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Genes, Volume 14, Issue 6 (June 2023) – 181 articles

Cover Story (view full-size image): Crop improvement is highly reliant on genetic diversity within crop gene pools. We investigated 104 Ethiopian durum wheat genotypes from various geopgraphic locations and revealed the substantial genetic diversity in their 10 morphological characters and 14 SSR markers. Both markers distinguished distinct groups of cultivars and landraces, demonstrating the potential of morphological markers to capture genetic variations. Favorable alleles at these SSRs can serve as markers for marker-assisted selection in national durum wheat breeding programs, both for parental selection for crossbreeding and for pyramiding desirable characteristics of agronomic and quality traits into a standard breeding line. This study emphasizes the value of Ethiopian durum wheat gene pools to improve the productivity and quality of the crop. View this paper
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15 pages, 2126 KiB  
Article
Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize
by Fuyan Jiang, Li Liu, Ziwei Li, Yaqi Bi, Xingfu Yin, Ruijia Guo, Jing Wang, Yudong Zhang, Ranjan Kumar Shaw and Xingming Fan
Genes 2023, 14(6), 1305; https://doi.org/10.3390/genes14061305 - 20 Jun 2023
Cited by 3 | Viewed by 1387
Abstract
Ear diameter (ED) is a critical component of grain yield (GY) in maize (Zea mays L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map [...] Read more.
Ear diameter (ED) is a critical component of grain yield (GY) in maize (Zea mays L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map the ED-related quantitative trait locus (QTL) and SNPs associated with ED; and (2) identify putative functional genes that may affect ED in maize. To accomplish this, an elite maize inbred line, Ye107, which belongs to the Reid heterotic group, was used as a common parent and crossed with seven elite inbred lines from three different heterotic groups (Suwan1, Reid, and nonReid) that exhibited abundant genetic variation in ED. This led to the construction of a multi-parent population consisting of 1215 F7 recombinant inbred lines (F7RILs). A genome-wide association study (GWAS) and linkage analysis were then conducted for the multi-parent population using 264,694 high-quality SNPs generated via the genotyping-by-sequencing method. Our study identified a total of 11 SNPs that were significantly associated with ED through the GWAS, and three QTLs were revealed by the linkage analysis for ED. The major QTL on chromosome 1 was co-identified in the region by the GWAS at SNP_143985532. SNP_143985532, located upstream of the Zm00001d030559 gene, encodes a callose synthase that is expressed in various tissues, with the highest expression level in the maize ear primordium. Haplotype analysis indicated that the haplotype B (allele AA) of Zm00001d030559 was positively correlated with ED. The candidate genes and SNPs identified in this study provide crucial insights for future studies on the genetic mechanism of maize ED formation, cloning of ED-related genes, and genetic improvement of ED. These results may help develop important genetic resources for enhancing maize yield through marker-assisted breeding. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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22 pages, 3357 KiB  
Review
Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications
by Aram Arshadi, Doron Tolomeo, Santina Venuto and Clelia Tiziana Storlazzi
Genes 2023, 14(6), 1304; https://doi.org/10.3390/genes14061304 - 20 Jun 2023
Viewed by 1809
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, [...] Read more.
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients. Full article
(This article belongs to the Special Issue Genetic and Genomic Abnormalities in Cancer)
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21 pages, 3244 KiB  
Article
Characterization and Genome Study of a Newly Isolated Temperate Phage Belonging to a New Genus Targeting Alicyclobacillus acidoterrestris
by Dziyana Shymialevich, Michał Wójcicki, Olga Świder, Paulina Średnicka and Barbara Sokołowska
Genes 2023, 14(6), 1303; https://doi.org/10.3390/genes14061303 - 20 Jun 2023
Viewed by 1811
Abstract
The spoilage of juices by Alicyclobacillus spp. remains a serious problem in industry and leads to economic losses. Compounds such as guaiacol and halophenols, which are produced by Alicyclobacillus, create undesirable flavors and odors and, thus, decrease the quality of juices. The [...] Read more.
The spoilage of juices by Alicyclobacillus spp. remains a serious problem in industry and leads to economic losses. Compounds such as guaiacol and halophenols, which are produced by Alicyclobacillus, create undesirable flavors and odors and, thus, decrease the quality of juices. The inactivation of Alicyclobacillus spp. constitutes a challenge because it is resistant to environmental factors, such as high temperatures, and active acidity. However, the use of bacteriophages seems to be a promising approach. In this study, we aimed to isolate and comprehensively characterize a novel bacteriophage targeting Alicyclobacillus spp. The Alicyclobacillus phage strain KKP 3916 was isolated from orchard soil against the Alicyclobacillus acidoterrestris strain KKP 3133. The bacterial host’s range and the effect of phage addition at different rates of multiplicity of infections (MOIs) on the host’s growth kinetics were determined using a Bioscreen C Pro growth analyzer. The Alicyclobacillus phage strain KKP 3916, retained its activity in a wide range of temperatures (from 4 °C to 30 °C) and active acidity values (pH from 3 to 11). At 70 °C, the activity of the phage decreased by 99.9%. In turn, at 80 °C, no activity against the bacterial host was observed. Thirty minutes of exposure to UV reduced the activity of the phages by almost 99.99%. Based on transmission-electron microscopy (TEM) and whole-genome sequencing (WGS) analyses, the Alicyclobacillus phage strain KKP 3916 was classified as a tailed bacteriophage. The genomic sequencing revealed that the newly isolated phage had linear double-stranded DNA (dsDNA) with sizes of 120 bp and 131 bp and 40.3% G+C content. Of the 204 predicted proteins, 134 were of unknown function, while the remainder were annotated as structural, replication, and lysis proteins. No genes associated with antibiotic resistance were found in the genome of the newly isolated phage. However, several regions, including four associated with integration into the bacterial host genome and excisionase, were identified, which indicates the temperate (lysogenic) life cycle of the bacteriophage. Due to the risk of its potential involvement in horizontal gene transfer, this phage is not an appropriate candidate for further research on its use in food biocontrol. To the best of our knowledge, this is the first article on the isolation and whole-genome analysis of the Alicyclobacillus-specific phage. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Microbiome)
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13 pages, 578 KiB  
Article
Inbreeding Effects on the Performance and Genomic Prediction for Polysomic Tetraploid Potato Offspring Grown at High Nordic Latitudes
by Rodomiro Ortiz, Fredrik Reslow, Ramesh Vetukuri, M. Rosario García-Gil, Paulino Pérez-Rodríguez and José Crossa
Genes 2023, 14(6), 1302; https://doi.org/10.3390/genes14061302 - 20 Jun 2023
Cited by 3 | Viewed by 2123
Abstract
Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation [...] Read more.
Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S1) and two hybrid (F1) offspring and their parents (S0) were used in the experiment, with a field layout of an augmented design with the four S0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umeå (63°49′30″ N 20°15′50″ E), Sweden. S0 was significantly (p < 0.01) better than both S1 and F1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F1 was significantly (p < 0.01) better than S1 for all tuber weight and uniformity traits. Some F1 hybrid offspring (15–19%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from −0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F1 full sib’s GEBV accuracy was higher, on average, than that of S1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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24 pages, 3777 KiB  
Article
Domestication over Speciation in Allopolyploid Cotton Species: A Stronger Transcriptomic Pull
by Josef J. Jareczek, Corrinne E. Grover, Guanjing Hu, Xianpeng Xiong, Mark A. Arick II, Daniel G. Peterson and Jonathan F. Wendel
Genes 2023, 14(6), 1301; https://doi.org/10.3390/genes14061301 - 20 Jun 2023
Cited by 1 | Viewed by 1461
Abstract
Cotton has been domesticated independently four times for its fiber, but the genomic targets of selection during each domestication event are mostly unknown. Comparative analysis of the transcriptome during cotton fiber development in wild and cultivated materials holds promise for revealing how independent [...] Read more.
