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Genes, Volume 13, Issue 12 (December 2022) – 241 articles

Cover Story (view full-size image): Clostridioides difficile is an obligate anaerobic pathogen that is among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, C. difficile infection can lead to fulminant colitis associated with shock, hypotension, megacolon, and, in severe cases, death. It is therefore of the utmost urgency to fully characterize this pathogen and to better understand its spread, in order to reduce infection rates and improve therapy success. Our work focuses on the genetic evolution of C. difficile virulence, antimicrobial resistance, the molecular typing techniques used to characterize this pathogen, the global distribution of the most common ribotypes, and novel genetic engineering strategies to control this threat. View this paper
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16 pages, 3269 KiB  
Article
Population Genetics and Anastomosis Group’s Geographical Distribution of Rhizoctonia solani Associated with Soybean
by Aqleem Abbas, Xiangling Fang, Shehzad Iqbal, Syed Atif Hasan Naqvi, Yasir Mehmood, Muhammad Junaid Rao, Zeshan Hassan, Roberto Miño Ortiz, Alaa Baazeem, Mahmoud Moustafa, Sulaiman Alrumman and Sally Negm
Genes 2022, 13(12), 2417; https://doi.org/10.3390/genes13122417 - 19 Dec 2022
Cited by 2 | Viewed by 2115
Abstract
Rhizoctonia solani is a species complex composed of many genetically diverse anastomosis groups (AG) and their subgroups. It causes economically important diseases of soybean worldwide. However, the global genetic diversity and distribution of R. solani AG associated with soybean are unknown to date. [...] Read more.
Rhizoctonia solani is a species complex composed of many genetically diverse anastomosis groups (AG) and their subgroups. It causes economically important diseases of soybean worldwide. However, the global genetic diversity and distribution of R. solani AG associated with soybean are unknown to date. In this study, the global genetic diversity and distribution of AG associated with soybean were investigated based on rDNA-ITS sequences deposited in GenBank and published literature. The most prevalent AG, was AG-1 (40%), followed by AG-2 (19.13%), AG-4 (11.30%), AG-7 (10.43%), AG-11 (8.70%), AG-3 (5.22%) and AG-5 (3.48%). Most of the AG were reported from the USA and Brazil. Sequence analysis of internal transcribed spacers of ribosomal DNA separated AG associated with soybean into two distinct clades. Clade I corresponded to distinct subclades containing AG-2, AG-3, AG-5, AG-7 and AG-11. Clade II corresponded to subclades of AG-1 subgroups. Furthermore, AG and/or AG subgroups were in close proximity without corresponding to their geographical origin. Moreover, AG or AG subgroups within clade or subclades shared higher percentages of sequence similarities. The principal coordinate analysis also supported the phylogenetic and genetic diversity analyses. In conclusion, AG-1, AG-2, and AG-4 were the most prevalent AG in soybean. The clade or subclades corresponded to AG or AG subgroups and did not correspond to the AG’s geographical origin. The information on global genetic diversity and distribution will be helpful if novel management measures are to be developed against soybean diseases caused by R. solani. Full article
(This article belongs to the Special Issue Phylogenetics, Genetics, and Breeding of Medicinal Plants)
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12 pages, 2885 KiB  
Article
Analysis of Breast Cancer Differences between China and Western Countries Based on Radiogenomics
by Yuanyuan Zhang, Lifeng Yang and Xiong Jiao
Genes 2022, 13(12), 2416; https://doi.org/10.3390/genes13122416 - 19 Dec 2022
Cited by 1 | Viewed by 1754
Abstract
Using radiogenomics methods, the differences between tumor imaging data and genetic data in Chinese and Western breast cancer (BC) patients were analyzed, and the correlation between phenotypic data and genetic data was explored. In this paper, we analyzed BC patients’ image characteristics and [...] Read more.
Using radiogenomics methods, the differences between tumor imaging data and genetic data in Chinese and Western breast cancer (BC) patients were analyzed, and the correlation between phenotypic data and genetic data was explored. In this paper, we analyzed BC patients’ image characteristics and transcriptome data separately, then correlated the magnetic resonance imaging (MRI) phenotype with the transcriptome data through a computational method to develop a radiogenomics feature. The data was fed into the designed random forest (RF) model, which used the area under the receiver operating curve (AUC) as the evaluation index. Next, we analyzed the hub genes in the differentially expressed genes (DEGs) and obtained seven hub genes, which may cause Chinese and Western BC patients to behave differently in the clinic. We demonstrated that combining relevant genetic data and imaging features could better classify Chinese and Western patients than using genes or imaging characteristics alone. The AUC values of 0.74, 0.81, and 0.95 were obtained separately using the image characteristics, DEGs, and radiogenomics features. We screened SYT4, GABRG2, CHGA, SLC6A17, NEUROG2, COL2A1, and MATN4 and found that these genes were positively or negatively correlated with certain imaging characteristics. In addition, we found that the SLC6A17, NEUROG2, CHGA, and MATN4 genes were associated with clinical features. Full article
(This article belongs to the Special Issue Bioinformatics Analysis for Cancers)
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11 pages, 917 KiB  
Review
Impact of X-Linked Hypophosphatemia on Muscle Symptoms
by Cecilia Romagnoli, Teresa Iantomasi and Maria Luisa Brandi
Genes 2022, 13(12), 2415; https://doi.org/10.3390/genes13122415 - 19 Dec 2022
Cited by 6 | Viewed by 4047
Abstract
X-linked hypophosphatemia (XLH) is the most common hereditary form of rickets and deficiency of renal tubular phosphate transport in humans. XLH is caused by the inactivation of mutations within the phosphate-regulating endopeptidase homolog X-linked (PHEX) gene and follows an X-dominant transmission. [...] Read more.
X-linked hypophosphatemia (XLH) is the most common hereditary form of rickets and deficiency of renal tubular phosphate transport in humans. XLH is caused by the inactivation of mutations within the phosphate-regulating endopeptidase homolog X-linked (PHEX) gene and follows an X-dominant transmission. It has an estimated frequency of 1 case per 20,000, and over 300 distinct pathogenic variations have been reported that result in an excess of fibroblast growth factor 23 (FGF23) in the serum. Increased levels of FGF23 lead to renal phosphate loss, decreased serum 1,25-dihydroxyvitamin D, and increased metabolism of 1,25-dihydoxyvitamin D, resulting in hypophosphatemia. Major clinical manifestations include rickets, bone deformities, and growth retardation that develop during childhood, and osteomalacia-related fractures or pseudo-fractures, degenerative osteoarthritis, enthesopathy, dental anomalies, and hearing loss during adulthood, which can affect quality of life. In addition, fatigue is also a common symptom in patients with XLH, who experience decreased motion, muscle weakness, and pain, contributing to altered quality of life. The clinical and biomedical characteristics of XLH are extensively defined in bone tissue since skeletal deformations and mineralization defects are the most evident effects of high FGF23 and low serum phosphate levels. However, despite the muscular symptoms that XLH causes, very few reports are available on the effects of FGF23 and phosphate in muscle tissue. Given the close relationship between bones and skeletal muscles, studying the effects of FGF23 and phosphate on muscle could provide additional opportunities to understand the interactions between these two important compartments of the body. By describing the current literature on XLH and skeletal muscle dysfunctions, the purpose of this review is to highlight future areas of research that could contribute to a better understanding of XLH muscular disability and its management. Full article
(This article belongs to the Special Issue Genetics and Genomics of Skeletal Disorders)
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13 pages, 1896 KiB  
Article
Marker-Assisted Pyramiding of CRa and CRd Genes to Improve the Clubroot Resistance of Brassica rapa
by Xiaonan Li, Yingxia Wei, Yingmei Ma, Guizhu Cao, Siwen Ma, Tianyu Zhang, Zongxiang Zhan and Zhongyun Piao
Genes 2022, 13(12), 2414; https://doi.org/10.3390/genes13122414 - 19 Dec 2022
Cited by 2 | Viewed by 1804
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an economically important soil-borne disease that threatens Brassicaceae crops worldwide. In recent years, the incidence area of Chinese cabbage (Brassica rapa ssp. pekinensis) clubroot disease has increased, which severely affects the yield and quality [...] Read more.
