Genes

9 pages, 3964 KiB

Open AccessArticle

A COL5A2 In-Frame Deletion in a Chihuahua with Ehlers-Danlos Syndrome

by Sarah Kiener, Lucie Chevallier, Vidhya Jagannathan, Amaury Briand, Noëlle Cochet-Faivre, Edouard Reyes-Gomez and Tosso Leeb

Genes 2022, 13(5), 934; https://doi.org/10.3390/genes13050934 - 23 May 2022

Cited by 5 | Viewed by 3415

Abstract

Ehlers-Danlos syndrome (EDS) is a group of heterogeneous, rare diseases affecting the connective tissues. The main clinical signs of EDS are skin hyperextensibility, joint hypermobility, and skin fragility. Currently, the classification of EDS in humans distinguishes 13 clinical subtypes associated with variants in [...] Read more.

Ehlers-Danlos syndrome (EDS) is a group of heterogeneous, rare diseases affecting the connective tissues. The main clinical signs of EDS are skin hyperextensibility, joint hypermobility, and skin fragility. Currently, the classification of EDS in humans distinguishes 13 clinical subtypes associated with variants in 20 different genes, reflecting the heterogeneity of this set of diseases. At present, variants in three of these genes have also been identified in dogs affected by EDS. The purpose of this study was to characterize the clinical and histopathological phenotype of an EDS-affected Chihuahua and to identify the causative genetic variant for the disease. The clinical examination suggested a diagnosis of classical EDS. Skin histopathology revealed an abnormally thin dermis, which is compatible with classical EDS. Whole-genome sequencing identified a heterozygous de novo 27 bp deletion in the COL5A2 gene, COL5A2:c.3388_3414del. The in-frame deletion is predicted to remove 9 amino acids in the triple-helical region of COL5A2. The molecular analysis and identification of a likely pathogenic variant in COL5A2 confirmed the subtype as a form of classical EDS. This is the first report of a COL5A2-related EDS in a dog. Full article

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

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12 pages, 4188 KiB

Open AccessArticle

Complete Chloroplast Genome Sequence of Triosteum sinuatum, Insights into Comparative Chloroplast Genomics, Divergence Time Estimation and Phylogenetic Relationships among Dipsacales

by HaiRui Liu, WenHui Liu, Israr Ahmad, QingMeng Xiao, XuMin Li, DeJun Zhang, Jie Fang, GuoFan Zhang, Bin Xu, QingBo Gao and ShiLong Chen

Genes 2022, 13(5), 933; https://doi.org/10.3390/genes13050933 - 23 May 2022

Cited by 2 | Viewed by 2101

Abstract

Triosteum himalayanum, Triosteum pinnatifidum (Triosteum L., Caprifoliaceae, Dipsacales) are widely distributed in China while Triosteum sinuatum mainly occurrs in northeast China. Few reports have been determined on the genus Triosteum. In the present research, we sequenced 2 chloroplast genomes of [...] Read more.

Triosteum himalayanum, Triosteum pinnatifidum (Triosteum L., Caprifoliaceae, Dipsacales) are widely distributed in China while Triosteum sinuatum mainly occurrs in northeast China. Few reports have been determined on the genus Triosteum. In the present research, we sequenced 2 chloroplast genomes of Triosteum and analyzed 18 chloroplast genomes, trying to explore the sequence variations and phylogeny of genus Triosteum in the order Dipsacales. The chloroplast genomes of the genus Triosteum ranged from 154,579 bp to 157,178 bp, consisting of 132 genes (86 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes). Comparative analyses and phylogenetic analysis supported the division of Dipsacales into two clades, Adoxaceae and six other families. Among the six families, a clade of Valerianaceae+Dipsacaceae was recovered as a sister to a clade of Morinaceae+Linnaeaceae. A closer relationship of T. himalayanum and T. pinnatifidum among three species was revealed. Our research supported that Loniceraferdinandi and Triosteum was closely related. Zabelia had a closer relationship with Linnaea borealis and Dipelta than Morinaceae. The divergence between T. sinuatum and two other species in Triosteum was dated to 13.4 mya. Full article

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

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16 pages, 2956 KiB

Open AccessArticle

In Silico Analysis of Seven PCR Markers Developed from the CHD1, NIPBL and SPIN Genes Followed by Laboratory Testing Shows How to Reliably Determine the Sex of Musophagiformes Species

by Aleksandra Kroczak, Heliodor Wierzbicki and Adam Dawid Urantówka

Genes 2022, 13(5), 932; https://doi.org/10.3390/genes13050932 - 23 May 2022

Cited by 1 | Viewed by 2084

Abstract

Sex determination in birds, due to the very common lack of sexual dimorphism, is challenging. Therefore, molecular sexing is often the only reliable way to differentiate between the sexes. However, for many bird species, very few genetic markers are available to accurately, quickly, [...] Read more.