Cotton has been domesticated independently four times for its fiber, but the genomic targets of selection during each domestication event are mostly unknown. Comparative analysis of the transcriptome during cotton fiber development in wild and cultivated materials holds promise for revealing how independent domestications led to the superficially similar modern cotton fiber phenotype in upland (G. hirsutum) and Pima (G. barbadense) cotton cultivars. Here we examined the fiber transcriptomes of both wild and domesticated G. hirsutum and G. barbadense to compare the effects of speciation versus domestication, performing differential gene expression analysis and coexpression network analysis at four developmental timepoints (5, 10, 15, or 20 days after flowering) spanning primary and secondary wall synthesis. These analyses revealed extensive differential expression between species, timepoints, domestication states, and particularly the intersection of domestication and species. Differential expression was higher when comparing domesticated accessions of the two species than between the wild, indicating that domestication had a greater impact on the transcriptome than speciation. Network analysis showed significant interspecific differences in coexpression network topology, module membership, and connectivity. Despite these differences, some modules or module functions were subject to parallel domestication in both species. Taken together, these results indicate that independent domestication led G. hirsutum and G. barbadense down unique pathways but that it also leveraged similar modules of coexpression to arrive at similar domesticated phenotypes. Full article
(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)
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14 pages, 754 KiB  
Review
Inherited Reticulate Pigmentary Disorders
by Min-Huei Lin, Pei-Chen Chou, I-Chen Lee, Syuan-Fei Yang, Hsin-Su Yu and Sebastian Yu
Genes 2023, 14(6), 1300; https://doi.org/10.3390/genes14061300 - 20 Jun 2023
Cited by 1 | Viewed by 1426
Abstract
Reticulate pigmentary disorders (RPDs) are a group of inherited and acquired skin conditions characterized by hyperpigmented and/or hypopigmented macules. Inherited RPDs include dyschromatosis symmetrica hereditaria (DSH), dyschromatosis universalis hereditaria (DUH), reticulate acropigmentation of Kitamura (RAK), Dowling-Degos disease (DDD), dyskeratosis congenita (DKC), Naegeli–Franceschetti–Jadassohn syndrome [...] Read more.
Reticulate pigmentary disorders (RPDs) are a group of inherited and acquired skin conditions characterized by hyperpigmented and/or hypopigmented macules. Inherited RPDs include dyschromatosis symmetrica hereditaria (DSH), dyschromatosis universalis hereditaria (DUH), reticulate acropigmentation of Kitamura (RAK), Dowling-Degos disease (DDD), dyskeratosis congenita (DKC), Naegeli–Franceschetti–Jadassohn syndrome (NFJS), dermatopathia pigmentosa reticularis (DPR), and X-linked reticulate pigmentary disorder. Although reticulate pattern of pigmentation is a common characteristic of this spectrum of disorders, the distribution of pigmentation varies among these disorders, and there may be clinical manifestations beyond pigmentation. DSH, DUH, and RAK are mostly reported in East Asian ethnicities. DDD is more common in Caucasians, although it is also reported in Asian countries. Other RPDs show no racial predilection. This article reviews the clinical, histological, and genetic variations of inherited RPDs. Full article
(This article belongs to the Special Issue Genetics of Complex Cutaneous Disorders)
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0 pages, 3288 KiB  
Article
Genotype–Environment Interaction and Horizontal and Vertical Distributions of Heartwood for Acacia melanoxylon R.Br
by Ruping Zhang, Bingshan Zeng, Tianxiao Chen and Bing Hu
Genes 2023, 14(6), 1299; https://doi.org/10.3390/genes14061299 - 20 Jun 2023
Cited by 4 | Viewed by 997 | Correction
Abstract
Acacia melanoxylon (blackwood) is a valuable wood with excellent-quality heartwood extensively utilized worldwide. The main aim of this study was to confirm the horizontal and vertical variation and provide estimated values of genetic gains and clonal repeatabilities for improving the breeding program of [...] Read more.
Acacia melanoxylon (blackwood) is a valuable wood with excellent-quality heartwood extensively utilized worldwide. The main aim of this study was to confirm the horizontal and vertical variation and provide estimated values of genetic gains and clonal repeatabilities for improving the breeding program of A. melanoxylon. Six blackwood clones at 10 years old were analyzed in Heyuan and Baise cities in China. Stem trunk analysis was conducted for sample trees to explore the differences between heartwood and sapwood. The heartwood radius (HR), heartwood area (HA), and heartwood volume (HV) in heartwood properties decreased as the tree height (H) in growth traits increased, and the HV = 1.2502 DBH (diameter at breast height)1.7009 model can accurately estimate the heartwood volume. Furthermore, G × E analysis showed that the heritabilities of the eleven indices, including DBH, DGH (diameter at ground height), H, HR, SW (sapwood width), BT (bark thickness), HA, SA (sapwood area), HV, HRP (heartwood radius percentage), HAP (heartwood area percentage), and HVP (heartwood volume percentage) were between 0.94 and 0.99, and repeatabilities of the eleven indices were between 0.74 and 0.90. Clonal repeatability of DBH (0.88), DGH (0.88), and H (0.90) in growth traits and HR (0.90), HVP (0.90), and HV (0.88) in heartwood properties were slightly higher than for SA (0.74), SW (0.75), HAP (0.75), HRP (0.75), and HVP (0.75). These data also implied that the growth characteristics of heartwood and sapwood of blackwood clones were less affected by the environment and had substantial heritability. Full article
(This article belongs to the Section Genes & Environments)
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17 pages, 5235 KiB  
Article
Dynamic Changes in the Global Transcriptome of Postnatal Skeletal Muscle in Different Sheep
by Yue Ai, Yaning Zhu, Linli Wang, Xiaosheng Zhang, Jinlong Zhang, Xianlei Long, Qingyi Gu and Hongbing Han
Genes 2023, 14(6), 1298; https://doi.org/10.3390/genes14061298 - 20 Jun 2023
Cited by 2 | Viewed by 1310
Abstract
Sheep growth performance, mainly skeletal muscle growth, provides direct economic benefits to the animal husbandry industry. However, the underlying genetic mechanisms of different breeds remain unclear. We found that the cross-sectional area (CSA) of skeletal muscle in Dorper (D) and binary cross-breeding (HD) [...] Read more.
