https://doi.org/10.3390/genes15070902 - 10 Jul 2024

Cited by 2 | Viewed by 1469

Abstract

The FK506 Binding Protein (FKBP), ubiquitously present across diverse species, is characterized by its evolutionarily conserved FK506 binding domain (FKBd). In plants, evidence suggests that this gene family plays integral roles in regulating growth, development, and responses to environmental stresses. Notably, research on [...] Read more.

The FK506 Binding Protein (FKBP), ubiquitously present across diverse species, is characterized by its evolutionarily conserved FK506 binding domain (FKBd). In plants, evidence suggests that this gene family plays integral roles in regulating growth, development, and responses to environmental stresses. Notably, research on the identification and functionality of FKBP genes in rice remains limited. Therefore, this study utilized bioinformatic tools to identify 30 FKBP-encoding genes in rice. It provides a detailed analysis of their chromosomal locations, evolutionary relationships with the Arabidopsis thaliana FKBP family, and gene structures. Further analysis of the promoter elements of these rice FKBP genes revealed a high presence of stress-responsive elements. Quantitative PCR assays under drought and heat stress conditions demonstrated that genes OsFKBP15-2, OsFKBP15-3, OsFKBP16-3, OsFKBP18, and OsFKBP42b are inducible by these adverse conditions. These findings suggest a significant role for the rice FKBP gene family in stress adaptation. This research establishes a critical foundation for deeper explorations of the functional roles of the OsFKBP genes in rice. Full article

(This article belongs to the Special Issue Genetics and Breeding of Rice)

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18 pages, 2782 KiB

Open AccessEditor’s ChoiceArticle

Revealing Differential RNA Editing Specificity of Human ADAR1 and ADAR2 in Schizosaccharomyces pombe

by Niubing Zhang, Ping Chen, Zilin Cui, Xiaojuan Zhou, Chenhui Hao, Bingran Xie, Pei Hao, Bang-Ce Ye, Xuan Li and Xinyun Jing

Genes 2024, 15(7), 898; https://doi.org/10.3390/genes15070898 - 9 Jul 2024

Viewed by 2278

Abstract

Adenosine-to-inosine (A-to-I) RNA editing is an important post-transcriptional modification mediated by the adenosine deaminases acting on RNA (ADAR) family of enzymes, expanding the transcriptome by altering selected nucleotides A to I in RNA molecules. Recently, A-to-I editing has been explored for correcting disease-causing [...] Read more.

Adenosine-to-inosine (A-to-I) RNA editing is an important post-transcriptional modification mediated by the adenosine deaminases acting on RNA (ADAR) family of enzymes, expanding the transcriptome by altering selected nucleotides A to I in RNA molecules. Recently, A-to-I editing has been explored for correcting disease-causing mutations in RNA using therapeutic guide oligonucleotides to direct ADAR editing at specific sites. Humans have two active ADARs whose preferences and specificities are not well understood. To investigate their substrate specificity, we introduced hADAR1 and hADAR2, respectively, into Schizosaccharomyces pombe (S. pombe), which lacks endogenous ADARs, and evaluated their editing activities in vivo. Using transcriptome sequencing of S. pombe cultured at optimal growth temperature (30 °C), we identified 483 A-to-I high-confident editing sites for hADAR1 and 404 for hADAR2, compared with the non-editing wild-type control strain. However, these sites were mostly divergent between hADAR1 and hADAR2-expressing strains, sharing 33 common sites that are less than 9% for each strain. Their differential specificity for substrates was attributed to their differential preference for neighboring sequences of editing sites. We found that at the -3-position relative to the editing site, hADAR1 exhibits a tendency toward T, whereas hADAR2 leans toward A. Additionally, when varying the growth temperature for hADAR1- and hADAR2-expressing strains, we observed increased editing sites for them at both 20 and 35 °C, compared with them growing at 30 °C. However, we did not observe a significant shift in hADAR1 and hADAR2’s preference for neighboring sequences across three temperatures. The vast changes in RNA editing sites at lower and higher temperatures were also observed for hADAR2 previously in budding yeast, which was likely due to the influence of RNA folding at these different temperatures, among many other factors. We noticed examples of longer lengths of dsRNA around the editing sites that induced editing at 20 or 35 °C but were absent at the other two temperature conditions. We found genes’ functions can be greatly affected by editing of their transcripts, for which over 50% of RNA editing sites for both hADAR1 and hADAR2 in S. pombe were in coding sequences (CDS), with more than 60% of them resulting in amino acid changes in protein products. This study revealed the extensive differences in substrate selectivity between the two active human ADARS, i.e., ADAR1 and ADAR2, and provided novel insight when utilizing the two different enzymes for in vivo treatment of human genetic diseases using the RNA editing approach. Full article

(This article belongs to the Special Issue RNAs in Biology)

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14 pages, 4204 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Identification and Evolutionary and Mutational Analysis of the Bos taurus Pax Gene Family

by Jintao Zhong, Wenliang Wang, Yifei Li, Jia Wei, Shuangshuang Cui, Ning Song, Yunhai Zhang and Hongyu Liu

Genes 2024, 15(7), 897; https://doi.org/10.3390/genes15070897 - 9 Jul 2024

Viewed by 2461

Abstract

Bos taurus is known for its tolerance of coarse grains, adaptability, high temperature, humidity, and disease resistance. Primarily, cattle are raised for their meat and milk, and pinpointing genes associated with traits relevant to meat production can enhance their overall productivity. The aim [...] Read more.

Bos taurus is known for its tolerance of coarse grains, adaptability, high temperature, humidity, and disease resistance. Primarily, cattle are raised for their meat and milk, and pinpointing genes associated with traits relevant to meat production can enhance their overall productivity. The aim of this study was to identify the genome, analyze the evolution, and explore the function of the Pax gene family in B. taurus to provide a new molecular target for breeding in meat-quality-trait cattle. In this study, 44 Pax genes were identified from the genome database of five species using bioinformatics technology, indicating that the genetic relationships of bovids were similar. The Pax3 and Pax7 protein sequences of the five animals were highly consistent. In general, the Pax gene of the buffalo corresponds to the domestic cattle. In summary, there are differences in affinity between the Pax family genes of buffalo and domestic cattle in the Pax1/9, Pax2/5/8, Pax3/7, and Pax4/6 subfamilies. We believe that Pax1/9 has an effect on the growth traits of buffalo and domestic cattle. The Pax3/7 gene is conserved in the evolution of buffalo and domestic animals and may be a key gene regulating the growth of B. taurus. The Pax2/5/8 subfamily affects coat color, reproductive performance, and milk production performance in cattle. The Pax4/6 subfamily had an effect on the milk fat percentage of B. taurus. The results provide a theoretical basis for understanding the evolutionary, structural, and functional characteristics of the Pax family members of B. taurus and for molecular genetics and the breeding of meat-production B. taurus species. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle Volume II)

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11 pages, 1481 KiB

Open AccessEditor’s ChoiceArticle

Analysis of Codon Usage Bias in Chloroplast Genomes of Dryas octopetala var. asiatica (Rosaceae)

by Lizhen Ling, Shudong Zhang and Tao Yang

Genes 2024, 15(7), 899; https://doi.org/10.3390/genes15070899 - 9 Jul 2024

Cited by 4 | Viewed by 1289

Abstract

Dryas octopetala var. asiatica, a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in the chloroplast genome of this species [...] Read more.

Dryas octopetala var. asiatica, a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in the chloroplast genome of this species have not yet been documented. This study sequenced and assembled the complete genome of D. octopetala var. asiatica. The annotated genes in the chloroplast genome were analyzed for codon composition through multivariate statistical methods including a neutrality plot, a parity rule 2 (PR2) bias plot, and an effective number of codons (ENC) plot using CodonW 1.4.2 software. The results indicated that the mean GC content of 53 CDSs was 38.08%, with the average GC content at the third codon base position being 27.80%, suggesting a preference for A/U(T) at the third codon position in chloroplast genes. Additionally, the chloroplast genes exhibited a weak overall codon usage bias (CUB) based on ENC values and other indicators. Correlation analysis showed a significant negative correlation between ENC value and GC2, an extremely positive correlation with GC3, but no correlation with GC1 content. These findings highlight the importance of the codon composition at the third position in influencing codon usage bias. Furthermore, our analysis indicated that the CUB of the chloroplast genome of D. octopetala var. asiatica was primarily influenced by natural selection and other factors. Finally, this study identified UCA, CCU, GCU, AAU, GAU, and GGU as the optimal codons. These results offer a foundational understanding for genetic modification and evolutionary dynamics of the chloroplast genome of D. octopetala var. asiatica. Full article

(This article belongs to the Special Issue Plant Plastid Genome and Phylogenetics)

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31 pages, 3267 KiB

Open AccessEditor’s ChoiceArticle

Identification and Candidate Gene Evaluation of a Large Fast Neutron-Induced Deletion Associated with a High-Oil Phenotype in Soybean Seeds

by William R. Serson, Mohammad Fazel Soltani Gishini, Robert M. Stupar, Adrian O. Stec, Paul R. Armstrong and David Hildebrand

Genes 2024, 15(7), 892; https://doi.org/10.3390/genes15070892 - 8 Jul 2024

Viewed by 2028

Abstract

Since the dawn of agriculture, crops have been genetically altered for desirable characteristics. This has included the selection of natural and induced mutants. Increasing the production of plant oils such as soybean (Glycine max) oil as a renewable resource for food [...] Read more.