Sex determination in birds, due to the very common lack of sexual dimorphism, is challenging. Therefore, molecular sexing is often the only reliable way to differentiate between the sexes. However, for many bird species, very few genetic markers are available to accurately, quickly, and cost-effectively type sex. Therefore, in our study, using 14 species belonging to the order Musophagiformes, we tested the usefulness of seven PCR markers (three of which have never been used to determine the sex of turacos), developed based on the CHD1, NIPBL, and SPIN genes, to validate existing and develop new strategies/methods of sex determination. After in silico analysis, for which we used the three turaco nuclear genomes available in GenBank, the suitability of the seven selected markers for sexing turacos was tested in the laboratory. It turned out that the best of the markers tested was the 17th intron in the NIPBL gene (not previously tested in turacos), allowing reliable sex determination in 13 of the 14 species tested. For the one species not sexed by this marker, the 9th intron in the CHD1 gene proved to be effective. The remaining markers were of little (4 markers developed based on the CHD1 gene) or no use (marker developed based on the SPIN gene). Full article

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

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16 pages, 3184 KiB

Open AccessArticle

The Chloroplast Genome of Wild Saposhnikovia divaricata: Genomic Features, Comparative Analysis, and Phylogenetic Relationships

by Shanyong Yi, Haibo Lu, Wei Wang, Guanglin Wang, Tao Xu, Mingzhi Li, Fangli Gu, Cunwu Chen, Bangxing Han and Dong Liu

Genes 2022, 13(5), 931; https://doi.org/10.3390/genes13050931 - 23 May 2022

Cited by 4 | Viewed by 1804

Abstract

Saposhnikovia divaricata, a well-known Chinese medicinal herb, is the sole species under the genus Saposhnikovia of the Apiaceae subfamily Apioideae Drude. However, information regarding its genetic diversity and evolution is still limited. In this study, the first complete chloroplast genome (cpDNA) of [...] Read more.

Saposhnikovia divaricata, a well-known Chinese medicinal herb, is the sole species under the genus Saposhnikovia of the Apiaceae subfamily Apioideae Drude. However, information regarding its genetic diversity and evolution is still limited. In this study, the first complete chloroplast genome (cpDNA) of wild S. divaricata was generated using de novo sequencing technology. Similar to the characteristics of Ledebouriella seseloides, the 147,834 bp-long S. divaricata cpDNA contained a large single copy, a small single copy, and two inverted repeat regions. A total of 85 protein-coding, 8 ribosomal RNA, and 36 transfer RNA genes were identified. Compared with five other species, the non-coding regions in the S. divaricata cpDNA exhibited greater variation than the coding regions. Several repeat sequences were also discovered, namely, 33 forward, 14 reverse, 3 complement, and 49 microsatellite repeats. Furthermore, phylogenetic analysis using 47 cpDNA sequences of Apioideae members revealed that L. seseloides and S. divaricata clustered together with a 100% bootstrap value, thereby supporting the validity of renaming L. seseloides to S. divaricata at the genomic level. Notably, S. divaricata was most closely related to Libanotis buchtormensis, which contradicts previous reports. Therefore, these findings provide a valuable foundation for future studies on the genetic diversity and evolution of S. divaricata. Full article

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

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13 pages, 1689 KiB

Open AccessEditor’s ChoiceArticle

Gut Microbiota as a Potential Predictive Biomarker in Relapsing-Remitting Multiple Sclerosis

by Vicente Navarro-López, María Ángeles Méndez-Miralles, Rosa Vela-Yebra, Ana Fríes-Ramos, Pedro Sánchez-Pellicer, Beatriz Ruzafa-Costas, Eva Núñez-Delegido, Humberto Gómez-Gómez, Sara Chumillas-Lidón, Jose A. Picó-Monllor and Laura Navarro-Moratalla

Genes 2022, 13(5), 930; https://doi.org/10.3390/genes13050930 - 23 May 2022

Cited by 11 | Viewed by 2832

Abstract

Background: The influence of the microbiome on neurological diseases has been studied for years. Recent findings have shown a different composition of gut microbiota detected in patients with multiple sclerosis (MS). The role of this dysbiosis is still unknown. Objective: We analyzed the [...] Read more.