Sheep growth performance, mainly skeletal muscle growth, provides direct economic benefits to the animal husbandry industry. However, the underlying genetic mechanisms of different breeds remain unclear. We found that the cross-sectional area (CSA) of skeletal muscle in Dorper (D) and binary cross-breeding (HD) was higher than that in Hu sheep (H) from 3 months to 12 months after birth. The transcriptomic analysis of 42 quadriceps femoris samples showed that a total of 5053 differential expression genes (DEGs) were identified. The differences in the global gene expression patterns, the dynamic transcriptome of skeletal muscle development, and the transcriptome of the transformation of fast and slow muscles were explored using weighted correlation network analysis (WGCNA) and allele-specific expression analysis. Moreover, the gene expression patterns of HD were more similar to D rather than H from 3 months to 12 months, which might be the reason for the difference in muscle growth in the three breeds. Additionally, several genes (GNB2L1, RPL15, DVL1, FBXO31, etc.) were identified as candidates related to skeletal muscle growth. These results should serve as an important resource revealing the molecular basis of muscle growth and development in sheep. Full article
(This article belongs to the Special Issue Genetics and Breeding of Sheep and Goats)
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12 pages, 1379 KiB  
Review
Genetics of Generalized Pustular Psoriasis: Current Understanding and Implications for Future Therapeutics
by Syuan-Fei Yang, Min-Huei Lin, Pei-Chen Chou, Sheng-Kai Hu, Sin-Yi Shih, Hsin-Su Yu and Sebastian Yu
Genes 2023, 14(6), 1297; https://doi.org/10.3390/genes14061297 - 20 Jun 2023
Cited by 7 | Viewed by 2385
Abstract
Psoriasis is a chronic inflammatory skin disease characterized by the appearance of clearly demarcated erythematous and scaly plaques. It can be divided into various types, including plaque, nail, guttate, inverse, and pustular psoriasis. Plaque psoriasis is the most commonly occurring type, though there [...] Read more.
Psoriasis is a chronic inflammatory skin disease characterized by the appearance of clearly demarcated erythematous and scaly plaques. It can be divided into various types, including plaque, nail, guttate, inverse, and pustular psoriasis. Plaque psoriasis is the most commonly occurring type, though there is another rare but severe pustular autoinflammatory skin disease called generalized pustular psoriasis (GPP), which manifests with acute episodes of pustulation and systemic symptoms. Though the etiopathogenesis of psoriasis is not yet fully understood, a growing body of literature has demonstrated that both genetic and environmental factors play a role. The discovery of genetic mutations associated with GPP has shed light on our comprehension of the mechanisms of the disease, promoting the development of targeted therapies. This review will summarize genetic determinants as known and provide an update on the current and potential treatments for GPP. The pathogenesis and clinical presentation of the disease are also included for a comprehensive discussion. Full article
(This article belongs to the Special Issue Genetics of Complex Cutaneous Disorders)
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9 pages, 2227 KiB  
Brief Report
Molecular and Clinical Characterization of CNGA3 and CNGB3 Genes in Brazilian Patients Affected with Achromatopsia
by Rebeca A. S. Amaral, Fabiana L. Motta, Olivia A. Zin, Mariana M. da Palma, Gabriela D. Rodrigues and Juliana M. F. Sallum
Genes 2023, 14(6), 1296; https://doi.org/10.3390/genes14061296 - 20 Jun 2023
Viewed by 1270
Abstract
Achromatopsia (ACHM) is a congenital cone photoreceptor disorder characterized by reduced visual acuity, nystagmus, photophobia, and very poor or absent color vision. Pathogenic variants in six genes encoding proteins composing the cone phototransduction cascade (CNGA3, CNGB3, PDE6C, PDE6H, [...] Read more.
Achromatopsia (ACHM) is a congenital cone photoreceptor disorder characterized by reduced visual acuity, nystagmus, photophobia, and very poor or absent color vision. Pathogenic variants in six genes encoding proteins composing the cone phototransduction cascade (CNGA3, CNGB3, PDE6C, PDE6H, GNAT2) and of the unfolded protein response (ATF6) have been related to ACHM cases, while CNGA3 and CNGB3 alone are responsible for most cases. Herein, we provide a clinical and molecular overview of 42 Brazilian patients from 38 families affected with ACHM related to biallelic pathogenic variants in the CNGA3 and CNGB3 genes. Patients’ genotype and phenotype were retrospectively evaluated. The majority of CNGA3 variants were missense, and the most prevalent CNGB3 variant was c.1148delC (p.Thr383Ilefs*13), resulting in a frameshift and premature stop codon, which is compatible with previous publications in the literature. A novel variant c.1893T>A (p.Tyr631*) in the CNGB3 gene is reported for the first time in this study. A great variability in morphologic findings was observed in our patients, although no consistent correlation with age and disease stage in OCT foveal morphology was found. The better understanding of the genetic variants landscape in the Brazilian population will help in the diagnosis of this disease. Full article
(This article belongs to the Special Issue Genetics in Retinal Diseases)
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12 pages, 3275 KiB  
Article
Histone Deacetylases (HDAC) Inhibitor—Valproic Acid Sensitizes Human Melanoma Cells to Dacarbazine and PARP Inhibitor
by Małgorzata Drzewiecka, Anna Gajos-Michniewicz, Grażyna Hoser, Dominika Jaśniak, Gabriela Barszczewska-Pietraszek, Przemysław Sitarek, Piotr Czarny, Janusz Piekarski, Maciej Radek, Małgorzata Czyż, Tomasz Skorski and Tomasz Śliwiński
Genes 2023, 14(6), 1295; https://doi.org/10.3390/genes14061295 - 20 Jun 2023
Cited by 3 | Viewed by 1901
Abstract
The inhibition of histone deacetylases (HDACs) holds promise as a potential anti-cancer therapy as histone and non-histone protein acetylation is frequently disrupted in cancer, leading to cancer initiation and progression. Additionally, the use of a histone deacetylase inhibitor (HDACi) such as the class [...] Read more.
The inhibition of histone deacetylases (HDACs) holds promise as a potential anti-cancer therapy as histone and non-histone protein acetylation is frequently disrupted in cancer, leading to cancer initiation and progression. Additionally, the use of a histone deacetylase inhibitor (HDACi) such as the class I HDAC inhibitor—valproic acid (VPA) has been shown to enhance the effectiveness of DNA-damaging factors, such as cisplatin or radiation. In this study, we found that the use of VPA in combination with talazoparib (BMN-673—PARP1 inhibitor—PARPi) and/or Dacarbazine (DTIC—alkylating agent) resulted in an increased rate of DNA double strand breaks (DSBs) and reduced survival (while not affecting primary melanocytes) and the proliferation of melanoma cells. Furthermore, the pharmacological inhibition of class I HDACs sensitizes melanoma cells to apoptosis following exposure to DTIC and BMN-673. In addition, the inhibition of HDACs causes the sensitization of melanoma cells to DTIV and BMN-673 in melanoma xenografts in vivo. At the mRNA and protein level, the histone deacetylase inhibitor downregulated RAD51 and FANCD2. This study aims to demonstrate that combining an HDACi, alkylating agent and PARPi could potentially enhance the treatment of melanoma, which is commonly recognized as being among the most aggressive malignant tumors. The findings presented here point to a scenario in which HDACs, via enhancing the HR-dependent repair of DSBs created during the processing of DNA lesions, are essential nodes in the resistance of malignant melanoma cells to methylating agent-based therapies. Full article
(This article belongs to the Special Issue DNA Damage Induced by Anti-cancer Agents)
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18 pages, 3517 KiB  
Article
Integration of GWAS and RNA-Seq Analysis to Identify SNPs and Candidate Genes Associated with Alkali Stress Tolerance at the Germination Stage in Mung Bean
by Ning Xu, Bingru Chen, Yuxin Cheng, Yufei Su, Mengyuan Song, Rongqiu Guo, Minghai Wang, Kunpeng Deng, Tianjiao Lan, Shuying Bao, Guifang Wang, Zhongxiao Guo and Lihe Yu
Genes 2023, 14(6), 1294; https://doi.org/10.3390/genes14061294 - 19 Jun 2023
Viewed by 2230
Abstract
Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association [...] Read more.
Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association study (GWAS) was performed to detect alkali-tolerant genetic loci and candidate genes in 277 mung bean accessions during germination. Using the relative values of two germination traits, 19 QTLs containing 32 SNPs significantly associated with alkali tolerance on nine chromosomes were identified, and they explained 3.6 to 14.6% of the phenotypic variance. Moreover, 691 candidate genes were mined within the LD intervals containing significant trait-associated SNPs. Transcriptome sequencing of alkali-tolerant accession 132–346 under alkali and control conditions after 24 h of treatment was conducted, and 2565 DEGs were identified. An integrated analysis of the GWAS and DEGs revealed six hub genes involved in alkali tolerance responses. Moreover, the expression of hub genes was further validated by qRT-PCR. These findings improve our understanding of the molecular mechanism of alkali stress tolerance and provide potential resources (SNPs and genes) for the genetic improvement of alkali tolerance in mung bean. Full article
(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)
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22 pages, 1482 KiB  
Review
Translation Arrest: A Key Player in Plant Antiviral Response
by Annemarie Vermeulen, Frank L. W. Takken and Victor A. Sánchez-Camargo
Genes 2023, 14(6), 1293; https://doi.org/10.3390/genes14061293 - 19 Jun 2023
Cited by 1 | Viewed by 2350
Abstract
Plants evolved several mechanisms to protect themselves against viruses. Besides recessive resistance, where compatible host factors required for viral proliferation are absent or incompatible, there are (at least) two types of inducible antiviral immunity: RNA silencing (RNAi) and immune responses mounted upon activation [...] Read more.
Plants evolved several mechanisms to protect themselves against viruses. Besides recessive resistance, where compatible host factors required for viral proliferation are absent or incompatible, there are (at least) two types of inducible antiviral immunity: RNA silencing (RNAi) and immune responses mounted upon activation of nucleotide-binding domain leucine-rich repeat (NLR) receptors. RNAi is associated with viral symptom recovery through translational repression and transcript degradation following recognition of viral double-stranded RNA produced during infection. NLR-mediated immunity is induced upon (in)direct recognition of a viral protein by an NLR receptor, triggering either a hypersensitive response (HR) or an extreme resistance response (ER). During ER, host cell death is not apparent, and it has been proposed that this resistance is mediated by a translational arrest (TA) of viral transcripts. Recent research indicates that translational repression plays a crucial role in plant antiviral resistance. This paper reviews current knowledge on viral translational repression during viral recovery and NLR-mediated immunity. Our findings are summarized in a model detailing the pathways and processes leading to translational arrest of plant viruses. This model can serve as a framework to formulate hypotheses on how TA halts viral replication, inspiring new leads for the development of antiviral resistance in crops. Full article
(This article belongs to the Collection Feature Papers: 'Plant Genetics and Genomics' Section)
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9 pages, 918 KiB  
Case Report
7p22.2 Microduplication: A Pathogenic CNV?
by Alessia Bauleo, Alberto Montesanto, Vincenza Pace, Francesco Guarasci, Rosalbina Apa, Rossella Brando, Laura De Stefano, Simona Sestito, Daniela Concolino and Elena Falcone
Genes 2023, 14(6), 1292; https://doi.org/10.3390/genes14061292 - 19 Jun 2023
Viewed by 1348
Abstract
Partial duplication of the short arm of chromosome 7 is a rare chromosome rearrangement. The phenotype spectrum associated with this rearrangement is extremely variable even if in the last decade the use of high-resolution microarray technology for the investigation of patients carrying this [...] Read more.
Partial duplication of the short arm of chromosome 7 is a rare chromosome rearrangement. The phenotype spectrum associated with this rearrangement is extremely variable even if in the last decade the use of high-resolution microarray technology for the investigation of patients carrying this rearrangement allowed for the identification of the 7p22.1 sub-band causative of this phenotype and to recognize the corresponding 7p22.1 microduplication syndrome. We report two unrelated patients that carry a microduplication involving the 7.22.2 sub-band. Unlike 7p22.1 microduplication carriers, both patients only show a neurodevelopmental disorder without malformations. We better characterized the clinical pictures of these two patients providing insight into the clinical phenotype associated with the microduplication of the 7p22.2 sub-band and support for a possible role of this sub-band in the 7p22 microduplication syndrome. Full article
(This article belongs to the Special Issue Advances in Clinical Cytogenetics)
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19 pages, 1200 KiB  
Article
Insights into the Adaptation to High Altitudes from Transcriptome Profiling: A Case Study of an Endangered Species, Kingdonia uniflora
by Man-Li Nong, Xiao-Hui Luo, Li-Xin Zhu, Ya-Nan Zhang, Xue-Yi Dun and Lei Huang
Genes 2023, 14(6), 1291; https://doi.org/10.3390/genes14061291 - 19 Jun 2023
Viewed by 1040
Abstract
Kingdonia uniflora is an endangered alpine herb that is distributed along an altitudinal gradient. The unique traits and important phylogenetic position make K. uniflora an ideal model for exploring how endangered plants react to altitude variation. In this study, we sampled nine individuals [...] Read more.
Kingdonia uniflora is an endangered alpine herb that is distributed along an altitudinal gradient. The unique traits and important phylogenetic position make K. uniflora an ideal model for exploring how endangered plants react to altitude variation. In this study, we sampled nine individuals from three representative locations and adopted RNA-seq technology to sequence 18 tissues, aiming to uncover how K. uniflora responded to different altitudes at the gene expression level. We revealed that genes that responded to light stimuli and circadian rhythm genes were significantly enriched in DEGs in the leaf tissue group, while genes that were related to root development and peroxidase activity or involved in the pathways of cutin, suberin, wax biosynthesis, and monoterpenoid biosynthesis were significantly enriched in DEGs in the flower bud tissue group. All of the above genes may play an important role in the response of K. uniflora to various stresses, such as low temperatures and hypoxia in high-altitude environments. Furthermore, we proved that the discrepancy in gene expression patterns between leaf and flower bud tissues varied along the altitudinal gradient. Overall, our findings provide new insights into the adaptation of endangered species to high-altitude environments and further encourage parallel research to focus on the molecular mechanisms of alpine plant evolution. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Phylogeography of Seed Plants)
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22 pages, 5031 KiB  
Article
Integrated Transcriptomics and Metabolomics Analysis of the Fructan Metabolism Response to Low-Temperature Stress in Garlic
by Haiyan Bian, Qianyi Zhou, Zhongping Du, Guangnan Zhang, Rui Han, Laisheng Chen, Jie Tian and Yi Li
Genes 2023, 14(6), 1290; https://doi.org/10.3390/genes14061290 - 19 Jun 2023
Cited by 2 | Viewed by 1487
Abstract
As the main reserve carbohydrate in garlic, fructan contributes to garlic’s yield and quality formation. Numerous studies have shown that plant fructan metabolism induces a stress response to adverse environments. However, the transcriptional regulation mechanism of garlic fructan in low-temperature environments is still [...] Read more.