Clubroot, caused by Plasmodiophora brassicae, is an economically important soil-borne disease that threatens Brassicaceae crops worldwide. In recent years, the incidence area of Chinese cabbage (Brassica rapa ssp. pekinensis) clubroot disease has increased, which severely affects the yield and quality of Chinese cabbage. The resistance of varieties harboring the single clubroot-resistance (CR) gene is easily broken through by P. brassicae pathotypes. CRa and CRd, genetically identified in B. rapa, are CR genes known to be highly resistant to different P. brassicaea pathotypes. In our study, we perform the gene pyramiding of CRa and CRd in Chinese cabbages through marker-assisted selection (MAS), and develop homozygous pyramided lines. The newly generated pyramided lines exhibit greater resistance to six different pathotypes than that of two parental lines carrying a single CR gene. This study provides new CR-gene-pyramided lines for the development of clubroot-resistant Brassica varieties for future breeding programs. Full article
(This article belongs to the Special Issue Molecular Genetics of Important Traits in Cruciferous Vegetables)
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14 pages, 2416 KiB  
Article
Heterologous Expression of Human Metallothionein Gene HsMT1L Can Enhance the Tolerance of Tobacco (Nicotiana nudicaulis Watson) to Zinc and Cadmium
by Yilin Zheng, Meng Cui, Lei Ni, Yafei Qin, Jinhua Li, Yu Pan and Xingguo Zhang
Genes 2022, 13(12), 2413; https://doi.org/10.3390/genes13122413 - 19 Dec 2022
Cited by 2 | Viewed by 1559
Abstract
Metallothionein (MT) is a multifunctional inducible protein in animals, plants, and microorganisms. MT is rich in cysteine residues (10−30%), can combine with metal ions, has a low molecular weight, and plays an essential biological role in various stages of the growth and development [...] Read more.
Metallothionein (MT) is a multifunctional inducible protein in animals, plants, and microorganisms. MT is rich in cysteine residues (10−30%), can combine with metal ions, has a low molecular weight, and plays an essential biological role in various stages of the growth and development of organisms. Due to its strong ability to bind metal ions and scavenge free radicals, metallothionein has been used in medicine, health care, and other areas. Zinc is essential for plant growth, but excessive zinc (Zn) is bound to poison plants, and cadmium (Cd) is a significant environmental pollutant. A high concentration of cadmium can significantly affect the growth and development of plants and even lead to plant death. In this study, the human metallothionein gene HsMT1L under the control of the CaMV 35S constitutive promoter was transformed into tobacco, and the tolerance and accumulation capacity of transgenic tobacco plants to Zn and Cd were explored. The results showed that the high-level expression of HsMT1L in tobacco could significantly enhance the accumulation of Zn2+ and Cd2+ in both the aboveground parts and the roots compared to wild-type tobacco plants and conferred a greater tolerance to Zn and Cd in transgenic tobacco. Subcellular localization showed that HsMT1L was localized to the nucleus and cytoplasm in the tobacco. Our study suggests that HsMT1L can be used for the phytoremediation of soil for heavy metal removal. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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23 pages, 17257 KiB  
Article
In Silico Prediction of Hub Genes Involved in Diabetic Kidney and COVID-19 Related Disease by Differential Gene Expression and Interactome Analysis
by Ulises Osuna-Martinez, Katia Aviña-Padilla, Vicente Olimon-Andalon, Carla Angulo-Rojo, Alma Guadron-Llanos, Jose Carlos Rivas-Ferreira, Francisco Urrea and Loranda Calderon-Zamora
Genes 2022, 13(12), 2412; https://doi.org/10.3390/genes13122412 - 19 Dec 2022
Cited by 2 | Viewed by 2732
Abstract
Diabetic kidney disease (DKD) is a frequently chronic kidney pathology derived from diabetes comorbidity. This condition has irreversible damage and its risk factor increases with SARS-CoV-2 infection. The prognostic outcome for diabetic patients with COVID-19 is dismal, even with intensive medical treatment. However, [...] Read more.
Diabetic kidney disease (DKD) is a frequently chronic kidney pathology derived from diabetes comorbidity. This condition has irreversible damage and its risk factor increases with SARS-CoV-2 infection. The prognostic outcome for diabetic patients with COVID-19 is dismal, even with intensive medical treatment. However, there is still scarce information on critical genes involved in the pathophysiological impact of COVID-19 on DKD. Herein, we characterize differential expression gene (DEG) profiles and determine hub genes undergoing transcriptional reprogramming in both disease conditions. Out of 995 DEGs, we identified 42 shared with COVID-19 pathways. Enrichment analysis elucidated that they are significantly induced with implications for immune and inflammatory responses. By performing a protein–protein interaction (PPI) network and applying topological methods, we determine the following five hub genes: STAT1, IRF7, ISG15, MX1 and OAS1. Then, by network deconvolution, we determine their co-expressed gene modules. Moreover, we validate the conservancy of their upregulation using the Coronascape database (DB). Finally, tissue-specific regulation of the five predictive hub genes indicates that OAS1 and MX1 expression levels are lower in healthy kidney tissue. Altogether, our results suggest that these genes could play an essential role in developing severe outcomes of COVID-19 in DKD patients. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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13 pages, 1906 KiB  
Article
Whole-Genome Sequence Analysis Reveals the Origin of the Chakouyi Horse
by Ying Li, Yu Liu, Min Wang, Xiaoran Lin, Yuanyuan Li, Tao Yang, Mo Feng, Yao Ling and Chunjiang Zhao
Genes 2022, 13(12), 2411; https://doi.org/10.3390/genes13122411 - 19 Dec 2022
Cited by 3 | Viewed by 1666
Abstract
The Chakouyi horse is an ancient Chinese indigenous horse breed distributed in Gansu Province in northwestern China, and is also one of the key breeds protected by the government. However, the origin of the Chakouyi horse remains unclear. As it is distributed in [...] Read more.
The Chakouyi horse is an ancient Chinese indigenous horse breed distributed in Gansu Province in northwestern China, and is also one of the key breeds protected by the government. However, the origin of the Chakouyi horse remains unclear. As it is distributed in a key region of the Silk Road, it was speculated that the origin of the Chakouyi horse might involve the foreign horse breeds found along this ancient commercial artery. In this study, whole-genome resequencing data of 12 horse breeds, including both indigenous and foreign horses, were applied to reveal the genetic relationships between the Chakouyi horse and other breeds, as well as the ancestry of this ancient breed. An analysis of the population structure and admixture showed that there is no close genetic affinity between the Chakouyi horse and the foreign horses while Chinese indigenous horse populations were grouped together in accordance with their geographic locations, and the Chakouyi horse showed a closer relationship with Kazak horses, Mongolian horses, and Tibetan horses. The results from the ancestral composition prediction indicated that the Kazak horse and the Mongolian horse might be two ancestors of the Chakouyi horse. Furthermore, the genome-wide selection signature analysis revealed that the DMRT3 gene was positively selected in the Chakouyi horse and related to the gait trait of the breed. Our results provide insights into the native origin of the Chakouyi horse and indicate that Kazak and Mongolian horses played important roles in the formation of the Chakouyi horse. Genetic communication between the Chakouyi horse and other horse populations could be attributed, at least partially, to population migrations and trade activities along the ancient commercial routes. Full article
(This article belongs to the Special Issue Equine Genetics and Genomics)
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12 pages, 3739 KiB  
Article
Complete Chloroplast Genome Sequence of Endangered Species in the Genus Opisthopappus C. Shih: Characterization, Species Identification, and Phylogenetic Relationships
by Xinke Zhang, Guoshuai Zhang, Yuan Jiang and Linfang Huang
Genes 2022, 13(12), 2410; https://doi.org/10.3390/genes13122410 - 19 Dec 2022
Cited by 2 | Viewed by 1344
Abstract
Opisthopappus C. Shih is a rare genus of the Asteraceae family native to the Taihang Mountains in China. Due to the narrow distribution area, poor reproduction ability and human harvesting, Opisthopappus is threatened by extinction. However, the limited genetic information within Opisthopappus impede [...] Read more.