Since the dawn of agriculture, crops have been genetically altered for desirable characteristics. This has included the selection of natural and induced mutants. Increasing the production of plant oils such as soybean (Glycine max) oil as a renewable resource for food and fuel is valuable. Successful breeding for higher oil levels in soybeans, however, usually results in reduced seed protein. A soybean fast neutron population was screened for oil content, and three high oil mutants with minimal reductions in protein levels were found. Three backcross F2 populations derived from these mutants exhibited segregation for seed oil content. DNA was pooled from the high-oil and normal-oil plants within each population and assessed by comparative genomic hybridization. A deletion encompassing 20 gene models on chromosome 14 was found to co-segregate with the high-oil trait in two of the three populations. Eighteen genes in the deleted region have known functions that appear unrelated to oil biosynthesis and accumulation pathways, while one of the unknown genes (Glyma.14G101900) may contribute to the regulation of lipid droplet formation. This high-oil trait can facilitate the breeding of high-oil soybeans without protein reduction, resulting in higher meal protein levels. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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12 pages, 2589 KiB

Open AccessEditor’s ChoiceArticle

Mitochondrial Genome Characteristics Reveal Evolution of Acanthopsetta nadeshnyi (Jordan and Starks, 1904) and Phylogenetic Relationships

by Li-min Yang, Jing-feng Xue, Xiao-man Zhao, Ke Ding, Zhao-wen Liu, Zhou-si-yu Wang, Jian-bing Chen and You-kun Huang

Genes 2024, 15(7), 893; https://doi.org/10.3390/genes15070893 - 8 Jul 2024

Cited by 1 | Viewed by 1343

Abstract

In the present study, the mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and have depicted the phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis of 13 PCGs, the TN93 model was used to review the neutral evolution and habitat evolution [...] Read more.

In the present study, the mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and have depicted the phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis of 13 PCGs, the TN93 model was used to review the neutral evolution and habitat evolution catalysis of the mitogenome to verify the distancing and purification selectivity of the mitogenome in Pleuronectidae. At the same time, a species differentiation and classification model based on mitogenome analysis data was established. This study is expected to provide a new perspective on the phylogenetic relationship and taxonomic status of A. nadeshnyi and lay a foundation for further exploration of environmental and biological evolutionary mechanisms. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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11 pages, 1470 KiB

Open AccessEditor’s ChoiceArticle

Influence of ACTN3 R577X Polymorphism on Blood Creatine Kinase Levels Relative to Number of Sprints in Brazilian Professional Soccer Players

by Kathleen Y. de Almeida, Hirofumi Zempo, Mika Saito, Tiago Cetolin, Rodrigo dos Santos Guimarães, Andrea Rita Marrero, Aderbal S. Aguiar, Jr. and Naoki Kikuchi

Genes 2024, 15(7), 896; https://doi.org/10.3390/genes15070896 - 8 Jul 2024

Viewed by 1690

Abstract

This study sought to assess how post-game creatine kinase (CK) levels correlate with the number of sprints and the impact of the ACTN3 polymorphism on this response. This research constituted a descriptive/observational, retrospective cross-sectional study. DNA was extracted from blood samples for ACTN3 [...] Read more.

This study sought to assess how post-game creatine kinase (CK) levels correlate with the number of sprints and the impact of the ACTN3 polymorphism on this response. This research constituted a descriptive/observational, retrospective cross-sectional study. DNA was extracted from blood samples for ACTN3 polymorphism genotyping. CK was measured 48 h after official matches, and the number of sprints (>19 km/h) was tracked using Global Positioning System (GPS) technology. The main cohort included 23 professional soccer players from the top tier of the Brazilian Championship. We analyzed 115 GPS + CK data sets. The replication cohort comprised 18 professional soccer players from the First Division of the Championship, had the same methodology applied, and featured a total of 90 GPS (sprints > 25.2 km/h) + CK data sets. For the main cohort, a significant positive correlation was seen between the number of sprints and the CK levels (p = 0.009). Athletes with the ACTN3 RR genotype had higher CK levels as more sprints were performed during the match (p = 0.017). However, the relationship was not found for X allele carriers (p > 0.05). For the replication cohort, there was a near-significant correlation between CK levels and the number of sprints (p = 0.05), and RR individuals showed a significant association (p = 0.01), whereas X allele carriers did not (p = 0.06). A greater number of sprints during matches is linked to higher CK levels, primarily among players with the ACTN3 RR genotype, which is potentially due to an increased presence of type II muscle fibers. These findings were replicated for both cohorts of elite Brazilian soccer players, emphasizing the importance of genetic factors in injury prevention. Full article

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

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7 pages, 213 KiB

Open AccessEditor’s ChoiceArticle

Early Non-Invasive Prenatal Testing at 6–9 Weeks of Gestation

by Alexandros Katrachouras, Harry Kontos, Kyriacos Konis, Chara Skentou and George Makrydimas

Genes 2024, 15(7), 895; https://doi.org/10.3390/genes15070895 - 8 Jul 2024

Cited by 1 | Viewed by 4284

Abstract

Non-invasive prenatal testing (NIPT) is usually performed beyond 10 weeks of gestation, because earlier in pregnancy, the fetal fraction is low, resulting in failure to obtain reliable results. This study aimed to evaluate the clinical performance of NIPT earlier in pregnancy using a [...] Read more.

Non-invasive prenatal testing (NIPT) is usually performed beyond 10 weeks of gestation, because earlier in pregnancy, the fetal fraction is low, resulting in failure to obtain reliable results. This study aimed to evaluate the clinical performance of NIPT earlier in pregnancy using a method for cell-free DNA (cfDNA) analysis that eliminates the need for polymerase chain reaction (PCR), DNA sequencing, or microarrays (Vanadis^® system, PerkinElmer, Waltham, MA, USA). Cell-free DNA was extracted from the maternal plasma of 30 singleton pregnancies at 6–9 weeks of gestation (group 1) and at 11–14 weeks of gestation of the same patients (group 2). The mean crown-rump length (CRL) and gestational age in group A was 16.12 mm and that in group B was 61.45 mm. In group A, results were obtained in all, but one, cases (97%). From the remaining pregnancies, one miscarried at 8 weeks and, therefore, the follow-up NIPT at 12 weeks could not be performed. The fetal sex was diagnosed correctly in the 28 cases that had a successful early test, and the results were in accordance with the examination at 12 weeks. There were no cases of aneuploidies and disomy was diagnosed correctly in all. The “Vanadis” prenatal NIPT assay can successfully be used early during the first trimester at 6–9 weeks of gestation (early NIPT) to identify the fetal sex. Further studies are needed to explore the diagnostic potential for aneuploidies. Full article

(This article belongs to the Topic Advances in Genetics and Precision Medicine in Human Diseases)

12 pages, 1000 KiB

Open AccessEditor’s ChoiceArticle

New Virus Variant Detection Based on the Optimal Natural Metric

by Hongyu Yu and Stephen S.-T. Yau

Genes 2024, 15(7), 891; https://doi.org/10.3390/genes15070891 - 7 Jul 2024

Viewed by 4897

Abstract

The highly variable SARS-CoV-2 virus responsible for the COVID-19 pandemic frequently undergoes mutations, leading to the emergence of new variants that present novel threats to public health. The determination of these variants often relies on manual definition based on local sequence characteristics, resulting [...] Read more.

The highly variable SARS-CoV-2 virus responsible for the COVID-19 pandemic frequently undergoes mutations, leading to the emergence of new variants that present novel threats to public health. The determination of these variants often relies on manual definition based on local sequence characteristics, resulting in delays in their detection relative to their actual emergence. In this study, we propose an algorithm for the automatic identification of novel variants. By leveraging the optimal natural metric for viruses based on an alignment-free perspective to measure distances between sequences, we devise a hypothesis testing framework to determine whether a given viral sequence belongs to a novel variant. Our method demonstrates high accuracy, achieving nearly 100% precision in identifying new variants of SARS-CoV-2 and HIV-1 as well as in detecting novel genera in Orthocoronavirinae. This approach holds promise for timely surveillance and management of emerging viral threats in the field of public health. Full article

(This article belongs to the Special Issue Statistical Methods for Genetic Epidemiology)

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12 pages, 2947 KiB

Open AccessEditor’s ChoiceArticle

Does Sunlight Affect the Quality for Purposes of DNA Analysis of Blood Stain Evidence Collected from Different Surfaces?

by Livia Sliskovic, Ivana Milos, Antonia Zecic, Sendi Kuret and Davorka Sutlovic

Genes 2024, 15(7), 888; https://doi.org/10.3390/genes15070888 - 6 Jul 2024

Cited by 1 | Viewed by 2953

Abstract

The aim of this study was to investigate the effect of sunlight on the degradation of DNA samples taken from blood stains from different types of surfaces. A blood sample obtained from a single male donor was placed on seven different surfaces (galvanized [...] Read more.

The aim of this study was to investigate the effect of sunlight on the degradation of DNA samples taken from blood stains from different types of surfaces. A blood sample obtained from a single male donor was placed on seven different surfaces (galvanized sheet, iron rod, newspaper, white printer paper, glass, soil, and ceramic panel). Samples were kept, during a 4-week summer period, in a room, but next to an open window. Every 7 days, 1 mm² of blood sample was collected from each substrate and stored in labeled tube for later analysis. DNA was extracted with the Chelex method, amplified using AmpFISTR^TM Minifiler^TM Plus Amplification Kit, and quantified using a Quantifiler^TM Human DNA Quantification kit. After 7 days of sun exposure, the highest DNA concentration was determined to be from the sample from a galvanized sheet stain, followed by, in order of decreasing concentration, the ceramic panel, glass, newspaper, iron rod, and white printer paper surface. As expected, the DNA concentration from all samples decreased as the sunlight exposure time progressed. The results obtained after the amplification in the MiniFiler^TM system were in correlation with the DNA concentrations measured by the qPCR method for all samples, except for the glass, soil, and white printer paper samples. The obtained data show that DNA degradation is correlated to the length of sunlight exposure and to the type of surface the samples are collected from. A negative qPCR result does not mean negative PCR amplification in the STR system; therefore, both methods should be applied when analyzing forensic samples collected from trace evidence. Full article

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

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10 pages, 3506 KiB

Open AccessEditor’s ChoiceArticle

Pathway-Based Mendelian Randomization for Pre-Infection IL-6 Levels Highlights Its Role in Coronavirus Disease

by Zoha Kamali, Nafiseh Esmaeil, Chris H. L. Thio, Ahmad Vaez and Harold Snieder

Genes 2024, 15(7), 889; https://doi.org/10.3390/genes15070889 - 6 Jul 2024

Viewed by 1797

Abstract

Objectives: Interleukin 6 (IL-6) levels at hospital admission have been suggested for disease prognosis, and IL-6 antagonists have been suggested for the treatment of patients with severe COVID-19. However, less is known about the relationship between pre-COVID-19 IL-6 levels and the risk of [...] Read more.