As the main reserve carbohydrate in garlic, fructan contributes to garlic’s yield and quality formation. Numerous studies have shown that plant fructan metabolism induces a stress response to adverse environments. However, the transcriptional regulation mechanism of garlic fructan in low-temperature environments is still unknown. In this study, the fructan metabolism of garlic seedlings under low-temperature stress was revealed by transcriptome and metabolome approaches. With the extension of stress time, the number of differentially expressed genes and metabolites increased. Using weighted gene co-expression network analysis (WGCNA), three key enzyme genes related to fructan metabolism were screened (a total of 12 transcripts): sucrose: sucrose 1-fructosyltransferase (1-SST) gene; fructan: fructan 6G fructosyltransferase (6G-FFT) gene; and fructan 1-exohydrolase (1-FEH) gene. Finally, two hub genes were obtained, namely Cluster-4573.161559 (6G-FFT) and Cluster-4573.153574 (1-FEH). The correlation network and metabolic heat map analysis between fructan genes and carbohydrate metabolites indicate that the expression of key enzyme genes in fructan metabolism plays a positive promoting role in the fructan response to low temperatures in garlic. The number of genes associated with the key enzyme of fructan metabolism in trehalose 6-phosphate was the highest, and the accumulation of trehalose 6-phosphate content may mainly depend on the key enzyme genes of fructan metabolism rather than the enzyme genes in its own synthesis pathway. This study not only obtained the key genes of fructan metabolism in garlic seedlings responding to low temperatures but also preliminarily analyzed its regulatory mechanism, providing an important theoretical basis for further elucidating the cold resistance mechanism of garlic fructan metabolism. Full article
(This article belongs to the Special Issue Genetics and Breeding of Horticulture Crops)
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13 pages, 9366 KiB  
Article
Complete Chloroplast Genome of Corethrodendron fruticosum (Papilionoideae: Fabaceae): Comparative and Phylogenetic Analysis
by Tianxiu Niu, Chunyu Tian, Yanting Yang, Qian Liu, Lemeng Liu, Qibo Tao, Zhiyong Li and Zinian Wu
Genes 2023, 14(6), 1289; https://doi.org/10.3390/genes14061289 - 19 Jun 2023
Cited by 1 | Viewed by 1474
Abstract
Corethrodendron fruticosum is an endemic forage grasses in China with high ecological value. In this study, the complete chloroplast genome of C. fruticosum was sequenced using Illumina paired-end sequencing. The C. fruticosum chloroplast genome was 123,100 bp and comprised 105 genes, including 74 [...] Read more.
Corethrodendron fruticosum is an endemic forage grasses in China with high ecological value. In this study, the complete chloroplast genome of C. fruticosum was sequenced using Illumina paired-end sequencing. The C. fruticosum chloroplast genome was 123,100 bp and comprised 105 genes, including 74 protein-coding genes, 4 rRNA-coding genes, and 27 tRNA-coding genes. The genome had a GC content of 34.53%, with 50 repetitive sequences and 63 simple repeat repetitive sequences that did not contain reverse repeats. The simple repeats included 45 single-nucleotide repeats, which accounted for the highest proportion and primarily comprised A/T repeats. A comparative analysis of C. fruticosum, C. multijugum, and four Hedysarum species revealed that the six genomes were highly conserved, with differentials primarily located in the conserved non-coding regions. Moreover, the accD and clpP genes in the coding regions exhibited high nucleotide variability. Accordingly, these genes may serve as molecular markers for the classification and phylogenetic analysis of Corethrodendron species. Phylogenetic analysis further revealed that C. fruticosum and C. multijugum appeared in different clades than the four Hedysarum species. The newly sequenced chloroplast genome provides further insights into the phylogenetic position of C. fruticosum, which is useful for the classification and identification of Corethrodendron. Full article
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome)
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11 pages, 1124 KiB  
Article
Genome-Wide Search for Associations with Meat Production Parameters in Karachaevsky Sheep Breed Using the Illumina BeadChip 600 K
by Alexander Krivoruchko, Andrey Likhovid, Anastasiya Kanibolotskaya, Tatiana Saprikina, Elena Safaryan and Olesya Yatsyk
Genes 2023, 14(6), 1288; https://doi.org/10.3390/genes14061288 - 19 Jun 2023
Cited by 2 | Viewed by 1228
Abstract
In a group of Karachaevsky rams, a genome-wide associations analysis of single nucleotide polymorphisms (SNPs) with live parameters of meat production was performed. We used for genotyping the Ovine Infinium HD BeadChip 600 K, which consists of points to detection of 606,000 polymorphisms. [...] Read more.
In a group of Karachaevsky rams, a genome-wide associations analysis of single nucleotide polymorphisms (SNPs) with live parameters of meat production was performed. We used for genotyping the Ovine Infinium HD BeadChip 600 K, which consists of points to detection of 606,000 polymorphisms. A total of 12 SNPs was found to be significantly associated with live meat quality parameters of the corpus and legs and ultrasonic traits. In this case, 11 candidate genes were described, the polymorphic variants of which can change in sheep body parameters. We found SNPs in the exons, introns, and other regions of some genes and transcripts: CLVS1, EVC2, KIF13B, ENSOART00000000511.1, KCNH5, NEDD4, LUZP2, MREG, KRT20, KRT23 and FZD6. The described genes involved in the metabolic pathways of cell differentiation, proliferation and apoptosis are connected with the regulation of the gastrointestinal, immune and nervous systems. In known productivity genes (MSTN, MEF2B, FABP4, etc.), loci were not found to be a significant presence of influence on the meat productivity of the Karachaevsky sheep phenotypes. Our study confirms the possible involvement of the identified candidate genes in the formation of the phenotypes of productivity traits in sheep and indicates the need for new research into candidate genes structure in point to detect their polymorphisms. Full article
(This article belongs to the Special Issue Genetics and Breeding of Sheep and Goats)
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32 pages, 13313 KiB  
Article
A Preliminary Survey of Transfer RNA Modifications and Modifying Enzymes of the Tropical Plant Cocos nucifera L.
by Meng Chu, Yichao Qin, Xiuying Lin, Li Ma, Dehai Deng, Daizhu Lv, Pengcheng Fu and Huan Lin
Genes 2023, 14(6), 1287; https://doi.org/10.3390/genes14061287 - 18 Jun 2023
Viewed by 1505
Abstract
The coconut (Cocos nucifera L.) is a commercial crop widely distributed among coastal tropical regions. It provides millions of farmers with food, fuel, cosmetics, folk medicine, and building materials. Among these, oil and palm sugar are representative extracts. However, this unique living [...] Read more.