Opisthopappus C. Shih is a rare genus of the Asteraceae family native to the Taihang Mountains in China. Due to the narrow distribution area, poor reproduction ability and human harvesting, Opisthopappus is threatened by extinction. However, the limited genetic information within Opisthopappus impede understanding of the conservation efforts and bioprospecting. Therefore, in this study, we reported the complete chloroplast (cp) genome sequences of two Opisthopappus species, including Opisthopappus taihangensis and Opisthopappus longilobus. The cp genomes of O. taihangensis and O. longilobus were 151,117 and 151,123 bp, which contained 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The repeat sequences, codon usage, RNA-editing sites, and comparative analyses revealed a high degree of conservation between the two species. The ycf1 gene was identified as a potential molecular marker. The phylogenetic tree demonstrated that O. longilobus was a separate species and not a synonym or variety of O. taihangensis. The molecular clock showed that two species diverge over a large time span, O. longilobus diverged at 15.24 Mya (Million years ago), whereas O. taihangensis diverged at 5.40 Mya We found that Opisthopappus and Ajania are closely related, which provides new ideas for the development of Opisthopappus. These results provide biological information and an essential basis to understand the evolutionary history of the Opisthopappus species, which will aid in the future the bioprospecting and conservation of endangered species. Full article
(This article belongs to the Section Cytogenomics)
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10 pages, 2510 KiB  
Article
Chromosomal Location of Pm12—A Novel Powdery Mildew Resistance Gene from Avena sterilis
by Tomasz Ociepa and Sylwia Okoń
Genes 2022, 13(12), 2409; https://doi.org/10.3390/genes13122409 - 19 Dec 2022
Cited by 4 | Viewed by 1472
Abstract
Identification of new, effective disease resistance genes is a very important aspect of plant breeding. Also important is the precise location of individual loci and tagging them with DNA markers for marker assisted selection. The aim of the present study was identification of [...] Read more.
Identification of new, effective disease resistance genes is a very important aspect of plant breeding. Also important is the precise location of individual loci and tagging them with DNA markers for marker assisted selection. The aim of the present study was identification of the molecular markers linked with Pm12, a new effective resistance gene to powdery mildew, and their location in the oat genome. The analysis was performed on 167 F2 individuals from a hybrid of Fuchs × CN67383, with the status of the locus in each individual verified by progeny test in F3. Segregation ratios confirmed the monogenic nature of resistance. Making use of the sequence data of DNA markers and the oat OT3098 v2 genome reference assembly, Pm12 is located on chromosome 7C. A comparison was also made with the reference consensus map, to which there are more reports of mapped genes to date. The mapping results suggest that Pm12 is located in the interval 103.8–111.7 cM on this map. No powdery mildew resistance locus has been identified in this region so far, suggesting that Avena sterilis CN67383 carries a novel locus offering effective resistance in oat breeding. The information included in the oat genome annotation allowed for the identification of candidate genes in the close region of the marker cluster for Pm12. This information may provide an interesting source of further analysis of the pathways of various genes in response to the stress of powdery mildew infection. Full article
(This article belongs to the Special Issue Molecular Markers in Plant Genetics and Breeding)
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13 pages, 743 KiB  
Article
Association of Inherited Copy Number Variation in ADAM3A and ADAM5 Pseudogenes with Oropharynx Cancer Risk and Outcome
by Juliana Carron, Caroline Torricelli, Janet Keller Silva, Yichuan Liu, Renata Pellegrino, Carmen Silvia Passos Lima and Gustavo Jacob Lourenço
Genes 2022, 13(12), 2408; https://doi.org/10.3390/genes13122408 - 19 Dec 2022
Cited by 2 | Viewed by 1479
Abstract
Inherited copy number variations (CNVs) can provide valuable information for cancer susceptibility and prognosis. However, their association with oropharynx squamous cell carcinoma (OPSCC) is still poorly studied. Using microarrays analysis, we identified three inherited CNVs associated with OPSCC risk, of which one was [...] Read more.
Inherited copy number variations (CNVs) can provide valuable information for cancer susceptibility and prognosis. However, their association with oropharynx squamous cell carcinoma (OPSCC) is still poorly studied. Using microarrays analysis, we identified three inherited CNVs associated with OPSCC risk, of which one was validated in 152 OPSCC patients and 155 controls and related to pseudogene-microRNA-mRNA interaction. Individuals with three or more copies of ADAM3A and ADAM5 pseudogenes (8p11.22 chromosome region) were under 6.49-fold increased risk of OPSCC. ADAM5 shared a highly homologous sequence with the ADAM9 3′-UTR, predicted to be a binding site for miR-122b-5p. Individuals carrying more than three copies of ADAM3A and ADAM5 presented higher ADAM9 expression levels. Moreover, patients with total deletion or one copy of pseudogenes and with higher expression of miR-122b-5p presented worse prognoses. Our data suggest, for the first time, that ADAM3A and ADAM5 pseudogene-inherited CNV could modulate OPSCC occurrence and prognosis, possibly through the interaction of ADAM5 pseudogene transcript, miR-122b-5p, and ADAM9. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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11 pages, 1319 KiB  
Article
Causal Association of Obesity and Dyslipidemia with Type 2 Diabetes: A Two-Sample Mendelian Randomization Study
by Young Lee, Ye An Kim and Je Hyun Seo
Genes 2022, 13(12), 2407; https://doi.org/10.3390/genes13122407 - 19 Dec 2022
Cited by 8 | Viewed by 2238
Abstract
Recent studies have suggested an association between obesity and dyslipidemia in the development of type 2 diabetes (T2D). The purpose of this study was to explore the causal effects of obesity and dyslipidemia on T2D risk in Asians. Two-sample Mendelian randomization (MR) analyses [...] Read more.
Recent studies have suggested an association between obesity and dyslipidemia in the development of type 2 diabetes (T2D). The purpose of this study was to explore the causal effects of obesity and dyslipidemia on T2D risk in Asians. Two-sample Mendelian randomization (MR) analyses were performed to assess genetically predicted obesity using body mass index (BMI) and dyslipidemia using high-density lipoprotein cholesterol (HDL), low-density lipoprotein cholesterol (LDL), total cholesterol (TCHL), and triglycerides (TG) versus T2D susceptibility using genome-wide association study (GWAS) results derived from the summary statistics of Biobank Japan (n = 179,000) and DIAbetes Meta-ANalysis of Trans-Ethnic association studies (n = 50,533). The MR analysis demonstrated evidence of a causal effect of higher BMI on the risk of T2D (odds ratio (OR) > 1.0, p < 0.05). In addition, TG showed a protective effect on the risk of T2D (ORs 0.68–0.85). However, HDL, LDL, and TCHL showed little genetic evidence supporting a causal association between dyslipidemia and T2D. We found strong genetic evidence supporting a causal association of BMI with T2D. Although HDL, LDL, and TCHL did not show a causal association with T2D, TG had a causal relationship with the decrease of T2D. Although it was predicted that TG would be linked to a higher risk of T2D, it actually exhibited a paradoxical protective effect against T2D, which requires further investigation. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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16 pages, 2635 KiB  
Article
Identification of Differentially Expressed miRNAs in Porcine Adipose Tissues and Evaluation of Their Effects on Feed Efficiency
by Mingxing Liao, Zhuqing Ren and Yuanxin Miao
Genes 2022, 13(12), 2406; https://doi.org/10.3390/genes13122406 - 19 Dec 2022
Viewed by 1501
Abstract
Feed efficiency (FE) is a very important trait affecting the economic benefits of pig breeding enterprises. Adipose tissue can modulate a variety of processes such as feed intake, energy metabolism and systemic physiological processes. However, the mechanism by which microRNAs (miRNAs) in adipose [...] Read more.