Background: The influence of the microbiome on neurological diseases has been studied for years. Recent findings have shown a different composition of gut microbiota detected in patients with multiple sclerosis (MS). The role of this dysbiosis is still unknown. Objective: We analyzed the gut microbiota of 15 patients with active relapsing-remitting multiple sclerosis (RRMS), comparing with diet-matched healthy controls. Method: To determine the composition of the gut microbiota, we performed high-throughput sequencing of the 16S ribosomal RNA gene. The specific amplified sequences were in the V3 and V4 regions of the 16S ribosomal RNA gene. Results: The gut microbiota of RRMS patients differed from healthy controls in the levels of the Lachnospiraceae, Ezakiella, Ruminococcaceae, Hungatella, Roseburia, Clostridium, Shuttleworthia, Poephyromonas, and Bilophila genera. All these genera were included in a logistic regression analysis to determine the sensitivity and the specificity of the test. Finally, the ROC (receiver operating characteristic) and AUC with a 95% CI were calculated and best-matched for Ezakiella (AUC of 75.0 and CI from 60.6 to 89.4) and Bilophila (AUC of 70.2 and CI from 50.1 to 90.4). Conclusions: There is a dysbiosis in the gut microbiota of RRMS patients. An analysis of the components of the microbiota suggests the role of some genera as a predictive factor of RRMS prognosis and diagnosis. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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13 pages, 1314 KiB

Open AccessArticle

Tissue-Specific Variations in Transcription Factors Elucidate Complex Immune System Regulation

by Hengwei Lu, Yi-Ching Tang and Assaf Gottlieb

Genes 2022, 13(5), 929; https://doi.org/10.3390/genes13050929 - 23 May 2022

Viewed by 2340

Abstract

Gene expression plays a key role in health and disease. Estimating the genetic components underlying gene expression can thus help understand disease etiology. Polygenic models termed “transcriptome imputation” are used to estimate the genetic component of gene expression, but these models typically consider [...] Read more.

Gene expression plays a key role in health and disease. Estimating the genetic components underlying gene expression can thus help understand disease etiology. Polygenic models termed “transcriptome imputation” are used to estimate the genetic component of gene expression, but these models typically consider only the cis regions of the gene. However, these cis-based models miss large variability in expression for multiple genes. Transcription factors (TFs) that regulate gene expression are natural candidates for looking for additional sources of the missing variability. We developed a hypothesis-driven approach to identify second-tier regulation by variability in TFs. Our approach tested two models representing possible mechanisms by which variations in TFs can affect gene expression: variability in the expression of the TF and genetic variants within the TF that may affect the binding affinity of the TF to the TF-binding site. We tested our TF models in whole blood and skeletal muscle tissues and identified TF variability that can partially explain missing gene expression for 1035 genes, 76% of which explains more than the cis-based models. While the discovered regulation patterns were tissue-specific, they were both enriched for immune system functionality, elucidating complex regulation patterns. Our hypothesis-driven approach is useful for identifying tissue-specific genetic regulation patterns involving variations in TF expression or binding. Full article

(This article belongs to the Special Issue DNA and RNA Epigenetics and Transcriptomics Research)

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9 pages, 648 KiB

Open AccessArticle

Major Histocompatibility Complex (MHC) Diversity of the Reintroduction Populations of Endangered Przewalski’s Horse

by Yongqing Tang, Gang Liu, Shasha Zhao, Kai Li, Dong Zhang, Shuqiang Liu and Defu Hu

Genes 2022, 13(5), 928; https://doi.org/10.3390/genes13050928 - 23 May 2022

Cited by 3 | Viewed by 1885

Abstract

Major histocompatibility complex (MHC) genes are the most polymorphic in vertebrates and the high variability in many MHC genes is thought to play a crucial role in pathogen recognition. The MHC class II locus DQA polymorphism was analyzed in the endangered Przewalski’s horse, [...] Read more.