Objectives: Interleukin 6 (IL-6) levels at hospital admission have been suggested for disease prognosis, and IL-6 antagonists have been suggested for the treatment of patients with severe COVID-19. However, less is known about the relationship between pre-COVID-19 IL-6 levels and the risk of severe COVID-19. To fill in this gap, here we extensively investigated the association of genetically instrumented IL-6 pathway components with the risk of severe COVID-19. Methods: We used a two-sample Mendelian randomization study design and retrieved genetic instruments for blood biomarkers of IL-6 activation, including IL-6, soluble IL-6 receptor, IL-6 signal transducer, and CRP, from respective large available GWASs. To establish associations of these instruments with COVID-19 outcomes, we used data from the Host Genetics Initiative and GenOMICC studies. Results: Our analyses revealed inverse associations of genetically instrumented levels of IL-6 and its soluble receptor with the risk of developing severe disease (OR = 0.60 and 0.94, respectively). They also demonstrated a positive association of severe disease with the soluble signal transducer level (OR = 1.13). Only IL-6 associations with severe COVID-19 outcomes reached the significance threshold corrected for multiple testing (p < 0.003; with COVID-19 hospitalization and critical illness). Conclusions: These potential causal relationships for pre-COVID-19 IL-6 levels with the risk of developing severe symptoms provide opportunities for further evaluation of these factors as prognostic/preventive markers of severe COVID-19. Further studies will need to clarify whether the higher risk for a severe disease course with lower baseline IL-6 levels may also extend to other infectious diseases. Full article

(This article belongs to the Special Issue Genetic Insights into Population Adaptations Associated with Immunity and Host Defense)

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15 pages, 5797 KiB

Open AccessEditor’s ChoiceArticle

Comparative Analysis and Phylogeny of the Complete Chloroplast Genomes of Nine Cynanchum (Apocynaceae) Species

by Erdong Zhang, Xueling Ma, Ting Guo, Yujie Wu and Lei Zhang

Genes 2024, 15(7), 884; https://doi.org/10.3390/genes15070884 - 5 Jul 2024

Cited by 4 | Viewed by 1545

Abstract

Cynanchum belongs to the Apocynaceae family and is a morphologically diverse genus that includes around 200 shrub or perennial herb species. Despite the utilization of CPGs, few molecular phylogenetic studies have endeavored to elucidate infrafamilial relationships within Cynanchum through extensive taxon sampling. In [...] Read more.

Cynanchum belongs to the Apocynaceae family and is a morphologically diverse genus that includes around 200 shrub or perennial herb species. Despite the utilization of CPGs, few molecular phylogenetic studies have endeavored to elucidate infrafamilial relationships within Cynanchum through extensive taxon sampling. In this research, we constructed a phylogeny and estimated divergence time based on the chloroplast genomes (CPGs) of nine Cynanchum species. We sequenced and annotated nine chloroplast (CP) genomes in this study. The comparative analysis of these genomes from these Cynanchum species revealed a typical quadripartite structure, with a total sequence length ranging from 158,283 to 161,241 base pairs (bp). The CP genome (CPG) was highly conserved and moderately differentiated. Through annotation, we identified a total of 129–132 genes. Analysis of the boundaries of inverted repeat (IR) regions showed consistent positioning: the rps19 gene was located in the IRb region, varying from 46 to 50 bp. IRb/SSC junctions were located between the trnN and ndhF genes. We did not detect major expansions or contractions in the IR region or rearrangements or insertions in the CPGs of the nine Cynanchum species. The results of SSR analysis revealed a variation in the number of SSRs, ranging from 112 to 150. In five types of SSRs, the largest number was mononucleotide repeats, and the smallest number was hexanucleotide repeats. The number of long repeats in the cp genomes of nine Cynanchum species was from 35 to 80. In nine species of Cynanchum, the GC3s values ranged from 26.80% to 27.00%, indicating a strong bias towards A/U-ending codons. Comparative analyses revealed four hotspot regions in the CPG, ndhA-ndhH, trnI-GAU-rrn16, psbI-trnS-GCU, and rps7-ndhB, which could potentially serve as molecular markers. In addition, phylogenetic tree construction based on the CPG indicated that the nine Cynanchum species formed a monophyletic group. Molecular dating suggested that Cynanchum diverged from its sister genus approximately 18.87 million years ago (Mya) and species diversification within the Cynanchum species primarily occurred during the recent Miocene epoch. The divergence time estimation presented in this study will facilitate future research on Cynanchum, aid in species differentiation, and facilitate diverse investigations into this economically and ecologically important genus. Full article

(This article belongs to the Section Genes & Environments)

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9 pages, 496 KiB

Open AccessEditor’s ChoiceArticle

Comparing Cancer Risk Management between Females with Truncating CHEK2 1100delC versus Missense CHEK2 I157T Variants

by Diego Garmendia, Anne Weidner, Lindsay Venton and Tuya Pal

Genes 2024, 15(7), 881; https://doi.org/10.3390/genes15070881 - 5 Jul 2024

Cited by 1 | Viewed by 2230

Abstract

Breast cancer (BC) risks imparted by CHEK2 c.1100delC (“1100delC”) germline pathogenic/likely pathogenic variant (GPV) are 20–30%, compared to CHEK2 c.470T>C (“I157T”) GPV with <20%, leading to different breast screening recommendations through MRI. We compared cancer risk management (CRM) across these two GPVs. Study [...] Read more.

Breast cancer (BC) risks imparted by CHEK2 c.1100delC (“1100delC”) germline pathogenic/likely pathogenic variant (GPV) are 20–30%, compared to CHEK2 c.470T>C (“I157T”) GPV with <20%, leading to different breast screening recommendations through MRI. We compared cancer risk management (CRM) across these two GPVs. Study participants were adult females with an 1100delC or I157T GPV drawn from the Inherited Cancer Registry (ICARE) across the United States. Cancer history, clinical characteristics, and CRM were compared using chi-squared tests, t-tests, and logistic regression. Of 150 CHEK2 carriers, 40.7% had BC, with a mean age of 50. Comparing 1100delC and I157T GPVs, there were no differences in rates of (1) breast MRI among those with (65.2% versus 55.6% of 23 and 9; p = 0.612) and without (44.0% versus 44.8% of 50 and 29; p = 0.943) BC; (2) risk-reducing mastectomy among those with (50% versus 38.9% of 46 and 15; p = 0.501) and without (13.8% versus 6.5% of 58 and 31; p = 0.296) BC; and (3) risk-reducing salpingo-oophorectomy among those with (24.2% versus 22.2% of 45 and 18; p = 0.852) and without (17.5% versus 16.7% of 57 and 30; p = 0.918) BC. The results suggest over-screening with breast MRI among CHEK2 I157T GPV carriers and possible overuse of risk-reducing surgeries among CHEK2 carriers. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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12 pages, 669 KiB

Open AccessEditor’s ChoiceArticle

Somatic Variants Acquired Later in Life Associated with Thoracic Aortic Aneurysms: JAK2 V617F

by Christina Waldron, Mohammad A. Zafar, Deqiong Ma, Hui Zhang, Daniel Dykas, Bulat A. Ziganshin, Andreea Popa, Alokkumar Jha, Jennifer M. Kwan and John A. Elefteriades

Genes 2024, 15(7), 883; https://doi.org/10.3390/genes15070883 - 5 Jul 2024

Cited by 1 | Viewed by 2214

Abstract

The JAK2 V617F somatic variant is a well-known driver of myeloproliferative neoplasms (MPN) associated with an increased risk for athero-thrombotic cardiovascular disease. Recent studies have demonstrated its role in the development of thoracic aortic aneurysm (TAA). However, limited clinical information and level of [...] Read more.

The JAK2 V617F somatic variant is a well-known driver of myeloproliferative neoplasms (MPN) associated with an increased risk for athero-thrombotic cardiovascular disease. Recent studies have demonstrated its role in the development of thoracic aortic aneurysm (TAA). However, limited clinical information and level of JAK2 V617F burden have been provided for a comprehensive evaluation of potential confounders. A retrospective genotype-first study was conducted to identify carriers of the JAK2 V617F variant from an internal exome sequencing database in Yale DNA Diagnostics Lab. Additionally, the overall incidence of somatic variants in the JAK2 gene across various tissue types in the healthy population was carried out based on reanalysis of SomaMutDB and data from the UK Biobank (UKBB) cohort to compare our dataset to the population prevalence of the variant. In our database of 12,439 exomes, 594 (4.8%) were found to have a thoracic aortic aneurysm (TAA), and 12 (0.049%) were found to have a JAK2 V617F variant. Among the 12 JAK2 V617F variant carriers, five had a TAA (42%), among whom four had an ascending TAA and one had a descending TAA, with a variant allele fraction ranging from 11.2% to 20%. Among these five patients, 60% were female, and average age at diagnosis was 70 (49–79). The mean ascending aneurysm size was 5.05 cm (range 4.6–5.5 cm), and four patients had undergone surgical aortic replacement or repair. UKBB data revealed a positive correlation between the JAK2 V617F somatic variant and aortic valve disease (effect size 0.0086, p = 0.85) and TAA (effect size = 0.004, p = 0.92), although not statistically significant. An unexpectedly high prevalence of TAA in our dataset (5/594, 0.84%) is greater than the prevalence reported before for the general population, supporting its association with TAA. JAK2 V617F may contribute a meaningful proportion of otherwise unexplained aneurysm patients. Additionally, it may imply a potential JAK2-specific disease mechanism in the developmental of TAA, which suggests a possible target of therapy that warrants further investigation. Full article

(This article belongs to the Special Issue Genetic and Genomic Research of Cardiovascular Diseases)

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13 pages, 2603 KiB

Open AccessEditor’s ChoiceArticle

CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal

by Zhen Lyu, Sabin Dahal, Shuai Zeng, Juexin Wang, Dong Xu and Trupti Joshi

Genes 2024, 15(7), 882; https://doi.org/10.3390/genes15070882 - 5 Jul 2024

Viewed by 2653

Abstract

In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible chromatin sequencing (scATAC-seq) data. Integrated analysis of diverse modalities has helped researchers [...] Read more.