Feed efficiency (FE) is a very important trait affecting the economic benefits of pig breeding enterprises. Adipose tissue can modulate a variety of processes such as feed intake, energy metabolism and systemic physiological processes. However, the mechanism by which microRNAs (miRNAs) in adipose tissues regulate FE remains largely unknown. Therefore, this study aimed to screen potential miRNAs related to FE through miRNA sequencing. The miRNA profiles in porcine adipose tissues were obtained and 14 miRNAs were identified differentially expressed in adipose tissues of pigs with extreme differences in FE, of which 9 were down-regulated and 5 were up-regulated. GO and KEGG analyses indicated that these miRNAs were significantly related to lipid metabolism and these miRNAs modulated FE by regulating lipid metabolism. Subsequently, quantitative reverse transcription–polymerase chain reaction (qRT-PCR) of five randomly selected DEMs was used to verify the reliability of miRNA-seq data. Furthermore, 39 differentially expressed target genes of these DEMs were obtained, and DEMs–target mRNA interaction networks were constructed. In addition, the most significantly down-regulated miRNAs, ssc-miR-122-5p and ssc-miR-192, might be the key miRNAs for FE. Our results reveal the mechanism by which adipose miRNAs regulate feed efficiency in pigs. This study provides a theoretical basis for the further study of swine feed efficiency improvement. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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10 pages, 1630 KiB  
Article
Analysis of Copy Number Variation in the Whole Genome of Normal-Haired and Long-Haired Tianzhu White Yaks
by Guangyao Meng, Qi Bao, Xiaoming Ma, Min Chu, Chun Huang, Xian Guo, Chunnian Liang and Ping Yan
Genes 2022, 13(12), 2405; https://doi.org/10.3390/genes13122405 - 18 Dec 2022
Cited by 2 | Viewed by 1813
Abstract
Long-haired individuals in the Tianzhu white yak population are a unique genetic resource, and have important landscape value. Copy number variation (CNV) is an important source of phenotypic variation in mammals. In this study, we used resequencing technology to detect the whole genome [...] Read more.
Long-haired individuals in the Tianzhu white yak population are a unique genetic resource, and have important landscape value. Copy number variation (CNV) is an important source of phenotypic variation in mammals. In this study, we used resequencing technology to detect the whole genome of 10 long-haired Tianzhu white yaks (LTWY) and 10 normal-haired Tianzhu white yaks (NTWY), and analyzed the differences of CNV in the genome of LTWYs and NTWYs. A total of 110268 CNVs were identified, 2006 CNVRs were defined, and the distribution map of these CNVRs on chromosomes was constructed. The comparison of LTWYs and NTWYs identified 80 differential CNVR-harbored genes, which were enriched in lipid metabolism, cell migration and other functions. Notably, some differential genes were identified as associated with hair growth and hair-follicle development (e.g., ASTN2, ATM, COL22A1, GK5, SLIT3, PM20D1, and SGCZ). In general, we present the first genome-wide analysis of CNV in LTWYs and NTWYs. Our results can provide new insights into the phenotypic variation of different hair lengths in Tianzhu white yaks. Full article
(This article belongs to the Special Issue Genetic Variation in Biological Traits)
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19 pages, 2842 KiB  
Article
Morphological Characteristics and Comparative Chloroplast Genome Analyses between Red and White Flower Phenotypes of Pyracantha fortuneana (Maxim.) Li (Rosaceae), with Implications for Taxonomy and Phylogeny
by Shi-Xiong Ding, Jia-Chen Li, Ke Hu, Zi-Jian Huang and Rui-Sen Lu
Genes 2022, 13(12), 2404; https://doi.org/10.3390/genes13122404 - 18 Dec 2022
Cited by 4 | Viewed by 1613
Abstract
Pyracantha fortuneana (Maxim.) Li (Rosaceae), commonly known as Chinese firethorn, is an evergreen shrub with high nutritional, medicinal, and horticultural importance. This species typically has white flowers, but a rare red flower phenotype has been found in very few wild populations in western [...] Read more.
Pyracantha fortuneana (Maxim.) Li (Rosaceae), commonly known as Chinese firethorn, is an evergreen shrub with high nutritional, medicinal, and horticultural importance. This species typically has white flowers, but a rare red flower phenotype has been found in very few wild populations in western Hubei, China, showing great ornamental potential. In this study, the complete chloroplast genome of the red flower phenotype of P. fortuneana was reported for the first time, using high-throughput sequencing technology. The complete chloroplast genome was 160,361 bp in length and showed a typical quadripartite structure with a pair of inverted repeat (IR) regions (26,350 bp) separated by a large single-copy (LSC) region (88,316 bp) and a small single-copy (SSC) region (19,345 bp). A total of 131 functional genes were annotated in this chloroplast genome, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. Comparative chloroplast genome analyses revealed that high genome similarity existed not only between red and white flower phenotypes of P. fortuneana, but also among Pyracantha species. No evidence for positive selection was found in any PCG, suggesting the evolutionary conservation of Pyracantha chloroplast genomes. Furthermore, four mutational hotspots (trnG-trnR-atpA, psbZ-trnG-trnfM-rps14, ycf3-trnS-rps4, and ndhF-rpl32) with π > 0.004 were identified as potential molecular markers for Pyracantha species. Phylogenomic analysis strongly supported that the red flower phenotype of P. fortuneana was nested within the common white flower phenotype. Based on both morphological and molecular evidence, we suggest that the red flower phenotype of P. fortuneana could be considered as a new forma. Overall, the availability of these genetic resources will not only offer valuable information for further studies on molecular taxonomy, phylogeny, and population genetics of Pyracantha species but also could be used as potential genetic resources for Chinese firethorn breeding. Full article
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome)
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13 pages, 3813 KiB  
Article
MDSN: A Module Detection Method for Identifying High-Order Epistatic Interactions
by Yan Sun, Yijun Gu, Qianqian Ren, Yiting Li, Junliang Shang, Jin-Xing Liu and Boxin Guan
Genes 2022, 13(12), 2403; https://doi.org/10.3390/genes13122403 - 18 Dec 2022
Cited by 1 | Viewed by 1374
Abstract
Epistatic interactions are referred to as SNPs (single nucleotide polymorphisms) that affect disease development and trait expression nonlinearly, and hence identifying epistatic interactions plays a great role in explaining the pathogenesis and genetic heterogeneity of complex diseases. Many methods have been proposed for [...] Read more.
Epistatic interactions are referred to as SNPs (single nucleotide polymorphisms) that affect disease development and trait expression nonlinearly, and hence identifying epistatic interactions plays a great role in explaining the pathogenesis and genetic heterogeneity of complex diseases. Many methods have been proposed for epistasis detection; nevertheless, they mainly focus on low-order epistatic interactions, two-order or three-order for instance, and often ignore high-order interactions due to computational burden. In this paper, a module detection method called MDSN is proposed for identifying high-order epistatic interactions. First, an SNP network is constructed by a construction strategy of interaction complementary, which consists of low-order SNP interactions that can be obtained from fast computations. Then, a node evaluation measure that integrates multi-topological features is proposed to improve the node expansion algorithm, where the importance of a node is comprehensively evaluated by the topological characteristics of the neighborhood. Finally, modules are detected in the constructed SNP network, which have high-order epistatic interactions associated with the disease. The MDSN was compared with four state-of-the-art methods on simulation datasets and a real Age-related Macular Degeneration dataset. The results demonstrate that MDSN has higher performance on detecting high-order interactions. Full article
(This article belongs to the Section Bioinformatics)
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16 pages, 3943 KiB  
Article
The Complete Chloroplast Genome Sequence of Machilus chuanchienensis (Lauraceae): Genome Structure and Phylogenetic Analysis
by Xue Bai, Juan Peng, Yongyi Yang and Biao Xiong
Genes 2022, 13(12), 2402; https://doi.org/10.3390/genes13122402 - 18 Dec 2022
Cited by 4 | Viewed by 2033
Abstract
Machilus chuanchienensis is an ecological tree distributed in southwestern China. It has a significant valuation with making Hawk tea using its leaves, an ethnic traditional tea-like beverage with a long history in Chinese tea culture. The whole chloroplast (cp) genome is an ideal [...] Read more.