The coconut (Cocos nucifera L.) is a commercial crop widely distributed among coastal tropical regions. It provides millions of farmers with food, fuel, cosmetics, folk medicine, and building materials. Among these, oil and palm sugar are representative extracts. However, this unique living species of Cocos has only been preliminarily studied at molecular levels. Benefiting from the genomic sequence data published in 2017 and 2021, we investigated the transfer RNA (tRNA) modifications and modifying enzymes of the coconut in this survey. An extraction method for the tRNA pool from coconut flesh was built. In total, 33 species of modified nucleosides and 66 homologous genes of modifying enzymes were confirmed using a nucleoside analysis using high-performance liquid chromatography combined with high-resolution mass spectrometry (HPLC-HRMS) and homologous protein sequence alignment. The positions of tRNA modifications, including pseudouridines, were preliminarily mapped using a oligonucleotide analysis, and the features of their modifying enzymes were summarized. Interestingly, we found that the gene encoding the modifying enzyme of 2′-O-ribosyladenosine at the 64th position of tRNA (Ar(p)64) was uniquely overexpressed under high-salinity stress. In contrast, most other tRNA-modifying enzymes were downregulated with mining transcriptomic sequencing data. According to previous physiological studies of Ar(p)64, the coconut appears to enhance the quality control of the translation process when subjected to high-salinity stress. We hope this survey can help advance research on tRNA modification and scientific studies of the coconut, as well as thinking of the safety and nutritional value of naturally modified nucleosides. Full article
(This article belongs to the Section RNA)
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13 pages, 3611 KiB  
Article
Genome-Wide Analysis of the BAHD Family in Welsh Onion and CER2-LIKEs Involved in Wax Metabolism
by Lecheng Liu, Huanhuan Xu, Wanyue Zhang, Jiayi Xing, Mingzhao Zhu, Yuchen Zhang and Yongqin Wang
Genes 2023, 14(6), 1286; https://doi.org/10.3390/genes14061286 - 18 Jun 2023
Cited by 2 | Viewed by 1233
Abstract
BAHD acyltransferases (BAHDs), especially those present in plant epidermal wax metabolism, are crucial for environmental adaptation. Epidermal waxes primarily comprise very-long-chain fatty acids (VLCFAs) and their derivatives, serving as significant components of aboveground plant organs. These waxes play an essential role in resisting [...] Read more.
BAHD acyltransferases (BAHDs), especially those present in plant epidermal wax metabolism, are crucial for environmental adaptation. Epidermal waxes primarily comprise very-long-chain fatty acids (VLCFAs) and their derivatives, serving as significant components of aboveground plant organs. These waxes play an essential role in resisting biotic and abiotic stresses. In this study, we identified the BAHD family in Welsh onion (Allium fistulosum). Our analysis revealed the presence of AfBAHDs in all chromosomes, with a distinct concentration in Chr3. Furthermore, the cis-acting elements of AfBAHDs were associated with abiotic/biotic stress, hormones, and light. The motif of Welsh onion BAHDs indicated the presence of a specific BAHDs motif. We also established the phylogenetic relationships of AfBAHDs, identifying three homologous genes of CER2. Subsequently, we characterized the expression of AfCER2-LIKEs in a Welsh onion mutant deficient in wax and found that AfCER2-LIKE1 plays a critical role in leaf wax metabolism, while all AfCER2-LIKEs respond to abiotic stress. Our findings provide new insights into the BAHD family and lay a foundation for future studies on the regulation of wax metabolism in Welsh onion. Full article
(This article belongs to the Section Bioinformatics)
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20 pages, 7151 KiB  
Article
Metabolic Pathway Pairwise-Based Signature as a Potential Non-Invasive Diagnostic Marker in Alzheimer’s Disease Patients
by Yunwen Feng, Xingyu Chen, Xiaohua Douglas Zhang and Chen Huang
Genes 2023, 14(6), 1285; https://doi.org/10.3390/genes14061285 - 17 Jun 2023
Cited by 2 | Viewed by 1841
Abstract
Alzheimer’s disease (AD) is an incurable neurodegenerative disorder. Early screening, particularly in blood plasma, has been demonstrated as a promising approach to the diagnosis and prevention of AD. In addition, metabolic dysfunction has been demonstrated to be closely related to AD, which might [...] Read more.
Alzheimer’s disease (AD) is an incurable neurodegenerative disorder. Early screening, particularly in blood plasma, has been demonstrated as a promising approach to the diagnosis and prevention of AD. In addition, metabolic dysfunction has been demonstrated to be closely related to AD, which might be reflected in the whole blood transcriptome. Hence, we hypothesized that the establishment of a diagnostic model based on the metabolic signatures of blood is a workable strategy. To that end, we initially constructed metabolic pathway pairwise (MPP) signatures to characterize the interplay among metabolic pathways. Then, a series of bioinformatic methodologies, e.g., differential expression analysis, functional enrichment analysis, network analysis, etc., were used to investigate the molecular mechanism behind AD. Moreover, an unsupervised clustering analysis based on the MPP signature profile via the Non-Negative Matrix Factorization (NMF) algorithm was utilized to stratify AD patients. Finally, aimed at distinguishing AD patients from non-AD groups, a metabolic pathway-pairwise scoring system (MPPSS) was established using multi-machine learning methods. As a result, many metabolic pathways correlated to AD were disclosed, including oxidative phosphorylation, fatty acid biosynthesis, etc. NMF clustering analysis divided AD patients into two subgroups (S1 and S2), which exhibit distinct activities of metabolism and immunity. Typically, oxidative phosphorylation in S2 exhibits a lower activity than that in S1 and non-AD group, suggesting the patients in S2 might possess a more compromised brain metabolism. Additionally, immune infiltration analysis showed that the patients in S2 might have phenomena of immune suppression compared with S1 and the non-AD group. These findings indicated that S2 probably has a more severe progression of AD. Finally, MPPSS could achieve an AUC of 0.73 (95%CI: 0.70, 0.77) in the training dataset, 0.71 (95%CI: 0.65, 0.77) in the testing dataset, and an AUC of 0.99 (95%CI: 0.96, 1.00) in one external validation dataset. Overall, our study successfully established a novel metabolism-based scoring system for AD diagnosis using the blood transcriptome and provided new insight into the molecular mechanism of metabolic dysfunction implicated in AD. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Alzheimer’s Disease)
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18 pages, 2593 KiB  
Article
A Lycopene ε-Cyclase TILLING Allele Enhances Lycopene and Carotenoid Content in Fruit and Improves Drought Stress Tolerance in Tomato Plants
by Angelo Petrozza, Stephan Summerer, Donato Melfi, Teresa Mango, Filippo Vurro, Manuele Bettelli, Michela Janni, Francesco Cellini and Filomena Carriero
Genes 2023, 14(6), 1284; https://doi.org/10.3390/genes14061284 - 17 Jun 2023
Cited by 1 | Viewed by 1191
Abstract
In the scenario of climate change, the availability of genetic resources for tomato cultivation that combine improved nutritional properties and more tolerance to water deficiency is highly desirable. Within this context, the molecular screenings of the Red Setter cultivar-based TILLING platform led to [...] Read more.
In the scenario of climate change, the availability of genetic resources for tomato cultivation that combine improved nutritional properties and more tolerance to water deficiency is highly desirable. Within this context, the molecular screenings of the Red Setter cultivar-based TILLING platform led to the isolation of a novel lycopene ε-cyclase gene (SlLCY-E) variant (G/3378/T) that produces modifications in the carotenoid content of tomato leaves and fruits. In leaf tissue, the novel G/3378/T SlLCY-E allele enhances β,β-xanthophyll content at the expense of lutein, which decreases, while in ripe tomato fruit the TILLING mutation induces a significant increase in lycopene and total carotenoid content. Under drought stress conditions, the G/3378/T SlLCY-E plants produce more abscisic acid (ABA) and still conserve their leaf carotenoid profile (reduction of lutein and increase in β,β-xanthophyll content). Furthermore, under said conditions, the mutant plants grow much better and are more tolerant to drought stress, as revealed by digital-based image analysis and in vivo monitoring of the OECT (Organic Electrochemical Transistor) sensor. Altogether, our data indicate that the novel TILLING SlLCY-E allelic variant is a valuable genetic resource that can be used for developing new tomato varieties, improved in drought stress tolerance and enriched in fruit lycopene and carotenoid content. Full article
(This article belongs to the Special Issue Genetic Control of Agronomic Traits in Plants)
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13 pages, 2953 KiB  
Article
Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach
by Mashooq Ahmad Dar, Basharat Bhat, Junaid Nazir, Afnan Saleem, Tasaduq Manzoor, Mahak Khan, Zulfqarul Haq, Sahar Saleem Bhat and Syed Mudasir Ahmad
Genes 2023, 14(6), 1283; https://doi.org/10.3390/genes14061283 - 17 Jun 2023
Viewed by 1712
Abstract
Potential single nucleotide polymorphisms (SNPs) were detected between two chicken breeds (Kashmir favorella and broiler) using deep RNA sequencing. This was carried out to comprehend the coding area alterations, which cause variances in the immunological response to Salmonella infection. In the present [...] Read more.