In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible chromatin sequencing (scATAC-seq) data. Integrated analysis of diverse modalities has helped researchers make more accurate predictions and gain a more comprehensive understanding than with single-modality analysis. However, generating such multimodal data is technically challenging and expensive, leading to limited availability of single-cell co-assay data. Here, we propose a model for cross-modal prediction between the transcriptome and chromatin profiles in single cells. Our model is based on a deep neural network architecture that learns the latent representations from the source modality and then predicts the target modality. It demonstrates reliable performance in accurately translating between these modalities across multiple paired human scATAC-seq and scRNA-seq datasets. Additionally, we developed CrossMP, a web-based portal allowing researchers to upload their single-cell modality data through an interactive web interface and predict the other type of modality data, using high-performance computing resources plugged at the backend. Full article

(This article belongs to the Collection Feature Papers in Bioinformatics)

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18 pages, 8717 KiB

Open AccessEditor’s ChoiceArticle

Complete Chloroplast Genome of Megacarpaea megalocarpa and Comparative Analysis with Related Species from Brassicaceae

by Zhuo Zhang, Xiaojun Shi, Haowen Tian, Juan Qiu, Hanze Ma and Dunyan Tan

Genes 2024, 15(7), 886; https://doi.org/10.3390/genes15070886 - 5 Jul 2024

Cited by 1 | Viewed by 1254

Abstract

Megacarpaea megalocarpa, a perennial herbaceous species belonging to the Brassicaceae family, has potential medicinal value. We isolated and characterized the chloroplast (cp) genome of M. megalocarpa and compared it with closely related species. The chloroplast genome displayed a typical quadripartite structure, spanning [...] Read more.

Megacarpaea megalocarpa, a perennial herbaceous species belonging to the Brassicaceae family, has potential medicinal value. We isolated and characterized the chloroplast (cp) genome of M. megalocarpa and compared it with closely related species. The chloroplast genome displayed a typical quadripartite structure, spanning 154,877 bp, with an overall guanine–cytosine (GC) content of 36.20%. Additionally, this genome contained 129 genes, 105 simple sequence repeats (SSRs), and 48 long repeat sequences. Significantly, the ycf1 gene exhibited a high degree of polymorphism at the small single copy (SSC) region and the inverted repeat a (IRa) boundary. Despite this polymorphism, relative synonymous codon usage (RSCU) values were found to be similar across species, and no large segment rearrangements or inversions were detected. The large single copy (LSC) and SSC regions showed higher sequence variations and nucleotide polymorphisms compared to the IR region. Thirteen distinct hotspot regions were identified as potential molecular markers. Our selection pressure analysis revealed that the protein-coding gene rpl20 is subjected to different selection pressures in various species. Phylogenetic analysis positioned M. megalocarpa within the expanded lineage II of the Brassicaceae family. The estimated divergence time suggests that M. megalocarpa diverged approximately 4.97 million years ago. In summary, this study provides crucial baseline information for the molecular identification, phylogenetic relationships, conservation efforts, and utilization of wild resources in Megacarpaea. Full article

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

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20 pages, 8533 KiB

Open AccessEditor’s ChoiceArticle

The Development of a Fluorescent Microsatellite Marker Assay for the Pitaya Canker Pathogen (Neoscytalidium dimidiatum)

by Rui Li, Xi Li, Jingcheng Tang, Changping Xie and Jianan Wang

Genes 2024, 15(7), 885; https://doi.org/10.3390/genes15070885 - 5 Jul 2024

Viewed by 1407

Abstract

Pitaya canker, caused by Neoscytalidium dimidiatum, is a destructive disease that significantly threatens the safety of the pitaya industry. The authors of previous studies have mainly focused on its biological characteristics and chemical control. However, there are no molecular markers available thus [...] Read more.

Pitaya canker, caused by Neoscytalidium dimidiatum, is a destructive disease that significantly threatens the safety of the pitaya industry. The authors of previous studies have mainly focused on its biological characteristics and chemical control. However, there are no molecular markers available thus far that can be used for the population genetics study of this pathogen. In the present study, a draft genome of N. dimidiatum with a total length of 41.46 MB was assembled in which 9863 coding genes were predicted and annotated. In particular, the microsatellite sequences in the draft genome were investigated. To improve the successful screening rate of potentially polymorphic microsatellite makers, another five N. dimidiatum isolates were resequenced and assembled. A total of eight pairs of polymorphic microsatellite primers were screened out based on the polymorphic microsatellite loci after investigating the sequencing and resequencing assemblies of the six isolates. A total of thirteen representative isolates sampled from different pitaya plantations were genotyped in order to validate the polymorphism of the resulting eight markers. The results indicated that these markers were able to distinguish the isolates well. Lastly, a neighbor-joining tree of 35 isolates, sampled from different pitaya plantations located in different regions, was constructed according to the genotypes of the eight molecular markers. The developed tree indicated that these molecular markers had sufficient genotyping capabilities for our test panel of isolates. In summary, we developed a set of polymorphic microsatellite markers in the following study that can effectively genotype and distinguish N. dimidiatum isolates and be utilized in the population genetics study of N. dimidiatum. Full article

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

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16 pages, 1873 KiB

Open AccessEditor’s ChoiceArticle

Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns

by Piaoran Xu, Lijuan Zhang, Liping Lu, Yanli Zhu, Dandan Gao and Shanshan Liu

Genes 2024, 15(7), 887; https://doi.org/10.3390/genes15070887 - 5 Jul 2024

Cited by 2 | Viewed by 1528

Abstract

The latest research shows that ferns and lycophytes have distinct evolutionary lineages. The codon usage patterns of lycophytes and ferns have not yet been documented. To investigate the gene expression profiles across various plant lineages with respect to codon usage, analyze the disparities [...] Read more.

The latest research shows that ferns and lycophytes have distinct evolutionary lineages. The codon usage patterns of lycophytes and ferns have not yet been documented. To investigate the gene expression profiles across various plant lineages with respect to codon usage, analyze the disparities and determinants of gene evolution in primitive plant species, and identify appropriate exogenous gene expression platforms, the whole-genome sequences of four distinct species were retrieved from the NCBI database. The findings indicated that Ceratopteris richardii, Adiantum capillus-veneris, and Selaginella moellendorffii exhibited an elevated A/U content in their codon base composition and a tendency to end with A/U. Additionally, S. capillus-veneris had more C/G in its codons and a tendency to end with C/G. The ENC values derived from both ENC-plot and ENC-ratio analyses deviated significantly from the standard curves, suggesting that the codon usage preferences of these four species were primarily influenced by genetic mutations and natural selection, with natural selection exerting a more prominent influence. This finding was further supported by PR2-Plot, neutrality plot analysis, and COA. A combination of RSCU and ENC values was used as a reference criterion to rank the codons and further identify the optimal codons. The study identified 24 high-frequency codons in C. richardii, A. capillus-veneris, and Diphasiastrum complanatum, with no shared optimal codons among the four species. Arabidopsis thaliana and Ginkgo biloba exhibited similar codon preferences to the three species, except for S. moellendorffii. This research offers a theoretical framework at the genomic codon level for investigating the phylogenetic relationships between lycophytes and ferns, shedding light on gene codon optimization and its implications for genetic engineering in breeding. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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14 pages, 7152 KiB

Open AccessEditor’s ChoiceArticle

Characterization and Phylogenetic Analysis of the Chloroplast Genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor

by Li-Li Wu, Ying-Min Geng and Lan-Ping Zheng

Genes 2024, 15(7), 877; https://doi.org/10.3390/genes15070877 - 3 Jul 2024

Cited by 2 | Viewed by 1360

Abstract

This study sequenced the complete chloroplast genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor using the Illumina NovaSeq and PacBio RSII platforms. Following sequencing, the genomes were assembled, annotated, comparatively analyzed, and used to construct a phylogenetic tree to explore [...] Read more.

This study sequenced the complete chloroplast genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor using the Illumina NovaSeq and PacBio RSII platforms. Following sequencing, the genomes were assembled, annotated, comparatively analyzed, and used to construct a phylogenetic tree to explore their phylogenetic positions. Results indicated that the chloroplast genomes of S. japonica var. timoriensis and S. japonica var. discolor both displayed a typical double-stranded circular tetrameric structure, measuring 157,609 and 157,748 bp in length, respectively. Each genome contained 130 annotated genes, with similar total GC content and relative codon usage patterns, showing a distinct preference for A/U at the third codon position. Simple sequence repeat analysis identified 207 and 211 repeats in S. japonica var. timoriensis and S. japonica var. discolor, respectively, primarily the A/T type. Boundary condition analysis indicated no significant expansion or contraction in the inverted repeat regions with consistent gene types and locations across both varieties. Nucleotide polymorphism analysis highlighted greater variation in the intergenic regions than in the coding sequences of Stephania chloroplast genomes. Phylogenetic analyses demonstrated that the species Stephania clustered into a distinct, well-supported clade. Notably, Stephania japonica, along with S. japonica var. discolor and S. japonica var. timoriensis, established a monophyletic lineage. Within this lineage, S. japonica and S. japonica var. discolor were closely related, with S. japonica var. timoriensis serving as their sister taxon. Full article

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

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17 pages, 3923 KiB

Open AccessEditor’s ChoiceArticle

Sequencing and Description of the Mitochondrial Genome of Orthopodomyia fascipes (Diptera: Culicidae)

by Fábio Silva da Silva, Bruna Laís Sena do Nascimento, Ana Cecília Ribeiro Cruz, Sandro Patroca da Silva, Carine Fortes Aragão, Daniel Damous Dias, Lucas Henrique da Silva e Silva, Lúcia Aline Moura Reis, Hanna Carolina Farias Reis, Liliane Leal das Chagas, José Wilson Rosa Jr., Durval Bertram Rodrigues Vieira, Roberto Carlos Feitosa Brandão, Daniele Barbosa de Almeida Medeiros and Joaquim Pinto Nunes Neto

Genes 2024, 15(7), 874; https://doi.org/10.3390/genes15070874 - 3 Jul 2024

Cited by 2 | Viewed by 1746

Abstract

The genus Orthopodomyia Theobald, 1904 (Diptera: Culicidae) comprises 36 wild mosquito species, with distribution largely restricted to tropical and temperate areas, most of which are not recognized as vectors of epidemiological importance due to the lack of information related to their bionomy and [...] Read more.