Major histocompatibility complex (MHC) genes are the most polymorphic in vertebrates and the high variability in many MHC genes is thought to play a crucial role in pathogen recognition. The MHC class II locus DQA polymorphism was analyzed in the endangered Przewalski’s horse, Equus przewalskii, a species that has been extinct in the wild and all the current living individuals descend from 12 founders. We used the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) to detect the polymorphism within the MHC DQA in 31 Przewalski’s horses from two reintroduced populations. Consequently, only seven alleles were identified, with only four presenting in each population. In comparison with other mammals, the Przewalski’s horse demonstrated less MHC variation. The nucleotide genetic distance of the seven ELA-DQA alleles was between 0.012 and 0.161. The Poisson corrected amino acid genetic distance of the founded alleles was 0.01–0.334. The allele and genotype frequencies of both reintroduced populations of Przewalski’s horse deviated from the Hardy–Weinberg equilibrium. Specific MHC DQA alleles may have been lost during the extreme bottleneck event that this species underwent throughout history. We suggest the necessity to detect the genetic background of individuals prior to performing the reintroduction project. Full article

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

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11 pages, 814 KiB

Open AccessArticle

Description of Two New Cases of AQP1 Related Pulmonary Arterial Hypertension and Review of the Literature

by Natalia Gallego-Zazo, Alejandro Cruz-Utrilla, María Jesús del Cerro, Nuria Ochoa Parra, Julián Nevado Blanco, Pedro Arias, Pablo Lapunzina, Pilar Escribano-Subias and Jair Tenorio-Castaño

Genes 2022, 13(5), 927; https://doi.org/10.3390/genes13050927 - 22 May 2022

Cited by 3 | Viewed by 2227

Abstract

Pulmonary arterial hypertension (PAH) is a severe clinical condition characterized by an increase in mean pulmonary artery pressure, which leads to a right ventricular hypertrophy and potentially heart failure and death. In the last several years, many genes have been associated with PAH, [...] Read more.

Pulmonary arterial hypertension (PAH) is a severe clinical condition characterized by an increase in mean pulmonary artery pressure, which leads to a right ventricular hypertrophy and potentially heart failure and death. In the last several years, many genes have been associated with PAH, particularly in idiopathic and heritable forms but also in associated forms. Here we described the identification of two unrelated families in which the AQP1 variant was found from a cohort of 300 patients. The variants were identified by whole exome sequencing (WES). In the first family, the variant was detected in three affected members from a hereditary PAH, and in the second family the proband had PAH associated with scleroderma. In addition, we have reviewed all cases published in the literature thus far of patients with PAH and AQP1 variants. Functional studies have led to some contradictory conclusions, and the evidence of the relationship of AQP1 and PAH is still limited. However, we describe two further families with PAH and variants in AQP1, expanding both the number of cases and the clinically associated phenotype. We provide further evidence of the association of AQP1 and the development of hereditary and associated forms of PAH. Full article

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

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16 pages, 767 KiB

Open AccessReview

Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods

by Paolo Abondio, Elisabetta Cilli and Donata Luiselli

Genes 2022, 13(5), 926; https://doi.org/10.3390/genes13050926 - 22 May 2022

Cited by 6 | Viewed by 3784

Abstract

Signatures of positive selection in the genome are a characteristic mark of adaptation that can reveal an ongoing, recent, or ancient response to environmental change throughout the evolution of a population. New sources of food, climate conditions, and exposure to pathogens are only [...] Read more.

Signatures of positive selection in the genome are a characteristic mark of adaptation that can reveal an ongoing, recent, or ancient response to environmental change throughout the evolution of a population. New sources of food, climate conditions, and exposure to pathogens are only some of the possible sources of selective pressure, and the rise of advantageous genetic variants is a crucial determinant of survival and reproduction. In this context, the ability to detect these signatures of selection may pinpoint genetic variants that are responsible for a significant change in gene regulation, gene expression, or protein synthesis, structure, and function. This review focuses on statistical methods that take advantage of linkage disequilibrium and haplotype determination to reveal signatures of positive selection in whole-genome sequencing data, showing that they emerge from different descriptions of the same underlying event. Moreover, considerations are provided around the application of these statistics to different species, their suitability for ancient DNA, and the usefulness of discovering variants under selection for biomedicine and public health in an evolutionary medicine framework. Full article

(This article belongs to the Special Issue Feature Papers in Technologies and Resources for Genetics)