Potential single nucleotide polymorphisms (SNPs) were detected between two chicken breeds (Kashmir favorella and broiler) using deep RNA sequencing. This was carried out to comprehend the coding area alterations, which cause variances in the immunological response to Salmonella infection. In the present study, we identified high impact SNPs from both chicken breeds in order to delineate different pathways that mediate disease resistant/susceptibility traits. Samples (liver and spleen) were collected from Salmonella resistant (K. favorella) and susceptible (broiler) chicken breeds. Salmonella resistance and susceptibility were checked by different pathological parameters post infection. To explore possible polymorphisms in genes linked with disease resistance, SNP identification analysis was performed utilizing RNA seq data from nine K. favorella and ten broiler chickens. A total of 1778 (1070 SNPs and 708 INDELs) and 1459 (859 SNPs and 600 INDELs) were found to be specific to K. favorella and broiler, respectively. Based on our results, we conclude that in broiler chickens the enriched pathways mostly included metabolic pathways like fatty acid metabolism, carbon metabolism and amino acid metabolism (Arginine and proline metabolism), while as in K. favorella genes with high impact SNPs were enriched in most of the immune-related pathways like MAPK signaling pathway, Wnt signaling pathway, NOD-like receptor signaling pathway, etc., which could be a possible resistance mechanism against salmonella infection. In K. favorella, protein–protein interaction analysis also shows some important hub nodes, which are important in providing defense against different infectious diseases. Phylogenomic analysis revealed that indigenous poultry breeds (resistant) are clearly separated from commercial breeds (susceptible). These findings will offer fresh perspectives on the genetic diversity in chicken breeds and will aid in the genomic selection of poultry birds. Full article
(This article belongs to the Special Issue Molecular Genetics in Livestock Production and Disease Resistance)
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13 pages, 3231 KiB  
Article
Metabolome and Transcriptome Integrated Analysis of Mulberry Leaves for Insight into the Formation of Bitter Taste
by Jin Huang, Yong Li, Cui Yu, Rongli Mo, Zhixian Zhu, Zhaoxia Dong, Xingming Hu and Wen Deng
Genes 2023, 14(6), 1282; https://doi.org/10.3390/genes14061282 - 17 Jun 2023
Cited by 1 | Viewed by 1432
Abstract
Mulberry leaves are excellent for health care, confirmed as a ‘drug homologous food’ by the Ministry of Health, China. The bitter taste of mulberry leaves is one of the main problems that hinders the development of the mulberry food industry. The bitter, unique [...] Read more.
Mulberry leaves are excellent for health care, confirmed as a ‘drug homologous food’ by the Ministry of Health, China. The bitter taste of mulberry leaves is one of the main problems that hinders the development of the mulberry food industry. The bitter, unique taste of mulberry leaves is difficult to eliminate by post-processing. In this study, the bitter metabolites in mulberry leaves were identified as flavonoids, phenolic acids, alkaloids, coumarins and L-amino acids by a combined analysis of the metabolome and transcriptome of mulberry leaves. The analysis of the differential metabolites showed that the bitter metabolites were diverse and the sugar metabolites were down-regulated, indicating that the bitter taste of mulberry leaves was a comprehensive reflection of various bitter-related metabolites. Multi-omics analysis showed that the main metabolic pathway related to bitter taste in mulberry leaves was galactose metabolism, indicating that soluble sugar was one of the main factors of bitter taste difference in mulberry leaves. Bitter metabolites play a great role in the medicinal and functional food of mulberry leaves, but the saccharides in mulberry leaves have a great influence on the bitter taste of mulberry. Therefore, we propose to retain bitter metabolites with drug activity in mulberry leaves and increase the content of sugars to improve the bitter taste of mulberry leaves as strategies for mulberry leaf food processing and mulberry breeding for vegetable use. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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36 pages, 4543 KiB  
Review
Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant’s Abiotic Stress Tolerance Responses
by Rajib Roychowdhury, Soumya Prakash Das, Amber Gupta, Parul Parihar, Kottakota Chandrasekhar, Umakanta Sarker, Ajay Kumar, Devade Pandurang Ramrao and Chinta Sudhakar
Genes 2023, 14(6), 1281; https://doi.org/10.3390/genes14061281 - 16 Jun 2023
Cited by 19 | Viewed by 5457
Abstract
The present day’s ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant’s innate growth and development, resulting in reduced yield and [...] Read more.
The present day’s ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant’s innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the ‘omics’ toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant’s genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence ‘multi-omics’) integrated-omics approaches can decipher the plant’s abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop’s variable abiotic stress tolerance to ensure food security under changing environmental circumstances. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Present and Future)
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16 pages, 5435 KiB  
Article
A Comprehensive Pan-Cancer Analysis of the Potential Biological Functions and Prognosis Values of RICTOR
by Ying Sun, Rui Li, Baoting Nong, Zhou Songyang, Xianren Wang, Wenbin Ma and Qin Zhou
Genes 2023, 14(6), 1280; https://doi.org/10.3390/genes14061280 - 16 Jun 2023
Cited by 2 | Viewed by 1721
Abstract
The importance of the network defined by phosphatidylinositol-3-kinase (PI3K), AKT and mammalian target of rapamycin (mTOR) downstream of Receptor Tyrosine Kinase (RTK) has been recognized for many years. However, the central role of RICTOR (rapamycin-insensitive companion of mTOR) in this pathway has only [...] Read more.
The importance of the network defined by phosphatidylinositol-3-kinase (PI3K), AKT and mammalian target of rapamycin (mTOR) downstream of Receptor Tyrosine Kinase (RTK) has been recognized for many years. However, the central role of RICTOR (rapamycin-insensitive companion of mTOR) in this pathway has only recently come to light. The function of RICTOR in pan-cancer still needs to be systematically elucidated. In this study, we examined RICTOR’s molecular characteristics and clinical prognostic value by pan-cancer analysis. Our findings indicate that RICTOR was overexpressed in twelve cancer types, and a high RICTOR expression was linked to poor overall survival. Moreover, the CRISPR Achilles’ knockout analysis revealed that RICTOR was a critical gene for the survival of many tumor cells. Function analysis revealed that RICTOR-related genes were mainly involved in TOR signaling and cell growth. We further demonstrated that the RICTOR expression was significantly influenced by genetic alteration and DNA-methylation in multiple cancer types. Additionally, we found a positive relationship between RICTOR expression and the immune infiltration of macrophages and cancer-associated fibroblasts in Colon adenocarcinoma and Head and Neck squamous cell carcinoma. Finally, we validated the ability of RICTOR in sustaining tumor growth and invasion in the Hela cell line using cell-cycle analysis, the cell proliferation assay, and wound-healing assay. Our pan-cancer analysis highlights the critical role of RICTOR in tumor progression and its potential as a prognostic marker for various cancer types. Full article
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16 pages, 2412 KiB  
Article
Sequencing and Characterization of M. morganii Strain UM869: A Comprehensive Comparative Genomic Analysis of Virulence, Antibiotic Resistance, and Functional Pathways
by Dibyajyoti Uttameswar Behera, Sangita Dixit, Mahendra Gaur, Rukmini Mishra, Rajesh Kumar Sahoo, Maheswata Sahoo, Bijay Kumar Behera, Bharat Bhusan Subudhi, Sutar Suhas Bharat and Enketeswara Subudhi
Genes 2023, 14(6), 1279; https://doi.org/10.3390/genes14061279 - 16 Jun 2023
Cited by 1 | Viewed by 2024
Abstract
Morganella morganii is a Gram-negative opportunistic Enterobacteriaceae pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study investigated the virulence factors, resistance mechanisms, functional pathways, and comparative genomic analysis of M. morganii strain UM869 with 79 publicly available [...] Read more.