The genus Orthopodomyia Theobald, 1904 (Diptera: Culicidae) comprises 36 wild mosquito species, with distribution largely restricted to tropical and temperate areas, most of which are not recognized as vectors of epidemiological importance due to the lack of information related to their bionomy and involvement in the cycle transmission of infectious agents. Furthermore, their evolutionary relationships are not completely understood, reflecting the scarcity of genetic information about the genus. Therefore, in this study, we report the first complete description of the mitochondrial genome of a Neotropical species representing the genus, Orthopodomyia fascipes Coquillet, 1906, collected in the Brazilian Amazon region. Using High Throughput Sequencing, we obtained a mitochondrial sequence of 15,598 bp, with an average coverage of 418.5×, comprising 37 functional subunits and a final portion rich in A + T, corresponding to the control region. The phylogenetic analysis, using Maximum Likelihood and Bayesian Inference based on the 13 protein-coding genes, corroborated the monophyly of Culicidae and its two subfamilies, supporting the proximity between the tribes Orthopodomyiini and Mansoniini, partially disagreeing with previous studies based on the use of molecular and morphological markers. The information generated in this study contributes to a better understanding of the taxonomy and evolutionary history of the genus and other groups of Culicidae. Full article

(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)

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11 pages, 1032 KiB

Open AccessEditor’s ChoiceArticle

Chronic Adolescent Restraint Stress Downregulates miRNA-200a Expression in Male and Female C57BL/6J and BALB/cJ Mice

by Helen M. Kamens, Emma K. Anziano, William J. Horton and Sonia A. Cavigelli

Genes 2024, 15(7), 873; https://doi.org/10.3390/genes15070873 - 3 Jul 2024

Cited by 1 | Viewed by 1816

Abstract

Adolescence is a critical developmental period when the brain is plastic, and stress exposure can have lasting physiological consequences. One mechanism through which adolescent stress may have lasting effects is by altering microRNAs (miRNAs), leading to wide-scale gene expression changes. Three prior independent [...] Read more.

Adolescence is a critical developmental period when the brain is plastic, and stress exposure can have lasting physiological consequences. One mechanism through which adolescent stress may have lasting effects is by altering microRNAs (miRNAs), leading to wide-scale gene expression changes. Three prior independent studies used unbiased approaches (RNA sequencing or microarray) to identify miRNAs differentially expressed by chronic variable stress in male rodents. In all three studies, miRNA-200a was differentially expressed in areas of the brain associated with emotion regulation. The current study extends this research to determine if chronic non-variable adolescent stress downregulates miRNA-200a expression by looking at two strains (BALB/cJ and C57BL/6J) of male and female mice. We utilized a 14-day (2 h/day) restraint stress protocol and verified stress effects on adolescent body weight gain and circulating corticosterone concentrations relative to non-restraint controls. Mice were then left undisturbed until they were euthanized in adulthood, at which time brains were collected to measure miRNA-200a in the ventral hippocampus. Three weeks after adolescent stress ended, differences in body weight between groups were no longer significant; however, animals exposed to stress had less miRNA-200a expression in the ventral hippocampus than control animals. These data implicate miRNA-200a expression as a potential mechanism by which adolescent stress can have persistent impacts on multiple outcomes in both male and female mice. Full article

(This article belongs to the Section Neurogenomics)

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11 pages, 1082 KiB

Open AccessEditor’s ChoiceArticle

The Evolution of Genetic Variability at the LRRK2 Locus

by Dylan T. Guenther, Jordan Follett, Rim Amouri, Samia Ben Sassi, Faycel Hentati and Matthew J. Farrer

Genes 2024, 15(7), 878; https://doi.org/10.3390/genes15070878 - 3 Jul 2024

Cited by 2 | Viewed by 1848

Abstract

Leucine-rich repeat kinase 2 (LRRK2) c.6055G>A (p.G2019S) is a frequent cause of Parkinson’s disease (PD), accounting for >30% of Tunisian Arab-Berber patients. LRRK2 is widely expressed in the immune system and its kinase activity confers a survival advantage against infection in [...] Read more.

Leucine-rich repeat kinase 2 (LRRK2) c.6055G>A (p.G2019S) is a frequent cause of Parkinson’s disease (PD), accounting for >30% of Tunisian Arab-Berber patients. LRRK2 is widely expressed in the immune system and its kinase activity confers a survival advantage against infection in animal models. Here, we assess haplotype variability in cis and in trans of the LRRK2 c.6055G>A mutation, define the age of the pathogenic allele, explore its relationship to the age of disease onset (AOO), and provide evidence for its positive selection. Full article

(This article belongs to the Section Genes & Environments)

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14 pages, 1960 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Association Analysis Identified Quantitative Trait Loci (QTLs) Underlying Drought-Related Traits in Cultivated Peanut (Arachis hypogaea L.)

by Phat Dang, Jinesh Patel, Ron Sorensen, Marshall Lamb and Charles Y. Chen

Genes 2024, 15(7), 868; https://doi.org/10.3390/genes15070868 - 2 Jul 2024

Cited by 2 | Viewed by 1504

Abstract

Drought is a destructive abiotic stress that affects all critical stages of peanut growth such as emergence, flowering, pegging, and pod filling. The development of a drought-tolerant variety is a sustainable strategy for long-term peanut production. The U.S. mini-core peanut germplasm collection was [...] Read more.

Drought is a destructive abiotic stress that affects all critical stages of peanut growth such as emergence, flowering, pegging, and pod filling. The development of a drought-tolerant variety is a sustainable strategy for long-term peanut production. The U.S. mini-core peanut germplasm collection was evaluated for drought tolerance to the middle-season drought treatment phenotyping for pod weight, pod count, relative water content (RWC), specific leaf area (SLA), leaf dry matter content (LDMC), and drought rating. A genome-wide association study (GWAS) was performed to identify minor and major QTLs. A total of 144 QTLs were identified, including 18 significant QTLs in proximity to 317 candidate genes. Ten significant QTLs on linkage groups (LGs) A03, A05, A06, A07, A08, B04, B05, B06, B09, and B10 were associated with pod weight and pod count. RWC stages 1 and 2 were correlated with pod weight, pod count, and drought rating. Six significant QTLs on LGs A04, A07, B03, and B04 were associated with RWC stages 1 and 2. Drought rating was negatively correlated with pod yield and pod count and was associated with a significant QTL on LG A06. Many QTLs identified in this research are novel for the evaluated traits, with verification that the pod weight shared a significant QTL on chromosome B06 identified in other research. Identified SNP markers and the associated candidate genes provide a resource for molecular marker development. Verification of candidate genes surrounding significant QTLs will facilitate the application of marker-assisted peanut breeding for drought tolerance. Full article

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

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15 pages, 620 KiB

Open AccessEditor’s ChoiceArticle

Objective Assessments of Smoking and Drinking Outperform Clinical Phenotypes in Predicting Variance in Epigenetic Aging

by Robert Philibert, Man-Kit Lei, Mei Ling Ong and Steven R. H. Beach

Genes 2024, 15(7), 869; https://doi.org/10.3390/genes15070869 - 2 Jul 2024

Cited by 4 | Viewed by 1325

Abstract

The reliability of the associations of the acceleration of epigenetic aging (EA) indices with clinical phenotypes other than for smoking and drinking is poorly understood. Furthermore, the majority of clinical phenotyping studies have been conducted using data from subjects of European ancestry. In [...] Read more.

The reliability of the associations of the acceleration of epigenetic aging (EA) indices with clinical phenotypes other than for smoking and drinking is poorly understood. Furthermore, the majority of clinical phenotyping studies have been conducted using data from subjects of European ancestry. In order to address these limitations, we conducted clinical, physiologic, and epigenetic assessments of a cohort of 278 middle-aged African American adults and analyzed the associations with the recently described principal-components-trained version of GrimAge (i.e., PC-GrimAge) and with the DunedinPACE (PACE) index using regression analyses. We found that 74% of PC-GrimAge accelerated aging could be predicted by a simple baseline model consisting of age, sex, and methylation-sensitive digital PCR (MSdPCR) assessments of smoking and drinking. The addition of other serological, demographic, and medical history variables or PACE values did not meaningfully improve the prediction, although some variables did significantly improve the model fit. In contrast, clinical variables mapping to cardiometabolic syndrome did independently contribute to the prediction of PACE values beyond the baseline model. The PACE values were poorly correlated with the GrimAge values (r = 0.2), with little overlap in variance explained other than that conveyed by smoking and drinking. The results suggest that EA indices may differ in the clinical information that they provide and may have significant limitations as screening tools to guide patient care. Full article

(This article belongs to the Section Epigenomics)

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15 pages, 6926 KiB

Open AccessEditor’s ChoiceArticle

Identification and Expression Analysis of UPS Gene Family in Potato

by Wenyue Huang, Yifei Lu, Bi Ren, Fuchun Zeng, Yongjian Liu, Liming Lu and Liqin Li

Genes 2024, 15(7), 870; https://doi.org/10.3390/genes15070870 - 2 Jul 2024

Viewed by 1170

Abstract

Ureide permeases (UPSs) mediate the transport of ureides, including allantoin and allantoate, which act as nitrogen-transporting compounds in plants and have recently been found to play a role in cellular signaling. To date, UPSs have not been reported in potato, and their identification [...] Read more.