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12 pages, 3201 KiB

Open AccessArticle

Clinical Phenotypes of CDHR1-Associated Retinal Dystrophies

by Volha V. Malechka, Catherine A. Cukras, Emily Y. Chew, Yuri V. Sergeev, Delphine Blain, Brett G. Jeffrey, Ehsan Ullah, Robert B. Hufnagel, Brian P. Brooks, Laryssa A. Huryn and Wadih M. Zein

Genes 2022, 13(5), 925; https://doi.org/10.3390/genes13050925 - 22 May 2022

Cited by 3 | Viewed by 2080

Abstract

The retinal dystrophy phenotype associated with CDHR1 retinopathy is clinically heterogenous. In this study, we describe the clinical and molecular findings of a retinal dystrophy cohort (10 patients) attributed to autosomal recessive CDHR1 and report novel variants in populations not previously identified with [...] Read more.

The retinal dystrophy phenotype associated with CDHR1 retinopathy is clinically heterogenous. In this study, we describe the clinical and molecular findings of a retinal dystrophy cohort (10 patients) attributed to autosomal recessive CDHR1 and report novel variants in populations not previously identified with CDHR1-related retinopathy. Seven patients had evaluations covering at least a three-year period. The mean age of individuals at first symptoms was 36 ± 8.5 years (range 5–45 years). Visual acuity at the last visit ranged from 20/20 to 20/2000 (mean LogMAR 0.8 or 20/125). Three clinical subgroups were identified: rod–cone dystrophy (RCD), cone–rod dystrophy (CRD), and maculopathy. Extinguished scotopic electroretinography responses were noted in the RCD patients. Macular involvement was noted in all patients and documented on color fundus photography, fundus autofluorescence, and optical coherence tomography. Notable asymmetry of the degree of macular atrophy was present in two patients. The possible association between CDHR1 variants and clinical findings was predicted using molecular modeling. Full article

(This article belongs to the Special Issue Genetics of Retinal and Vitreoretinal Diseases)

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10 pages, 257 KiB

Open AccessProtocol

Benefits and Harms of Treatment and Preventive Interventions for Hereditary Angioedema: Protocol for a Systematic Review and Network Meta-Analysis of Randomized Controlled Trials

by Mati Chuamanochan, Sutthinee Phuprasertsak, Puncharas Weesasubpong, Chidchanok Ruengorn, Chabaphai Phosuya, Ratanaporn Awiphan, Brian Hutton, Kednapa Thavorn, Jonathan A. Bernstein and Surapon Nochaiwong

Genes 2022, 13(5), 924; https://doi.org/10.3390/genes13050924 - 22 May 2022

Cited by 1 | Viewed by 1983

Abstract

Background: Hereditary angioedema (HAE) is a rare genetic disease that can lead to potentially life-threatening airway attacks. Although novel therapies for HAE treatment have become available over the past decades, a comparison of all available treatments has not yet been conducted. As such, [...] Read more.

Background: Hereditary angioedema (HAE) is a rare genetic disease that can lead to potentially life-threatening airway attacks. Although novel therapies for HAE treatment have become available over the past decades, a comparison of all available treatments has not yet been conducted. As such, we will perform a systematic review and network meta-analysis to identify the best evidence-based treatments for the management of acute attacks and prophylaxis of HAE. Methods: This study will include both parallel and crossover randomized controlled trials that have investigated prevention or treatment strategies for HAE attacks. We will search electronic databases, including Medline, Embase, PubMed, Cochrane Library, Scopus, and CINAHL, from inception with no language restrictions. Potential trials will be supplemented through a gray literature search. The process of study screening, selection, data extraction, risk-of-bias assessment, certainty assessment and classification of treatments will be performed independently by a pair of reviewers. Any discrepancy will be addressed through team discussion. A two-step approach of pairwise and network meta-analysis will be performed. The summarized effect estimates of direct and indirect treatment comparisons will be pooled using DerSimonion–Laird random-effects models. The incoherence assumption, in terms of the consistency of direct and indirect effects, will be assessed. An evidence-based synthesis will be performed, based on the magnitudes of effect size, evidence certainty, and ranking of treatment effects, with respect to treatment benefits and harms. Discussion: This systematic review and network meta-analysis will summarize evidence-based conclusions with respect to the ratio of benefits and harms arising from interventions for the treatment of acute attacks and prophylaxis of HAE. Evidence from this network estimate could promote the rational use of interventions among people living with HAE in clinical practice settings. PROSPERO registration number: CRD42021251367. Full article