Machilus chuanchienensis is an ecological tree distributed in southwestern China. It has a significant valuation with making Hawk tea using its leaves, an ethnic traditional tea-like beverage with a long history in Chinese tea culture. The whole chloroplast (cp) genome is an ideal model for the phylogenetic study of Lauraceae because of its simple structure and highly conserved features. There have been numerous reports of complete cp genome sequences in Lauraceae, but little is known about M. chuanchienensis. Here, the next-generation sequencing (NGS) was used to sequence the M. chuanchienensis cp genome. Then, a comprehensive comparative genome analysis was performed. The results revealed that the M. chuanchienensis’s cp genome measured 152,748 base pairs (bp) with a GC content of 39.15% and coded 126 genes annotated, including comprising eight ribosomal RNA (rRNA), 36 transporter RNA (tRNA), and 82 protein-coding genes. In addition, the cp genome presented a typical quadripartite structure comprising a large single-copy (LSC; 93,811) region, a small single-copy (SSC; 18,803) region, and the inverted repeats (IRs; 20,067) region and contained 92 simple sequence repeat (SSR) locus in total. Phylogenetic relationships of 37 species indicated that M. chuanchienensis was a sister to M. balansae, M. melanophylla, and M. minutiflora. Further research on this crucial species may benefit significantly from these findings. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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7 pages, 272 KiB  
Article
Some New Aspects of Genetic Variability in Patients with Cutaneous T-Cell Lymphoma
by Vladimír Vašků, Jan Máchal, Filip Zlámal and Anna Vašků
Genes 2022, 13(12), 2401; https://doi.org/10.3390/genes13122401 - 18 Dec 2022
Cited by 1 | Viewed by 1287
Abstract
Aim: Cutaneous T-cell lymphoma (CTCL) is a group of T-cell malignancies that develop in the skin. Though studied intensively, the etiology and pathogenesis of CTCL remain elusive. This study evaluated the survival of CTCL patients in the 1st Department of Dermatovenereology of St. [...] Read more.
Aim: Cutaneous T-cell lymphoma (CTCL) is a group of T-cell malignancies that develop in the skin. Though studied intensively, the etiology and pathogenesis of CTCL remain elusive. This study evaluated the survival of CTCL patients in the 1st Department of Dermatovenereology of St. Anne’s University Hospital Brno. It included analysis of 19 polymorphic gene variants based on their expected involvement in CTCL severity. Material and methods: 75 patients with CTCL, evaluated and treated at the 1st Department of Dermatovenereology of St. Anne´s University Hospital Brno, Faculty of Medicine, Masaryk University, were recruited for the study over the last 28 years (44 men and 31 women, average age 58 years, range 20–82 years). All patients were genotyped for 19 chosen gene polymorphisms by the conventional PCR method with restriction analysis. A multivariate Cox regression model was calculated to reveal genetic polymorphisms and other risk factors for survival. Results: The model identified MDR Ex21 2677 (rs2032582) as a significant genetic factor influencing the survival of the patients, with the T-allele playing a protective role. A multivariate stepwise Cox regression model confirmed the following as significant independent risk factors for overall survival: increased age at admission, clinical staging of the tumor, and male sex. Conclusion: We showed that the TT genotype at position 2677 of the MDR1 gene exhibited statistically significant longer survival in CTCL patients. As such, the TT genotype of MDR1 confers a significant advantage for the CTCL patients who respond to treatment. Full article
(This article belongs to the Special Issue Feature Papers in Human Genomics and Genetic Diseases)
17 pages, 4055 KiB  
Article
Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer
by Xingda Zhang, Jiaqi Zeng, Jianyu Wang, Zihan Yang, Song Gao, Honghao Liu, Guozheng Li, Xin Zhang, Yue Gu and Da Pang
Genes 2022, 13(12), 2400; https://doi.org/10.3390/genes13122400 - 18 Dec 2022
Cited by 10 | Viewed by 2038
Abstract
Understanding the causes of tumorigenesis and progression in triple-receptor negative breast cancer (TNBC) can help the design of novel and personalized therapies and prognostic assessments. Abnormal RNA modification is a recently discovered process in TNBC development. TNBC samples from The Cancer Genome Atlas [...] Read more.
Understanding the causes of tumorigenesis and progression in triple-receptor negative breast cancer (TNBC) can help the design of novel and personalized therapies and prognostic assessments. Abnormal RNA modification is a recently discovered process in TNBC development. TNBC samples from The Cancer Genome Atlas database were categorized according to the expression level of NAT10, which drives acetylation of cytidine in RNA to N(4)-acetylcytidine (ac4C) and affects mRNA stability. A total of 703 differentially expressed long non-coding RNAs (lncRNAs) were found between high- and low-expressed NAT10 groups in TNBC. Twenty of these lncRNAs were significantly associated with prognosis. Two breast cancer tissues and their paired normal tissues were sequenced at the whole genome level using acetylated RNA immunoprecipitation sequencing (acRIP-seq) technology to identify acetylation features in TNBC, and 180 genes were significantly differentially ac4c acetylated in patients. We also analyzed the genome-wide lncRNA expression profile and constructed a co-expression network, containing 116 ac4C genes and 1080 lncRNAs. Three of these lncRNAs were prognostic risk lncRNAs affected by NAT10 and contained in the network. The corresponding reciprocal pairs were “LINC01614-COL3A1”, “OIP5-AS1-USP8”, and “RP5-908M14.9-TRIR”. These results indicate that RNA ac4c acetylation involves lncRNAs and affects the tumor process and prognosis of TNBC. This will aid the prediction of drug targets and drug sensitivity. Full article
(This article belongs to the Special Issue DNA and RNA Epigenetics and Transcriptomics Research)
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14 pages, 553 KiB  
Article
Fragile X-Associated Neuropsychiatric Disorders (FXAND) in Young Fragile X Premutation Carriers
by Ramkumar Aishworiya, Dragana Protic, Si Jie Tang, Andrea Schneider, Flora Tassone and Randi Hagerman
Genes 2022, 13(12), 2399; https://doi.org/10.3390/genes13122399 - 17 Dec 2022
Cited by 4 | Viewed by 2289
Abstract
Background: The fragile X premutation carrier state (PM) (55–200 CGG repeats in the fragile X messenger ribonucleoprotein 1, FMR1 gene) is associated with several conditions, including fragile X-associated primary ovarian insufficiency (FXPOI) and fragile X-associated tremor ataxia (FXTAS), with current literature largely primarily [...] Read more.
Background: The fragile X premutation carrier state (PM) (55–200 CGG repeats in the fragile X messenger ribonucleoprotein 1, FMR1 gene) is associated with several conditions, including fragile X-associated primary ovarian insufficiency (FXPOI) and fragile X-associated tremor ataxia (FXTAS), with current literature largely primarily investigating older PM individuals. The aim of this study was to identify the prevalence of fragile X-associated neurodevelopmental disorders (FXAND) in a sample of young PM individuals. Methods: This was a retrospective study conducted through a medical record review of PM individuals who were seen either for clinical concerns (probands, 45.9%) or identified through the cascade testing (non-probands, 54.1%) of an affected sibling with fragile X syndrome. Information on the presence of autism spectrum disorder, attention deficit hyperactivity disorder, anxiety, depression, long-term psychiatric medication intake, and cognitive function, based on standardized assessments, was obtained. Molecular data, including CGG repeat number and FMR1 mRNA levels, were also available for a subset of participants. Analysis included descriptive statistics and a test of comparison to describe the clinical profile of PM individuals pertinent to FXAND. Results: Participants included 61 individuals (52 males and 9 females) aged 7.8 to 20.0 years (mean 12.6 ± 3.4) with a mean full-scale IQ of 90.9 ± 22.7. The majority (N = 52; 85.2%) had at least one mental health disorder, with anxiety being the most common (82.0% of subjects), followed by ADHD (66.5%), and ASD (32.8%). Twenty-seven (87.1%) of non-probands also had at least one mental health condition, with probands having lower cognitive and adaptive skills than non-probands. ASD was present in 20 participants (17/52 males and 3/9 females; 15 probands) with significantly lower FSIQ in those with ASD (mean 73.5 vs. 98.0, p < 0.001). Participants with ASD had a higher number of long-term medications compared to those without (2.32 vs. 1.3, p = 0.002). Conclusions: Our findings indicate a high rate of FXAND diagnoses within a cohort of young PM individuals, including those identified via cascade testing, although this was not a population sample. An awareness of the entity of FXAND and the early recognition of the symptoms of associated conditions may facilitate timely and appropriate care for PM individuals. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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11 pages, 2097 KiB  
Article
Ssc-miR-141 Attenuates Hypoxia-Induced Alveolar Type II Epithelial Cell Injury in Tibetan Pigs by Targeting PDCD4
by Linna Xu, Haonan Yuan, Zongli Wang, Shengguo Zhao and Yanan Yang
Genes 2022, 13(12), 2398; https://doi.org/10.3390/genes13122398 - 17 Dec 2022
Cited by 2 | Viewed by 1221
Abstract
The Tibetan pig is an endemic economic animal in the plateau region of China, and has a unique adaptation mechanism to the plateau hypoxic environment. Research into microRNAs (miRNAs) involved in the mechanism underlying hypoxia adaptation of Tibetan pig is very limited. Therefore, [...] Read more.