Ureide permeases (UPSs) mediate the transport of ureides, including allantoin and allantoate, which act as nitrogen-transporting compounds in plants and have recently been found to play a role in cellular signaling. To date, UPSs have not been reported in potato, and their identification is important for further function studies and for understanding molecular mechanisms of plant adverse responses. Based on potato genomic data, we identified 10 StUPS genes in potato (Solanum tuberosum L.). Then, we conducted a comprehensive study of the identified StUPS genes using bioinformatics methods. Genome phylogenetic and genomic localization analyses revealed that StUPSs can be classified into four categories, are highly homologous to Arabidopsis thaliana UPS members, and are distributed on three chromosomes. The six StUPS genes were investigated by RT–qPCR, and the findings indicated that all of these genes are involved in the response to several stresses, including low nitrogen, cold, ABA, salt, H₂O_2, and drought. This study establishes a strong theoretical framework for investigating the function of potato UPS genes, as well as the molecular mechanisms underlying the responses of these genes to various environmental stresses. Full article

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

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17 pages, 2179 KiB

Open AccessEditor’s ChoiceArticle

A-to-I Editing Is Subtype-Specific in Non-Hodgkin Lymphomas

by Cai Chen and Ralf Bundschuh

Genes 2024, 15(7), 864; https://doi.org/10.3390/genes15070864 - 1 Jul 2024

Cited by 1 | Viewed by 1298

Abstract

Cancer is a complex and heterogeneous disease, in which a number of genetic and epigenetic changes occur in tumor onset and progression. Recent studies indicate that changes at the RNA level are also involved in tumorigenesis, such as adenosine-to-inosine (A-to-I) RNA editing. Here, [...] Read more.

Cancer is a complex and heterogeneous disease, in which a number of genetic and epigenetic changes occur in tumor onset and progression. Recent studies indicate that changes at the RNA level are also involved in tumorigenesis, such as adenosine-to-inosine (A-to-I) RNA editing. Here, we systematically investigate transcriptome-wide A-to-I editing events in a large number of samples from Non-Hodgkin lymphomas (NHLs). Using a computational pipeline that determines significant differences in editing level between NHL and normal samples at known A-to-I editing sites, we identify a number of differentially edited editing sites between NHL subtypes and normal samples. Most of the differentially edited sites are located in non-coding regions, and many such sites show a strong correlation between gene expression level and editing efficiency, indicating that RNA editing might have direct consequences for the cancer cell’s aberrant gene regulation status in these cases. Moreover, we establish a strong link between RNA editing and NHL by demonstrating that NHL and normal samples and even NHL subtypes can be distinguished based on genome-wide RNA editing profiles alone. Our study establishes a strong link between RNA editing, cancer and aberrant gene regulation in NHL. Full article

(This article belongs to the Section RNA)

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18 pages, 2397 KiB

Open AccessEditor’s ChoiceArticle

Gene Expression Profiling and Qualitative Characteristics in Delaying Flesh Softening of Avocado Fruits

by Ourania Anagnostopoulou, Georgios Tsaniklidis, Konstantinos Paschalidis and Filippos Ververidis

Genes 2024, 15(7), 860; https://doi.org/10.3390/genes15070860 - 1 Jul 2024

Cited by 1 | Viewed by 1333

Abstract

In this research, qualitative characteristics were studied under different post-harvest treatments in Hass and Fuerte cultivars of avocado (Persea americana) fruits. The post-harvest treatments performed in fruits of these cultivars comprised Ethrel application and plastic film (membrane) covering. The measurements of [...] Read more.

In this research, qualitative characteristics were studied under different post-harvest treatments in Hass and Fuerte cultivars of avocado (Persea americana) fruits. The post-harvest treatments performed in fruits of these cultivars comprised Ethrel application and plastic film (membrane) covering. The measurements of qualitative characteristics were related to color; flesh consistency; measurements of titratable acidity, total soluble solids, percentage of total phenolic contents, and ascorbic peroxidase activity; and the real-time (quantitative) polymerase chain reaction (qPCR) of gene expression and enzyme activities of phenylalanine ammonia-lyase (PAL) and beta-galactosidase (β-gal). The experiments found that the application of plastic film has excellent results in retaining qualitative characteristics and enzyme activities via maintaining firmness in higher levels. The plastic film covering appeared to delay ripening without the use of chemicals and, therefore, it has the potential to extend the duration of the post-harvest life of the avocado fruit. Variations between the two cultivars were found in the measurements of total soluble solids (Fuerte cultivar showed an increase of 22%, whereas Hass cultivar showed an increase of 120% in Brix values) and total phenolic contents (Fuerte cultivar showed a decrease of 16% and Hass cultivar showed an increase of 29%). It is worth noting that PAL’s activity increased significantly (over 44%), as compared to other treatments, and β-galactosidase’s activity decreased, as compared to other treatments. In conclusion, plastic film covering results in a decrease in the activity of β-galactosidase, as shown by the reaction of hydrolysis (enzyme activity) but also from the expression of the related genes. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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23 pages, 4160 KiB

Open AccessEditor’s ChoiceArticle

Intermolecular Gene Conversion for the Equalization of Genome Copies in the Polyploid Haloarchaeon Haloferax volcanii: Identification of Important Proteins

by Hanna Özer, Daniel Wasser, Lara Sandner and Jörg Soppa

Genes 2024, 15(7), 861; https://doi.org/10.3390/genes15070861 - 1 Jul 2024

Cited by 2 | Viewed by 1685

Abstract

The model haloarchaeon Haloferax volcanii is polyploid with about 20 copies of its major chromosome. Recently it has been described that highly efficient intermolecular gene conversion operates in H. volcanii to equalize the chromosomal copies. In the current study, 24 genes were selected [...] Read more.

The model haloarchaeon Haloferax volcanii is polyploid with about 20 copies of its major chromosome. Recently it has been described that highly efficient intermolecular gene conversion operates in H. volcanii to equalize the chromosomal copies. In the current study, 24 genes were selected that encode proteins with orthologs involved in gene conversion or homologous recombination in archaea, bacteria, or eukaryotes. Single gene deletion strains of 22 genes and a control gene were constructed in two parent strains for a gene conversion assay; only radA and radB were shown to be essential. Protoplast fusions were used to generate strains that were heterozygous for the gene HVO_2528, encoding an enzyme for carotinoid biosynthesis. It was revealed that a lack of six of the proteins did not influence the efficiency of gene conversion, while sixteen mutants had severe gene conversion defects. Notably, lack of paralogous proteins of gene families had very different effects, e.g., mutant Δrad25b had no phenotype, while mutants Δrad25a, Δrad25c, and Δrad25d were highly compromised. Generation of a quadruple rad25 and a triple sph deletion strain also indicated that the paralogs have different functions, in contrast to sph2 and sph4, which cannot be deleted simultaneously. There was no correlation between the severity of the phenotypes and the respective transcript levels under non-stressed conditions, indicating that gene expression has to be induced at the onset of gene conversion. Phylogenetic trees of the protein families Rad3/25, MutL/S, and Sph/SMC/Rad50 were generated to unravel the history of the paralogous proteins of H. volcanii. Taken together, unselected intermolecular gene conversion in H. volcanii involves at least 16 different proteins, the molecular roles of which can be studied in detail in future projects. Full article

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

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22 pages, 2894 KiB

Open AccessEditor’s ChoiceArticle

Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities

by Liliana Hopkins, Kayla Yim, Ana Rumora, Melissa F. Baykus, Luisa Martinez and Luis Jimenez

Genes 2024, 15(7), 865; https://doi.org/10.3390/genes15070865 - 1 Jul 2024

Cited by 2 | Viewed by 1530

Abstract

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. [...] Read more.

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site. Full article

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

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11 pages, 3049 KiB

Open AccessEditor’s ChoiceArticle

Expanding Genetic Counselor Roles: A Model for Global Research Development

by Colleen C. Muraresku, Elizabeth M. McCormick, Lydia Rockart, T. Blaine Crowley, Stephanie Asher, Amanda Back, Sarah M. Baldino, Emma Bedoukian, Allison D. Britt, Natalie Burrill, Cara Cacioppo, Dana Farengo Clark, Mary Egan Clark, Laura Conway, Laynie Dratch, Holly A. Dubbs, Nicole M. Engelhardt, Natalie Ginn, Christopher Gray, Tiff Hartman, Evan R. Hathaway, Katherine L. Helbig, Lily Hoffman-Andrews, Stefanie Kasperski, Beth A. Keena, Kierstin N. Keller, Jessica M. Long, Lauren Lulis, Laina Lusk, Daniel E. McGinn, Rebecca Mueller, Rache A. Paul, Lisa Pilchman, Jacquelyn Powers, Sarah E. Raible, Sara Reichert, Alyssa L. Rippert, Angela G. Arnold, Sarah M. Ruggiero, Erica Schindewolf, Katie Rose Sullivan, Shannon Terek, Bekah Wang, McKenzie Wells, Natalia Wisniewski, Renee Wright, Elisabeth McCarty Wood, Stacy Woyciechowski, Kristin Zelley, Kathleen D. Valverde and Donna M. McDonald-McGinn Show full author list Hide full author list

Genes 2024, 15(7), 867; https://doi.org/10.3390/genes15070867 - 1 Jul 2024

Viewed by 2428

Abstract

Purpose: Genetic counselors (GCs) increasingly play key roles in advancing genomic medicine through innovative research. Here, we examine one large cohort of GCs’ evolving contributions to the literature, with the goal of facilitating worldwide professional development for GCs through scholarly activities. Methods: Publications [...] Read more.