(This article belongs to the Special Issue Autoimmunity and Genetic Syndromes)

12 pages, 619 KiB

Open AccessArticle

A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data

by Dao Minh Hai, Duong Thuy Yen, Pham Thanh Liem, Bui Minh Tam, Do Thi Thanh Huong, Bui Thi Bich Hang, Dang Quang Hieu, Mutien-Marie Garigliany, Wouter Coppieters, Patrick Kestemont, Nguyen Thanh Phuong and Frédéric Farnir

Genes 2022, 13(5), 923; https://doi.org/10.3390/genes13050923 - 22 May 2022

Cited by 1 | Viewed by 3037

Abstract

The HiFi sequencing technology yields highly accurate long-read data with accuracies greater than 99.9% that can be used to improve results for complex applications such as genome assembly. Our study presents a high-quality chromosome-scale genome assembly of striped catfish (Pangasianodon hypophthalmus), [...] Read more.

The HiFi sequencing technology yields highly accurate long-read data with accuracies greater than 99.9% that can be used to improve results for complex applications such as genome assembly. Our study presents a high-quality chromosome-scale genome assembly of striped catfish (Pangasianodon hypophthalmus), a commercially important species cultured mainly in Vietnam, integrating HiFi reads and Hi-C data. A 788.4 Mb genome containing 381 scaffolds with an N50 length of 21.8 Mb has been obtained from HiFi reads. These scaffolds have been further ordered and clustered into 30 chromosome groups, ranging from 1.4 to 57.6 Mb, based on Hi-C data. The present updated assembly has a contig N50 of 14.7 Mb, representing a 245-fold and 4.2-fold improvement over the previous Illumina and Illumina-Nanopore-Hi-C based version, respectively. In addition, the proportion of repeat elements and BUSCO genes identified in our genome is remarkably higher than in the two previously released striped catfish genomes. These results highlight the power of using HiFi reads to assemble the highly repetitive regions and to improve the quality of genome assembly. The updated, high-quality genome assembled in this work will provide a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of striped catfish. Full article

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

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19 pages, 2036 KiB

Open AccessArticle

Application of Dual Metabarcoding Platforms for the Meso- and Macrozooplankton Taxa in the Ross Sea

by Ji-Hyun Lee, Hyoung Sul La, Jeong-Hoon Kim, Wuju Son, Hyun Park, Young-Mog Kim and Hyun-Woo Kim

Genes 2022, 13(5), 922; https://doi.org/10.3390/genes13050922 - 21 May 2022

Cited by 1 | Viewed by 1788

Abstract

Meso- and macrozooplankton play crucial roles in the trophic web and the biological carbon pump in the ocean by transferring energy from lower to higher trophic levels and vertically exporting carbon from the surface to the deep ocean and seabed. In this study, [...] Read more.

Meso- and macrozooplankton play crucial roles in the trophic web and the biological carbon pump in the ocean by transferring energy from lower to higher trophic levels and vertically exporting carbon from the surface to the deep ocean and seabed. In this study, zooplankton community structures in the Ross Sea, Antarctica, were analyzed using metabarcoding methods. Both regular barcode (RB) (using a PacBio Sequel system) and mini barcode (MB) (using the Illumina MiSeq platform) methods were utilized. As the result of a combination of the two bioinformatic pipelines used in the RB, 55 reliable haplotypes were obtained from the pooled zooplankton net samples, whereas 183 amplicon sequence variants (ASVs) were isolated from the MB metabarcoding analyses of 14 individual stations. Among these, 39 (70.9%) and 125 (90.6%) showed higher than 99% sequence identity to the database, indicating that there were sufficient reference sequences to employ metabarcoding analysis—except for several taxa, including small-sized copepods, cnidarians, and pneumodermatids. A high degree of shared taxa showed that both metabarcoding analyses were feasible for use in the analysis of zooplankton assemblages in the Ross Sea. However, RB would be more useful for the construction of a reference database due to its relatively high cost, whereas MB would be more economic for ecological surveys due to its relatively low cost (albeit, only if reference sequences were well documented using RB). Zooplankton assemblages were highly diverse in each sample site, presumably due to the narrow covered volumes of the vertical net-towed samples from polynyas in the Ross Sea. As metabarcoding data accumulate, we will gain better insights into zooplankton communities and their ecological implications in the Ross Sea. Full article