The Tibetan pig is an endemic economic animal in the plateau region of China, and has a unique adaptation mechanism to the plateau hypoxic environment. Research into microRNAs (miRNAs) involved in the mechanism underlying hypoxia adaptation of Tibetan pig is very limited. Therefore, we isolated alveolar type II epithelial (ATII) cells from the lungs of the Tibetan pig, cultured them in normoxia/hypoxia (21% O2; 2% O2) for 48 h, and performed high-throughput sequencing analysis. We identified a hypoxic stress-related ssc-miR-141 and predicted its target genes. The target genes of ssc-miR-141 were mainly enriched in mitogen-activated protein kinase (MAPK), autophagy-animal, and Ras signaling pathways. Further, we confirmed that PDCD4 may serve as the target gene of ssc-miR-141. Real-time quantitative polymerase chain reaction (RT-qPCR) analysis was performed to confirm the expression levels of ssc-miR-141 and PDCD4, and a dual-luciferase gene reporter system was used to verify the targeted linkage of ssc-miR-141 to PDCD4. The results showed that the expression level of ssc-miR-141 in the hypoxia group was higher than that in the normoxia group, while the expression level of PDCD4 tended to show the opposite trend and significantly decreased under hypoxia. These findings suggest that ssc-miR-141 is associated with hypoxia adaptation and provide a new insight into the role of miRNAs from ATII cells of Tibetan pig in hypoxia adaptation. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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15 pages, 3359 KiB  
Article
Folic Acid and Vitamin B12 Prevent Deleterious Effects of Rotenone on Object Novelty Recognition Memory and Kynu Expression in an Animal Model of Parkinson’s Disease
by Gabriela Canalli Kretzschmar, Adriano D. S. Targa, Sheila Coelho Soares-Lima, Priscila Ianzen dos Santos, Lais S. Rodrigues, Daniel A. Macedo, Luis Felipe Ribeiro Pinto, Marcelo M. S. Lima and Angelica Beate Winter Boldt
Genes 2022, 13(12), 2397; https://doi.org/10.3390/genes13122397 - 17 Dec 2022
Cited by 2 | Viewed by 3012
Abstract
Parkinson’s disease (PD) is characterized by a range of motor signs, but cognitive dysfunction is also observed. Supplementation with folic acid and vitamin B12 is expected to prevent cognitive impairment. To test this in PD, we promoted a lesion within the substantia nigra [...] Read more.
Parkinson’s disease (PD) is characterized by a range of motor signs, but cognitive dysfunction is also observed. Supplementation with folic acid and vitamin B12 is expected to prevent cognitive impairment. To test this in PD, we promoted a lesion within the substantia nigra pars compacta of rats using the neurotoxin rotenone. In the sequence, the animals were supplemented with folic acid and vitamin B12 for 14 consecutive days and subjected to the object recognition test. We observed an impairment in object recognition memory after rotenone administration, which was prevented by supplementation (p < 0.01). Supplementation may adjust gene expression through efficient DNA methylation. To verify this, we measured the expression and methylation of the kynureninase gene (Kynu), whose product metabolizes neurotoxic metabolites often accumulated in PD as kynurenine. Supplementation prevented the decrease in Kynu expression induced by rotenone in the substantia nigra (p < 0.05), corroborating the behavioral data. No differences were observed concerning the methylation analysis of two CpG sites in the Kynu promoter. Instead, we suggest that folic acid and vitamin B12 increased global DNA methylation, reduced the expression of Kynu inhibitors, maintained Kynu-dependent pathway homeostasis, and prevented the memory impairment induced by rotenone. Our study raises the possibility of adjuvant therapy for PD with folic acid and vitamin B12. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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14 pages, 961 KiB  
Article
Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum
by Dongxiao Ma, Qin Zhang, Jintao Zhou, Yu Lu, Xiaomeng Duan, Chengzhong He and Jinde Yu
Genes 2022, 13(12), 2396; https://doi.org/10.3390/genes13122396 - 17 Dec 2022
Viewed by 1131
Abstract
Toxicodendron succedaneum (L.) Kuntze (T. succedaneum) is an economic tree species that produces urushiol and urushi wax, and it is of great value in industry and medicine. However, the stability of reference genes (RGs) has not been systematically reported in T. [...] Read more.
Toxicodendron succedaneum (L.) Kuntze (T. succedaneum) is an economic tree species that produces urushiol and urushi wax, and it is of great value in industry and medicine. However, the stability of reference genes (RGs) has not been systematically reported in T. succedaneum to date. In this study, the expression of 10 candidate RGs was analyzed by RT-qPCR in different tissues (roots, stems, leaves), stress treatments (high/low temperature, drought), and hormone stimulation (jasmonic acid, JA). Then, the stability ranking of 10 candidate genes was evaluated by ∆Ct analysis and three software programs: geNorm, NormFinder, and BestKeeper. Finally, RefFinder was used to comprehensively analyze the expression stability of 10 candidate genes. The comprehensive analysis showed that TsRG05/06, TsRG01/06, and TsRG03/ACT were stable under high/low-temperature stress, drought stress, and JA treatment, respectively. TsRG03 and ACT had stable expression in different tissues. While the TsRG03 and ACT were recommended as the suitable RGs for T. succedaneum in all samples. Meanwhile, UBQ was the least suitable as a reference gene for T. succedaneum. In addition, the results of geNorm showed that the combination of two stable RGs could make the results of gene expression more accurate. These results provide alternative RGs for the study of gene function, correction, and normalization of target gene expression and directed molecular breeding in T. succedaneum. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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12 pages, 3816 KiB  
Communication
Cloning and Functional Characterization of SpZIP2
by Tian-Long Han, Ting-Wei Tang, Pei-Hong Zhang, Min Liu, Jing Zhao, Jia-Shi Peng and Shuan Meng
Genes 2022, 13(12), 2395; https://doi.org/10.3390/genes13122395 - 17 Dec 2022
Cited by 1 | Viewed by 1549
Abstract
Zinc (Zn)-regulated and iron (Fe)-regulated transporter-like proteins (ZIP) are key players involved in the accumulation of cadmium (Cd) and Zn in plants. Sedum plumbizincicola X.H. Guo et S.B. Zhou ex L.H. Wu (S. plumbizincicola) is a Crassulaceae Cd/Zn hyperaccumulator found in [...] Read more.
Zinc (Zn)-regulated and iron (Fe)-regulated transporter-like proteins (ZIP) are key players involved in the accumulation of cadmium (Cd) and Zn in plants. Sedum plumbizincicola X.H. Guo et S.B. Zhou ex L.H. Wu (S. plumbizincicola) is a Crassulaceae Cd/Zn hyperaccumulator found in China, but the role of ZIPs in S. plumbizincicola remains largely unexplored. Here, we identified 12 members of ZIP family genes by transcriptome analysis in S. plumbizincicola and cloned the SpZIP2 gene with functional analysis. The expression of SpZIP2 in roots was higher than that in the shoots, and Cd stress significantly decreased its expression in the roots but increased its expression in leaves. Protein sequence characteristics and structural analysis showed that the content of alanine and leucine residues in the SpZIP2 sequence was higher than other residues, and several serine, threonine and tyrosine sites can be phosphorylated. Transmembrane domain analysis showed that SpZIP2 has the classic eight transmembrane regions. The evolutionary analysis found that SpZIP2 is closely related to OsZIP2, followed by AtZIP11, OsZIP1 and AtZIP2. Sequence alignment showed that most of the conserved sequences among these members were located in the transmembrane regions. A further metal sensitivity assay using yeast mutant Δyap1 showed that the expression of SpZIP2 increased the sensitivity of the transformants to Cd but failed to change the resistance to Zn. The subsequent ion content determination showed that the expression of SpZIP2 increased the accumulation of Cd in yeast. Subcellular localization showed that SpZIP2 was localized to membrane systems, including the plasma membrane and endoplasmic reticulum. The above results indicate that ZIP member SpZIP2 participates in the uptake and accumulation of Cd into cells and might contribute to Cd hyperaccumulation in S. plumbizincicola. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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19 pages, 5024 KiB  
Article
Genome-Wide Identification of Common Bean PvLTP Family Genes and Expression Profiling Analysis in Response to Drought Stress
by Xue Dong, Huijun Zhu, Xiaopeng Hao, Yan Wang, Xiaolei Ma, Jiandong Zhao and Jianwu Chang
Genes 2022, 13(12), 2394; https://doi.org/10.3390/genes13122394 - 16 Dec 2022
Cited by 2 | Viewed by 1673
Abstract
Common bean is one of the most important legume crops for human consumption. Its yield is adversely affected by environmental stress. Plant non-specific lipid transfer proteins (nsLTPs) are essential for plant growth, development, and resistance to abiotic stress, such as salt, drought, and [...] Read more.