Purpose: Genetic counselors (GCs) increasingly play key roles in advancing genomic medicine through innovative research. Here, we examine one large cohort of GCs’ evolving contributions to the literature, with the goal of facilitating worldwide professional development for GCs through scholarly activities. Methods: Publications were cataloged by members of the Section of Genetic Counseling (Section), established at the Children’s Hospital of Philadelphia and the University of Pennsylvania in 2014, including publication year, journal, impact factor, and author position. Data were organized using the “My Bibliography” tool on the National Center for Biotechnology Information website and a Research Electronic Data Capture database created to initially collect manuscripts published through 30 June 2020. A subsequent survey captured publications through 5 February 2024. Results: An amount of 52 of 120 (43%) GCs shared their curriculum vitae/papers. 992 unique publications were identified from 1986 to 2024. Since 2013, no less than 32 papers were published annually by Section members and no less than 10 GCs contributed to publications yearly. Impact factors typically averaged >5.0 per year. Areas of foci diversified considerably since 2015. Conclusions: Here, we establish that GCs indeed contribute to scholarly work as evidenced by the number of publications alone. The establishment of an academic home may have contributed, given publications increased concurrent to launching the Section, providing a model for organizing GCs at institutions nationally and internationally. Highlighting such achievements will foster the expansion of GC roles in the era of precision genomic medicine and therapy. Considering ways to support GCs towards expanding these activities is equally important. Full article

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

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13 pages, 4120 KiB

Open AccessEditor’s ChoiceArticle

Genetic Insights into the Historical Attribution of Variety Names of Sweet Chestnut (Castanea sativa Mill.) in Northern Italy

by Marta Cavallini, Gianluca Lombardo, Claudio Cantini, Mauro Gerosa and Giorgio Binelli

Genes 2024, 15(7), 866; https://doi.org/10.3390/genes15070866 - 1 Jul 2024

Viewed by 1544

Abstract

The sweet chestnut (Castanea sativa Mill.) is subject to the progressive disappearance of its traditional chestnut groves. In the northern part of Italy, where distribution of the sweet chestnut is fragmented, many local varieties continue to be identified mostly by oral tradition. [...] Read more.

The sweet chestnut (Castanea sativa Mill.) is subject to the progressive disappearance of its traditional chestnut groves. In the northern part of Italy, where distribution of the sweet chestnut is fragmented, many local varieties continue to be identified mostly by oral tradition. We characterised by SSRs eleven historically recognised varieties of sweet chestnut in the area surrounding Lake Como, with the goal of giving a genetic basis to the traditional classification. We performed classical analysis about differentiation and used Bayesian approaches to detect population structure and to reconstruct demography. The results revealed that historical and genetic classifications are loosely linked when chestnut fruits are just “castagne”, that is, normal fruits, but increasingly overlap where “marroni” (the most prized fruits) are concerned. Bayesian classification allowed us to identify a homogeneous gene cluster not recognised in the traditional assessment of the varieties and to reconstruct possible routes used for the propagation of sweet chestnut. We also reconstructed ancestral relationships between the different gene pools involved and dated ancestral lineages whose results fit with palynological data. We suggest that conservation strategies based on a genetic evaluation of the resource should also rely on traditional cultural heritage, which could reveal new sources of germplasm. Full article

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

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8 pages, 548 KiB

Open AccessEditor’s ChoiceArticle

Lynch Syndrome and Thyroid Nodules: A Single Center Experience

by Irene Spinelli, Simona Moffa, Francesca Fianchi, Teresa Mezza, Francesca Cinti, Gianfranco Di Giuseppe, Clelia Marmo, Gianluca Ianiro, Francesca Romana Ponziani, Annalisa Tortora, Maria Elena Riccioni, Andrea Giaccari and Antonio Gasbarrini

Genes 2024, 15(7), 859; https://doi.org/10.3390/genes15070859 - 30 Jun 2024

Cited by 1 | Viewed by 2006

Abstract

Background: Lynch syndrome (LS) is a genetic disease with increased risk of colorectal cancer and other malignancies. There are few reported cases of thyroid cancer in LS patients. The aim of this study is to investigate the presence of thyroid nodules in LS [...] Read more.

Background: Lynch syndrome (LS) is a genetic disease with increased risk of colorectal cancer and other malignancies. There are few reported cases of thyroid cancer in LS patients. The aim of this study is to investigate the presence of thyroid nodules in LS patients and to explore their association with the genetic features of the disease. Methods: A retrospective and descriptive analysis was conducted to include all LS patients followed at the CEMAD (Centro Malattie Apparato Digerente) of Fondazione Policlinico Universitario A. Gemelli IRCCS. The characteristics of LS disease, gene mutations, and previous history of thyroid disease were evaluated. Majority of patients underwent thyroid ultrasound (US), and nodule cytology was performed when needed. Results: Of a total of 139 patients with LS, 110 patients were included in the study. A total of 103 patients (74%) underwent thyroid ultrasound examinations, and 7 patients (5%) had a previous history of thyroid disease (cancer or multinodular goiter). The mean age was 51.9 years. Thyroid nodules were found in 62 patients (60%) who underwent US, and 9 of them (14%) had suspicious features of malignancy, inducing a fine-needle aspiration biopsy. A cytologic analysis classified 7 of 9 cases (78%) as TIR2 and 2 (22%) as TIR3a. Between patients with nodular thyroid disease (single nodule, multinodular goiter, and cancer), most of them (25 patients, 36% of total) were carriers of the MSH6 mutation, while 22 (32%), 17 (24%), and 5 (7%) had MSH2, MLH1, and PMS2 mutations, respectively. Conclusions: A high prevalence of thyroid nodules was found in patients with LS, especially in MSH6-carrying patients. Performing at least one thyroid ultrasound examination is suggested for the detection of nodular thyroid disease in LS patients. Systematic investigations are needed to estimate their prevalence, features, and risk of malignant transformation. Full article

(This article belongs to the Section Genetic Diagnosis)

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11 pages, 733 KiB

Open AccessEditor’s ChoiceArticle

Variation of the 3’RR1 HS1.2 Enhancer and Its Genomic Context

by Carla Jodice, Patrizia Malaspina, Bianca Maria Ciminelli, Cristina Martinez-Labarga, Michela Biancolella, Giuseppe Novelli and Andrea Novelletto

Genes 2024, 15(7), 856; https://doi.org/10.3390/genes15070856 - 29 Jun 2024

Cited by 1 | Viewed by 1363

Abstract

In humans, the HS1.2 enhancer in the Ig heavy-chain locus is modular, with length polymorphism. Previous studies have shown the following features for this variation: (i) strong population structuring; (ii) association with autoimmune diseases; and (iii) association with developmental changes in Ig expression. [...] Read more.

In humans, the HS1.2 enhancer in the Ig heavy-chain locus is modular, with length polymorphism. Previous studies have shown the following features for this variation: (i) strong population structuring; (ii) association with autoimmune diseases; and (iii) association with developmental changes in Ig expression. The HS1.2 region could then be considered as a contributor to inter-individual diversity in humoral response in adaptive immunity. We experimentally determined the HS1.2-length class genotype in 72 of the 1000 Genomes CEU cell lines and assigned the HS1.2 alleles to haplotypes defined by 18 landmark SNPs. We also sequenced the variable portion and ~200 bp of the flanking DNA of 34 HS1.2 alleles. Furthermore, we computationally explored the ability of different allelic arrangements to bind transcription factors. Non-random association between HS1.2 and Gm allotypes in the European population clearly emerged. We show a wealth of variation in the modular composition of HS1.2, with five SNPs further contributing to diversity. Longer alleles offer more potential sites for binding but, for same-length alleles, SNP variation creates/destroys potential binding sites. Altogether, the arrangements of modules and SNP alleles both inside and outside HS1.2 denote an organization of diversity far from randomness. In the context of the strong divergence of human populations for this genomic region and the reported disease associations, our results suggest that selective forces shaped the pattern of its diversity. Full article

(This article belongs to the Special Issue Evolution of Non-coding Elements in Genome Biology)

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12 pages, 5286 KiB

Open AccessEditor’s ChoiceArticle

Potential Involvement of MnCYP710A11 in Botrytis cinerea Resistance in Arabidopsis thaliana and Morus notabilis

by Hui An, Donghao Wang, Lin Yu, Hongshun Wu, Yue Qin, Shihao Zhang, Xianling Ji, Youchao Xin and Xiaodong Li

Genes 2024, 15(7), 853; https://doi.org/10.3390/genes15070853 - 28 Jun 2024

Viewed by 1187

Abstract

Cytochrome P450 (CYP) is a crucial oxidoreductase enzyme that plays a significant role in plant defense mechanisms. In this study, a specific cytochrome P450 gene (MnCYP710A11) was discovered in mulberry (Morus notabilis). Bioinformatic analysis and expression pattern analysis were [...] Read more.

Cytochrome P450 (CYP) is a crucial oxidoreductase enzyme that plays a significant role in plant defense mechanisms. In this study, a specific cytochrome P450 gene (MnCYP710A11) was discovered in mulberry (Morus notabilis). Bioinformatic analysis and expression pattern analysis were conducted to elucidate the involvement of MnCYP710A11 in combating Botrytis cinerea infection. After the infection of B. cinerea, there was a notable increase in the expression of MnCYP710A11. MnCYP710A11 is overexpressed in Arabidopsis and mulberry and strongly reacts to B. cinerea. The overexpression of the MnCYP710A11 gene in Arabidopsis and mulberry led to a substantial enhancement in resistance against B. cinerea, elevated catalase (CAT) activity, increased proline content, and reduced malondialdehyde (MDA) levels. At the same time, H₂O₂ and O₂⁻ levels in MnCYP710A11 transgenic Arabidopsis were decreased, which reduced the damage of ROS accumulation to plants. Furthermore, our research indicates the potential involvement of MnCYP710A11 in B. cinerea resistance through the modulation of other resistance-related genes. These findings establish a crucial foundation for gaining deeper insights into the role of cytochrome P450 in mulberry plants. Full article

(This article belongs to the Collection Feature Papers: 'Plant Genetics and Genomics' Section)

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19 pages, 2854 KiB

Open AccessEditor’s ChoiceArticle

New Observations of the Effects of the Cytoplasm of Aegilops kotschyi Boiss. in Bread Wheat Triticum aestivum L.

by Chaolan Fan, Joanna Melonek and Adam J. Lukaszewski

Genes 2024, 15(7), 855; https://doi.org/10.3390/genes15070855 - 28 Jun 2024

Cited by 1 | Viewed by 1617

Abstract

The cytoplasm of Aegilops kotschyi is known for the induction of male sterility and haploidy in wheat. Both systems originally appeared rather simple, but manipulation of the standard chromosome constitution of the nuclear genome revealed additional interactions. This study shows that while there [...] Read more.