Morganella morganii is a Gram-negative opportunistic Enterobacteriaceae pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study investigated the virulence factors, resistance mechanisms, functional pathways, and comparative genomic analysis of M. morganii strain UM869 with 79 publicly available genomes. The multidrug resistance strain UM869 harbored 65 genes associated with 30 virulence factors, including efflux pump, hemolysin, urease, adherence, toxin, and endotoxin. Additionally, this strain contained 11 genes related to target alteration, antibiotic inactivation, and efflux resistance mechanisms. Further, the comparative genomic study revealed a high genetic relatedness (98.37%) among the genomes, possibly due to the dissemination of genes between adjoining countries. The core proteome of 79 genomes contains the 2692 core, including 2447 single-copy orthologues. Among them, six were associated with resistance to major antibiotic classes manifested through antibiotic target alteration (PBP3, gyrB) and antibiotic efflux (kpnH, rsmA, qacG; rsmA; CRP). Similarly, 47 core orthologues were annotated to 27 virulence factors. Moreover, mostly core orthologues were mapped to transporters (n = 576), two-component systems (n = 148), transcription factors (n = 117), ribosomes (n = 114), and quorum sensing (n = 77). The presence of diversity in serotypes (type 2, 3, 6, 8, and 11) and variation in gene content adds to the pathogenicity, making them more difficult to treat. This study highlights the genetic similarity among the genomes of M. morganii and their restricted emergence, mostly in Asian countries, in addition to their growing pathogenicity and resistance. However, steps must be taken to undertake large-scale molecular surveillance and to direct suitable therapeutic interventions. Full article
(This article belongs to the Special Issue Omics and Bioinformatics)
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15 pages, 1160 KiB  
Article
Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM) Can Potentially Define the ALT Positivity of Cancer
by Kaitlin Raseley, Zeal Jinwala, Dong Zhang and Ming Xiao
Genes 2023, 14(6), 1278; https://doi.org/10.3390/genes14061278 - 16 Jun 2023
Viewed by 2175
Abstract
Telomeres play an essential role in protecting the ends of linear chromosomes and maintaining the integrity of the human genome. One of the key hallmarks of cancers is their replicative immortality. As many as 85–90% of cancers activate the expression of telomerase (TEL+) [...] Read more.
Telomeres play an essential role in protecting the ends of linear chromosomes and maintaining the integrity of the human genome. One of the key hallmarks of cancers is their replicative immortality. As many as 85–90% of cancers activate the expression of telomerase (TEL+) as the telomere maintenance mechanism (TMM), and 10–15% of cancers utilize the homology-dependent repair (HDR)-based Alternative Lengthening of Telomere (ALT+) pathway. Here, we performed statistical analysis of our previously reported telomere profiling results from Single Molecule Telomere Assay via Optical Mapping (SMTA-OM), which is capable of quantifying individual telomeres from single molecules across all chromosomes. By comparing the telomeric features from SMTA-OM in TEL+ and ALT+ cancer cells, we demonstrated that ALT+ cancer cells display certain unique telomeric profiles, including increased fusions/internal telomere-like sequence (ITS+), fusions/internal telomere-like sequence loss (ITS−), telomere-free ends (TFE), super-long telomeres, and telomere length heterogeneity, compared to TEL+ cancer cells. Therefore, we propose that ALT+ cancer cells can be differentiated from TEL+ cancer cells using the SMTA-OM readouts as biomarkers. In addition, we observed variations in SMTA-OM readouts between different ALT+ cell lines that may potentially be used as biomarkers for discerning subtypes of ALT+ cancer and monitoring the response to cancer therapy. Full article
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15 pages, 974 KiB  
Review
Enhancer Function in the 3D Genome
by Sergey V. Razin, Sergey V. Ulianov and Olga V. Iarovaia
Genes 2023, 14(6), 1277; https://doi.org/10.3390/genes14061277 - 16 Jun 2023
Cited by 2 | Viewed by 2221
Abstract
In this review, we consider various aspects of enhancer functioning in the context of the 3D genome. Particular attention is paid to the mechanisms of enhancer-promoter communication and the significance of the spatial juxtaposition of enhancers and promoters in 3D nuclear space. A [...] Read more.
In this review, we consider various aspects of enhancer functioning in the context of the 3D genome. Particular attention is paid to the mechanisms of enhancer-promoter communication and the significance of the spatial juxtaposition of enhancers and promoters in 3D nuclear space. A model of an activator chromatin compartment is substantiated, which provides the possibility of transferring activating factors from an enhancer to a promoter without establishing direct contact between these elements. The mechanisms of selective activation of individual promoters or promoter classes by enhancers are also discussed. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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16 pages, 2528 KiB  
Article
Suppression of NANOG Expression Reduces Drug Resistance of Cancer Stem Cells in Glioblastoma
by Jonhoi Smith, Melvin Field and Kiminobu Sugaya
Genes 2023, 14(6), 1276; https://doi.org/10.3390/genes14061276 - 16 Jun 2023
Cited by 3 | Viewed by 1786
Abstract
Glioblastoma (GBM) is an aggressive and incurable primary brain tumor that harbors therapy-resistant cancer stem cells (CSCs). Due to the limited effectiveness of conventional chemotherapies and radiation treatments against CSCs, there is a critical need for the development of innovative therapeutic approaches. Our [...] Read more.
Glioblastoma (GBM) is an aggressive and incurable primary brain tumor that harbors therapy-resistant cancer stem cells (CSCs). Due to the limited effectiveness of conventional chemotherapies and radiation treatments against CSCs, there is a critical need for the development of innovative therapeutic approaches. Our previous research revealed the significant expression of embryonic stemness genes, NANOG and OCT4, in CSCs, suggesting their role in enhancing cancer-specific stemness and drug resistance. In our current study, we employed RNA interference (RNAi) to suppress the expression of these genes and observed an increased susceptibility of CSCs to the anticancer drug, temozolomide (TMZ). Suppression of NANOG expression induced cell cycle arrest in CSCs, specifically in the G0 phase, and it concomitantly decreased the expression of PDK1. Since PDK1 activates the PI3K/AKT pathway to promote cell proliferation and survival, our findings suggest that NANOG contributes to chemotherapy resistance in CSCs through PI3K/AKT pathway activation. Therefore, the combination of TMZ treatment with RNAi targeting NANOG holds promise as a therapeutic strategy for GBM. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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