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

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10 pages, 5309 KiB

Open AccessArticle

Identification of the CKM Gene as a Potential Muscle-Specific Safe Harbor Locus in Pig Genome

by Youcai Xiong, Rongzhi Zhuang, Guangxing Zhao, Yanwen Liu, Yinyu Su, Wei Wang, Xiaoning Xi, Yanyu Yang, Xiaosong Han, Shengsong Xie, Heng Wang, Xinyun Li, Bo Zuo, Shuhong Zhao, Zheng Feng and Jinxue Ruan

Genes 2022, 13(5), 921; https://doi.org/10.3390/genes13050921 - 21 May 2022

Cited by 2 | Viewed by 2077

Abstract

Genetically modified pigs have shown considerable application potential in the fields of life science research and livestock breeding. Nevertheless, a barrier impedes the production of genetically modified pigs. There are too few safe harbor loci for the insertion of foreign genes into the [...] Read more.

Genetically modified pigs have shown considerable application potential in the fields of life science research and livestock breeding. Nevertheless, a barrier impedes the production of genetically modified pigs. There are too few safe harbor loci for the insertion of foreign genes into the pig genome. Only a few loci (pRosa26, pH11 and Pifs501) have been successfully identified to achieve the ectopic expression of foreign genes and produce gene-edited pigs. Here, we use CRISPR/Cas9-mediated homologous directed repair (HDR) to accurately knock the exogenous gene-of-interest fragments into an endogenous CKM gene in the porcine satellite cells. After porcine satellite cells are induced to differentiate, the CKM gene promoter simultaneously initiates the expression of the CKM gene and the exogenous gene. We infer preliminarily that the CKM gene can be identified as a potential muscle-specific safe harbor locus in pigs for the integration of exogenous gene-of-interest fragments. Full article

(This article belongs to the Special Issue Application of New Gene Editing Techniques in Pig Breeding)

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17 pages, 1338 KiB

Open AccessArticle

A Study of the Genomic Variations Associated with Autistic Spectrum Disorders in a Russian Cohort of Patients Using Whole-Exome Sequencing

by Ekaterina A. Gibitova, Pavel V. Dobrynin, Ekaterina A. Pomerantseva, Elizaveta V. Musatova, Anna Kostareva, Igor Evsyukov, Sergey Y. Rychkov, Olga V. Zhukova, Oxana Y. Naumova and Elena L. Grigorenko

Genes 2022, 13(5), 920; https://doi.org/10.3390/genes13050920 - 20 May 2022

Cited by 3 | Viewed by 2342

Abstract

This study provides new data on the whole-exome sequencing of a cohort of children with autistic spectrum disorders (ASD) from an underexplored Russian population. Using both a cross-sectional approach involving a control cohort of the same ancestry and an annotation-based approach involving relevant [...] Read more.

This study provides new data on the whole-exome sequencing of a cohort of children with autistic spectrum disorders (ASD) from an underexplored Russian population. Using both a cross-sectional approach involving a control cohort of the same ancestry and an annotation-based approach involving relevant public databases, we explored exonic single nucleotide variants and copy-number variation potentially involved in the manifestation of ASD. The study results reveal new potential ASD candidate-variants found in the studied Russian cohort and show a high prevalence of common ASD-associated genomic variants, especially those in the genes known to be associated with the manifestation of intellectual disabilities. Our screening of an ASD cohort from a previously understudied population allowed us to flag at least a few novel genes (IGLJ2, FAM21A, OR11H12, HIP1, PRAMEF10, and ZNF717) regarding their potential involvement in ASD. Full article

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

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16 pages, 1671 KiB

Open AccessArticle

Annotation and Analysis of 3902 Odorant Receptor Protein Sequences from 21 Insect Species Provide Insights into the Evolution of Odorant Receptor Gene Families in Solitary and Social Insects

by Pablo Mier, Jean-Fred Fontaine, Marah Stoldt, Romain Libbrecht, Carlotta Martelli, Susanne Foitzik and Miguel A. Andrade-Navarro

Genes 2022, 13(5), 919; https://doi.org/10.3390/genes13050919 - 20 May 2022

Cited by 3 | Viewed by 2573

Abstract

The gene family of insect olfactory receptors (ORs) has expanded greatly over the course of evolution. ORs enable insects to detect volatile chemicals and therefore play an important role in social interactions, enemy and prey recognition, and foraging. The sequences of several thousand [...] Read more.