Common bean is one of the most important legume crops for human consumption. Its yield is adversely affected by environmental stress. Plant non-specific lipid transfer proteins (nsLTPs) are essential for plant growth, development, and resistance to abiotic stress, such as salt, drought, and alkali. However, changes in nsLTP family genes responding to drought stress are less known. The PvLTP gene family in the common bean was identified by a comprehensive genome-wide analysis. Molecular weights, theoretical isoelectric points, phylogenetic tree, conserved motifs, gene structures, gene duplications, chromosome localization, and expression profiles were analyzed by SignalP 5.0, ExPASy, ClustalX 2.1, MEGA 7.0, NCBI-CDD, MEME, Weblogo, and TBtools 1.09876, respectively. Heatmap and qRT-PCR analyses were performed to validate the expression profiles of PvLTP genes in different organs. In addition, the expression patterns of nine PvLTP genes in common beans treated with drought stress were investigated by qRT-PCR. We obtained 58 putative PvLTP genes in the common bean genome via genome-wide analyses. Based on the diversity of the eight-cysteine motif (ECM), these genes were categorized into five types (I, II, IV, V, and VIII). The signal peptides of the PvLTP precursors were predicted to be from 16 to 42 amino acid residues. PvLTPs had a predicated theoretical isoelectric point of 3.94–10.34 and a molecular weight of 7.15–12.17 kDa. The phylogenetic analysis showed that PvLTPs were closer to AtLTPs than OsLTPs. Conserved motif and gene structure analyses indicated that PvLTPs were randomly distributed on all chromosomes except chromosome 9. In addition, 23 tandem duplicates of PvLTP genes were arranged in 10 gene clusters on chromosomes 1 and 2. The heatmap and qRT-PCR showed that PvLTP expression significantly varied in different tissues. Moreover, 9 PvLTP genes were up-regulated under drought treatment. Our results reveal that PvLTPs play potentially vital roles in plants and provide a comprehensive reference for studies on PvLTP genes and a theoretical basis for further analysis of regulatory mechanisms influencing drought tolerance in the common bean. Full article
(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)
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13 pages, 1081 KiB  
Article
Identification of Genetic Effects of ACADVL and IRF6 Genes with Milk Production Traits of Holstein Cattle in China
by Peng Peng, Yanan Liu, Weijie Zheng, Bo Han, Kun Wang and Dongxiao Sun
Genes 2022, 13(12), 2393; https://doi.org/10.3390/genes13122393 - 16 Dec 2022
Viewed by 2898
Abstract
With the development of high-throughput sequencing, RNA sequencing has been widely used in the identification of candidate genes for complex traits in livestock, and the functional genes and mutations with large genetic effects on milk production traits can provide molecular information for marker-assisted [...] Read more.
With the development of high-throughput sequencing, RNA sequencing has been widely used in the identification of candidate genes for complex traits in livestock, and the functional genes and mutations with large genetic effects on milk production traits can provide molecular information for marker-assisted selection to increase the selection accuracy and accelerate genetic gain in dairy cattle. Our previous study on the liver transcriptome of Holstein cows found that acyl-CoA dehydrogenase (ACADVL) and interferon regulatory factor 6 (IRF6) are differentially expressed between dry and peak lactation periods, as well as that they are involved in lipid metabolism and the proliferation and differentiation of mammary epithelial cells. Thus, the two genes were considered candidates for milk traits. Hence, this study further collected 1186 Holstein cows from 110 sire families to investigate their genetic associations with milk yield and composition traits. By resequencing the entire exons and 2000 bp of the 5′ and 3′ flanking regions of the two genes, we identified eight SNPs in ACADVL and eight SNPs in IRF6. Subsequent single-locus association analyses showed that the eight SNPs in ACADVL were all significantly associated with milk fat yield, fat percentage, and protein yield (p values ≤ 0.0001–0.0414), and the eight SNPs in IRF6 were associated with milk, fat, and protein yields in the first or second lactation (p values ≤ 0.0001–0.0467). Using Haploview 4.2, one haplotype block with eight of the SNPs in ACADVL (D’ = 0.99–1.00) and two haplotype blocks in IRF6 with three of the SNPs in each were observed (D’ = 0.98–1.00). Similarly, the haplotype combinations of ACADVL were significantly associated with milk yield, fat percentage, fat yield, and protein yield in the two lactations (p values ≤ 0.0001–0.0125), and those of IRF6 were associated with five milk traits (p values ≤ 0.0001–0.0263). Furthermore, with the JASPAR software, it was predicted that the SNPs 19:g.26933503T>C in ACADVL and 16:g.73501985G>A in IRF6 changed the transcription factor binding sites of ZEB1, PLAGL2, and RHOXF1, implying their impacts on the expressions of the corresponding genes. Our findings demonstrated that the ACADVL and IRF6 genes have significant genetic effects on milk yield and composition traits, and the valuable SNPs might be used as genetic markers for genomic selection programs in dairy cattle. Full article
(This article belongs to the Special Issue Genetics and Breeding of Cattle)
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22 pages, 4244 KiB  
Article
A Whole-Genome Sequencing Study Implicates GRAMD1B in Multiple Sclerosis Susceptibility
by Federica Esposito, Ana Maria Osiceanu, Melissa Sorosina, Linda Ottoboni, Bryan Bollman, Silvia Santoro, Barbara Bettegazzi, Andrea Zauli, Ferdinando Clarelli, Elisabetta Mascia, Andrea Calabria, Daniele Zacchetti, Ruggero Capra, Maurizio Ferrari, Paolo Provero, Dejan Lazarevic, Davide Cittaro, Paola Carrera, Nikolaos Patsopoulos, Daniela Toniolo, A Dessa Sadovnick, Gianvito Martino, Philip L. De Jager, Giancarlo Comi, Elia Stupka, Carles Vilariño-Güell, Laura Piccio and Filippo Martinelli Boneschiadd Show full author list remove Hide full author list
Genes 2022, 13(12), 2392; https://doi.org/10.3390/genes13122392 - 16 Dec 2022
Cited by 1 | Viewed by 2538
Abstract
While the role of common genetic variants in multiple sclerosis (MS) has been elucidated in large genome-wide association studies, the contribution of rare variants to the disease remains unclear. Herein, a whole-genome sequencing study in four affected and four healthy relatives of a [...] Read more.