The cytoplasm of Aegilops kotschyi is known for the induction of male sterility and haploidy in wheat. Both systems originally appeared rather simple, but manipulation of the standard chromosome constitution of the nuclear genome revealed additional interactions. This study shows that while there is little or no allelic variation at the main fertility restorer locus Rf^multi on chromosome arm 1BS, additional genes may also be involved in the nuclear–mitochondrial genome interactions, affecting not only male fertility but also the growth rate, from pollen competition for fertilization and early endosperm divisions all the way to seed size and plant maturity. Some of these effects appear to be of a sporophytic nature; others are gametophytic. Induction of parthenogenesis by a rye inducer in conjunction with the Ae. kotschyi cytoplasm is well known. However, here we show that the cytoplasmic-nuclear interactions affect all aspects of double fertilization: producing maternal haploids from unfertilized eggs, diploids from fertilized eggs or synergids, embryo-less kernels, and fertilized eggs without fertilization of the double nucleus in the embryo sack. It is unclear how frequent the inducers of parthenogenesis are, as variation, if any, is obscured by suppressors present in the wheat genome. Genetic dissection of a single wheat accession revealed five distinct loci affecting the rate of maternal haploid production: four acting as suppressors and one as an enhancer. Only when the suppressing haplotypes are confirmed may it be possible to the identify genetic variation of haploidy inducers, map their position(s), and determine their nature and the mode of action. Full article

(This article belongs to the Special Issue Genetics and Breeding of Polyploid Plants)

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16 pages, 304 KiB

Open AccessEditor’s ChoiceArticle

Genetic Markers Related to Meat Quality Properties in Fattened HF and HF x Charolaise Steers

by Piotr Kostusiak, Emilia Bagnicka, Beata Żelazowska, Magdalena Zalewska, Tomasz Sakowski, Jan Slósarz, Marcin Gołębiewski and Kamila Puppel

Genes 2024, 15(7), 843; https://doi.org/10.3390/genes15070843 - 27 Jun 2024

Cited by 1 | Viewed by 2319

Abstract

This study involved 45 Holstein and 60 Holstein-Charolaise steers, tailored with specific diets according to breed and rearing systems. DNA genotyping was conducted for DGAT1, LEP, SCD1, SREBF1, and TG genes to investigate their impact on carcass conformation traits, beef quality traits, and [...] Read more.

This study involved 45 Holstein and 60 Holstein-Charolaise steers, tailored with specific diets according to breed and rearing systems. DNA genotyping was conducted for DGAT1, LEP, SCD1, SREBF1, and TG genes to investigate their impact on carcass conformation traits, beef quality traits, and sensory quality traits. The results showed associations between the genetic variants and the analyzed traits. Specifically, DGAT1 was found to affect drip loss, meat brightness, and color saturation. The TG gene was associated with marbling and meat color. LEP influenced trim fat and pH levels, while SCD1 was linked to metabolic energy live weight gains, and pH levels. SREBF1 was related to fatness. Full article

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

15 pages, 1980 KiB

Open AccessEditor’s ChoiceArticle

Deafness DFNB128 Associated with a Recessive Variant of Human MAP3K1 Recapitulates Hearing Loss of Map3k1-Deficient Mice

by Rabia Faridi, Rizwan Yousaf, Sayaka Inagaki, Rafal Olszewski, Shoujun Gu, Robert J. Morell, Elizabeth Wilson, Ying Xia, Tanveer Ahmed Qaiser, Muhammad Rashid, Cristina Fenollar-Ferrer, Michael Hoa, Sheikh Riazuddin and Thomas B. Friedman

Genes 2024, 15(7), 845; https://doi.org/10.3390/genes15070845 - 27 Jun 2024

Viewed by 1768

Abstract

Deafness in vertebrates is associated with variants of hundreds of genes. Yet, many mutant genes causing rare forms of deafness remain to be discovered. A consanguineous Pakistani family segregating nonsyndromic deafness in two sibships were studied using microarrays and exome sequencing. A 1.2 [...] Read more.

Deafness in vertebrates is associated with variants of hundreds of genes. Yet, many mutant genes causing rare forms of deafness remain to be discovered. A consanguineous Pakistani family segregating nonsyndromic deafness in two sibships were studied using microarrays and exome sequencing. A 1.2 Mb locus (DFNB128) on chromosome 5q11.2 encompassing six genes was identified. In one of the two sibships of this family, a novel homozygous recessive variant NM_005921.2:c.4460G>A p.(Arg1487His) in the kinase domain of MAP3K1 co-segregated with nonsyndromic deafness. There are two previously reported Map3k1-kinase-deficient mouse models that are associated with recessively inherited syndromic deafness. MAP3K1 phosphorylates serine and threonine and functions in a signaling pathway where pathogenic variants of HGF, MET, and GAB1 were previously reported to be associated with human deafness DFNB39, DFNB97, and DFNB26, respectively. Our single-cell transcriptome data of mouse cochlea mRNA show expression of Map3k1 and its signaling partners in several inner ear cell types suggesting a requirement of wild-type MAP3K1 for normal hearing. In contrast to dominant variants of MAP3K1 associated with Disorders of Sex Development 46,XY sex-reversal, our computational modeling of the recessive substitution p.(Arg1487His) predicts a subtle structural alteration in MAP3K1, consistent with the limited phenotype of nonsyndromic deafness. Full article

(This article belongs to the Special Issue Molecular Basis of Rare Genetic Diseases)

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14 pages, 1740 KiB

Open AccessEditor’s ChoiceArticle

Genomic Regions Associated with Resistance to Gastrointestinal Parasites in Australian Merino Sheep

by Brenda Vera, Elly A. Navajas, Pablo Peraza, Beatriz Carracelas, Elize Van Lier and Gabriel Ciappesoni

Genes 2024, 15(7), 846; https://doi.org/10.3390/genes15070846 - 27 Jun 2024

Cited by 2 | Viewed by 2055

Abstract

The objective of this study was to identify genomic regions and genes associated with resistance to gastrointestinal nematodes in Australian Merino sheep in Uruguay, using the single-step GWAS methodology (ssGWAS), which is based on genomic estimated breeding values (GEBVs) obtained from a combination [...] Read more.

The objective of this study was to identify genomic regions and genes associated with resistance to gastrointestinal nematodes in Australian Merino sheep in Uruguay, using the single-step GWAS methodology (ssGWAS), which is based on genomic estimated breeding values (GEBVs) obtained from a combination of pedigree, genomic, and phenotypic data. This methodology converts GEBVs into SNP effects. The analysis included 26,638 animals with fecal egg count (FEC) records obtained in two independent parasitic cycles (FEC1 and FEC2) and 1700 50K SNP genotypes. The comparison of genomic regions was based on genetic variances (gVar(%)) explained by non-overlapping regions of 20 SNPs. For FEC1 and FEC2, 18 and 22 genomic windows exceeded the significance threshold (gVar(%) ≥ 0.22%), respectively. The genomic regions with strong associations with FEC1 were located on chromosomes OAR 2, 6, 11, 21, and 25, and for FEC2 on OAR 5, 6, and 11. The proportion of genetic variance attributed to the top windows was 0.83% and 1.9% for FEC1 and FEC2, respectively. The 33 candidate genes shared between the two traits were subjected to enrichment analysis, revealing a marked enrichment in biological processes related to immune system functions. These results contribute to the understanding of the genetics underlying gastrointestinal parasite resistance and its implications for other productive and welfare traits in animal breeding programs. Full article

(This article belongs to the Special Issue Advances in Cattle, Sheep, and Goats Molecular Genetics and Breeding)

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13 pages, 2998 KiB

Open AccessEditor’s ChoiceArticle

Identification and Spatiotemporal Expression of a Putative New GABA Receptor Subunit in the Human Body Louse Pediculus humanus humanus

by Omar Hashim, Berthine Toubaté, Claude L. Charvet, Aimun A. E. Ahmed, Cédric Neveu, Isabelle Dimier-Poisson, Françoise Debierre-Grockiego and Catherine Dupuy

Genes 2024, 15(7), 844; https://doi.org/10.3390/genes15070844 - 27 Jun 2024

Viewed by 1231

Abstract

The human louse (Pediculus humanus) is an obligatory blood feeding ectoparasite with two ecotypes: the human body louse (Pediculus humanus humanus), a competent vector of several bacterial pathogens, and the human head louse (Pediculus humanus capitis), responsible [...] Read more.

The human louse (Pediculus humanus) is an obligatory blood feeding ectoparasite with two ecotypes: the human body louse (Pediculus humanus humanus), a competent vector of several bacterial pathogens, and the human head louse (Pediculus humanus capitis), responsible for pediculosis and affecting millions of people around the globe. GABA (γ-aminobutyric acid) receptors, members of the cys-loop ligand gated ion channel superfamily, are among the main pharmacological targets for insecticides. In insects, there are four subunits of GABA receptors: resistant-to-dieldrin (RDL), glycin-like receptor of drosophila (GRD), ligand-gated chloride channel homologue3 (LCCH3), and 8916 are well described and form distinct phylogenetic clades revealing orthologous relationships. Our previous studies in the human body louse confirmed that subunits Phh-RDL, Phh-GRD, and Phh-LCCH3 are well clustered in their corresponding clades. In the present work, we cloned and characterized a putative new GABA receptor subunit in the human body louse that we named HoCas, for Homologous to Cys-loop α like subunit. Extending our analysis to arthropods, HoCas was found to be conserved and clustered in a new (fifth) phylogenetic clade. Interestingly, the gene encoding this subunit is ancestral and has been lost in some insect orders. Compared to the other studied GABA receptor subunits, HoCas exhibited a relatively higher expression level in all development stages and in different tissues of human body louse. These findings improved our understanding of the complex nature of GABA receptors in Pediculus humanus and more generally in arthropods. Full article

(This article belongs to the Special Issue Advances in Molecular Microbiology and Parasitology)

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