While the role of common genetic variants in multiple sclerosis (MS) has been elucidated in large genome-wide association studies, the contribution of rare variants to the disease remains unclear. Herein, a whole-genome sequencing study in four affected and four healthy relatives of a consanguineous Italian family identified a novel missense c.1801T > C (p.S601P) variant in the GRAMD1B gene that is shared within MS cases and resides under a linkage peak (LOD: 2.194). Sequencing GRAMD1B in 91 familial MS cases revealed two additional rare missense and two splice-site variants, two of which (rs755488531 and rs769527838) were not found in 1000 Italian healthy controls. Functional studies demonstrated that GRAMD1B, a gene with unknown function in the central nervous system (CNS), is expressed by several cell types, including astrocytes, microglia and neurons as well as by peripheral monocytes and macrophages. Notably, GRAMD1B was downregulated in vessel-associated astrocytes of active MS lesions in autopsied brains and by inflammatory stimuli in peripheral monocytes, suggesting a possible role in the modulation of inflammatory response and disease pathophysiology. Full article
(This article belongs to the Special Issue Genetic and Molecular Mechanisms in Multiple Sclerosis)
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16 pages, 1490 KiB  
Article
Diagnostic and Prognostic Risk Assessment of Heat Shock Protein HSPA1B rs2763979 Gene Variant in Asthma
by Salwa Faisal, Sherouk Abdelaal, Mohammed A. Jeraiby, Fatihi Hassan Soliman Toaimah, Shahad W. Kattan, Abdelhady Ragab Abdel-Gawad, Eman Riad, Eman A. Toraih, Manal S. Fawzy and Ahmed Ibrahim
Genes 2022, 13(12), 2391; https://doi.org/10.3390/genes13122391 - 16 Dec 2022
Cited by 2 | Viewed by 1805
Abstract
Given the significant role the heat shock protein Hsp70 plays in modulating cellular homeostasis in several chronic inflammatory disorders, the genetic variation of the inducible HSP70 (HSPA1B) gene may impact protein expression and disease phenotype. The HSPA1B rs2763979 variant has been [...] Read more.
Given the significant role the heat shock protein Hsp70 plays in modulating cellular homeostasis in several chronic inflammatory disorders, the genetic variation of the inducible HSP70 (HSPA1B) gene may impact protein expression and disease phenotype. The HSPA1B rs2763979 variant has been associated with multiple inflammatory scenarios, but no previous studies have explored its association with asthma. In this sense, this cross-sectional study enrolled 90 children with asthma and 218 age-/sex-matched healthy volunteers for rs2763979 variant genotyping by TaqMan allelic discrimination analysis. The results were investigated under several genetic models and associated with disease susceptibility and clinicolaboratory data. Overall analysis, including the 308 participants, revealed a higher C allele frequency among patients relative to controls (43.0% vs. 33%, p = 0.006). Furthermore, patients with the C variant initially had a higher risk of asthma under heterozygous (OR = 2.75, 95%CI = 1.46–5.18, p = 0.003), homozygous (OR = 3.35, 95%CI = 1.19–9.39, p = 0.008), dominant (OR = 2.83, 95%CI = 1.52–5.25, p < 0.001), and overdominant (OR = 2.12, 95%CI = 1.20–3.74, p = 0.008) models. However, after employing a 1:1 nearest propensity matching analysis, the studied variant showed only borderline significance with asthma under the dominant model in 71 matched cohorts. Interestingly, patients who carry the rs2763979 CC genotype showed favorable spirometric parameters in terms of better (mean ± SD) forced vital capacity (86.3 ± 7.4 vs. 77.7 ± 6.1 and 75.7 ± 7.2 for CT and TT, respectively, p = 0.021), forced expiratory volume in one second before bronchodilation (60.7 ± 12.9 vs. 54.9 ± 7.6 and 56.1 ± 7.5 for CT and TT, respectively, p = 0.021), and an improvement in peak expiratory flow rate after inhaled salbutamol bronchodilator (p = 0.044) relative to the counterpart genotypes. In conclusion, the HSPA1B rs2763979 variant might have prognostic utility as a genetic marker for asthma in our population. Further larger studies on different ethnicities are recommended to validate the results. Full article
(This article belongs to the Collection Genotype-Phenotype Study in Disease)
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21 pages, 2452 KiB  
Review
53BP1: Keeping It under Control, Even at a Distance from DNA Damage
by Emilie Rass, Simon Willaume and Pascale Bertrand
Genes 2022, 13(12), 2390; https://doi.org/10.3390/genes13122390 - 16 Dec 2022
Cited by 12 | Viewed by 6351
Abstract
Double-strand breaks (DSBs) are toxic lesions that can be generated by exposure to genotoxic agents or during physiological processes, such as during V(D)J recombination. The repair of these DSBs is crucial to prevent genomic instability and to maintain cellular homeostasis. Two main pathways [...] Read more.
Double-strand breaks (DSBs) are toxic lesions that can be generated by exposure to genotoxic agents or during physiological processes, such as during V(D)J recombination. The repair of these DSBs is crucial to prevent genomic instability and to maintain cellular homeostasis. Two main pathways participate in repairing DSBs, namely, non-homologous end joining (NHEJ) and homologous recombination (HR). The P53-binding protein 1 (53BP1) plays a pivotal role in the choice of DSB repair mechanism, promotes checkpoint activation and preserves genome stability upon DSBs. By preventing DSB end resection, 53BP1 promotes NHEJ over HR. Nonetheless, the balance between DSB repair pathways remains crucial, as unscheduled NHEJ or HR events at different phases of the cell cycle may lead to genomic instability. Therefore, the recruitment of 53BP1 to chromatin is tightly regulated and has been widely studied. However, less is known about the mechanism regulating 53BP1 recruitment at a distance from the DNA damage. The present review focuses on the mechanism of 53BP1 recruitment to damage and on recent studies describing novel mechanisms keeping 53BP1 at a distance from DSBs. Full article
(This article belongs to the Special Issue Dynamics of DNA Double Strand Breaks)
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11 pages, 263 KiB  
Article
Clinical, Cytogenetic and Molecular Cytogenetic Outcomes of Cell-Free DNA Testing for Rare Chromosomal Anomalies
by Seher Basaran, Recep Has, Ibrahim Halil Kalelioglu, Tugba Sarac Sivrikoz, Birsen Karaman, Melike Kirgiz, Tahir Dehgan, Tugba Kalayci, Bilge Ozsait Selcuk, Peter Miny and Atil Yuksel
Genes 2022, 13(12), 2389; https://doi.org/10.3390/genes13122389 - 16 Dec 2022
Cited by 2 | Viewed by 1658
Abstract
The scope of cell-free DNA (cfDNA) testing was expanded to the genome, which allowed screening for rare chromosome anomalies (RCAs). Since the efficiency of the test for RCAs remains below the common aneuploidies, there is a debate on the usage of expanded tests. [...] Read more.
The scope of cell-free DNA (cfDNA) testing was expanded to the genome, which allowed screening for rare chromosome anomalies (RCAs). Since the efficiency of the test for RCAs remains below the common aneuploidies, there is a debate on the usage of expanded tests. This study focuses on the confirmatory and follow-up data of cases with positive cfDNA testing for RCAs and cases with screen-negative results in a series of 912 consecutive cases that underwent invasive testing following cfDNA testing. Chorion villus sampling (CVS), amniocentesis (AS), fetal blood sampling, and term placenta samples were investigated using classical cytogenetic and molecular cytogenetic techniques. Out of 593 screen-positive results, 504 (85%) were for common aneuploidies, 40 (6.7%) for rare autosomal trisomies (RATs), and 49 (8.3%) for structural chromosome anomalies (SAs). Of the screen-positives for RATs, 20 cases were evaluated only in fetal tissue, and confined placental mosaicism (CPM) could not be excluded. Among cases with definitive results (n = 20), the rates of true positives, placental mosaics, and false positives were 35%, 45%, and 10%, respectively. Among screen-positives for SAs, 32.7% were true positives. The confirmation rate was higher for duplications than deletions (58.3% vs. 29.4%). The rate of chromosomal abnormality was 10.9% in the group of 256 screen-negatives with pathological ultrasound findings. This study provides further data to assess the efficiency of expanded cfDNA testing for RATs and SAs. The test efficiency for cfDNA seems to be higher for duplications than for deletions, which is evidence of the role of expert ultrasound in identifying pregnancies at increased risk for chromosome anomalies, even in pregnancies with screen-negatives. Furthermore, we discussed the efficiency of CVS vs. AC in screen-positives for RATs. Full article
23 pages, 439 KiB  
Review
Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update
by Sara Jarmakiewicz-Czaja, Magdalena Zielińska, Aneta Sokal and Rafał Filip
Genes 2022, 13(12), 2388; https://doi.org/10.3390/genes13122388 - 16 Dec 2022
Cited by 20 | Viewed by 5349
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them [...] Read more.
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics. Full article
(This article belongs to the Special Issue Genomics and Epigenomics of Gastrointestinal Disorders)
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