The gene family of insect olfactory receptors (ORs) has expanded greatly over the course of evolution. ORs enable insects to detect volatile chemicals and therefore play an important role in social interactions, enemy and prey recognition, and foraging. The sequences of several thousand ORs are known, but their specific function or their ligands have only been identified for very few of them. To advance the functional characterization of ORs, we have assembled, curated, and aligned the sequences of 3902 ORs from 21 insect species, which we provide as an annotated online resource. Using functionally characterized proteins from the fly Drosophila melanogaster, the mosquito Anopheles gambiae and the ant Harpegnathos saltator, we identified amino acid positions that best predict response to ligands. We examined the conservation of these predicted relevant residues in all OR subfamilies; the results showed that the subfamilies that expanded strongly in social insects had a high degree of conservation in their binding sites. This suggests that the ORs of social insect families are typically finely tuned and exhibit sensitivity to very similar odorants. Our novel approach provides a powerful tool to exploit functional information from a limited number of genes to study the functional evolution of large gene families. Full article

(This article belongs to the Special Issue Molecular Evolution and Functional Bioinformatics of Arthropods)

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14 pages, 3193 KiB

Open AccessArticle

Expression Pattern of nos1 in the Developing Nervous System of Ray-Finned Fish

by Giovanni Annona, José Luis Ferran, Pasquale De Luca, Ivan Conte, John H. Postlethwait and Salvatore D’Aniello

Genes 2022, 13(5), 918; https://doi.org/10.3390/genes13050918 - 20 May 2022

Cited by 4 | Viewed by 1789

Abstract

Fish have colonized nearly all aquatic niches, making them an invaluable resource to understand vertebrate adaptation and gene family evolution, including the evolution of complex neural networks and modulatory neurotransmitter pathways. Among ancient regulatory molecules, the gaseous messenger nitric oxide (NO) is involved [...] Read more.

Fish have colonized nearly all aquatic niches, making them an invaluable resource to understand vertebrate adaptation and gene family evolution, including the evolution of complex neural networks and modulatory neurotransmitter pathways. Among ancient regulatory molecules, the gaseous messenger nitric oxide (NO) is involved in a wide range of biological processes. Because of its short half-life, the modulatory capability of NO is strictly related to the local activity of nitric oxide synthases (Nos), enzymes that synthesize NO from L-arginine, making the localization of Nos mRNAs a reliable indirect proxy for the location of NO action domains, targets, and effectors. Within the diversified actinopterygian nos paralogs, nos1 (alias nnos) is ubiquitously present as a single copy gene across the gnathostome lineage, making it an ideal candidate for comparative studies. To investigate variations in the NO system across ray-finned fish phylogeny, we compared nos1 expression patterns during the development of two well-established experimental teleosts (zebrafish and medaka) with an early branching holostean (spotted gar), an important evolutionary bridge between teleosts and tetrapods. Data reported here highlight both conserved expression domains and species-specific nos1 territories, confirming the ancestry of this signaling system and expanding the number of biological processes implicated in NO activities. Full article

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

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26 pages, 3468 KiB

Open AccessArticle

Characterization, Selection, and Trans-Species Polymorphism in the MHC Class II of Heermann’s Gull (Charadriiformes)

by Misael Daniel Mancilla-Morales, Enriqueta Velarde, Araceli Contreras-Rodríguez, Zulema Gómez-Lunar, Jesús A. Rosas-Rodríguez, Joseph Heras, José G. Soñanez-Organis and Enrico A. Ruiz

Genes 2022, 13(5), 917; https://doi.org/10.3390/genes13050917 - 20 May 2022

Viewed by 2513

Abstract

The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull [...] Read more.

The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull MHC class II (MHCIIB) and compare these loci with other Charadriiformes. Fifty-nine MHCIIB haplotypes were recovered from sixty-eight Heermann’s Gulls by cloning, of them, twelve were identified as putative true alleles, forty-five as unique alleles, and two as pseudogenes. Intra and interspecific relationships indicated at least two loci in Heermann’s Gull MHCIIB and trans-species polymorphism among Charadriiformes (coinciding with the documented evidence of two ancient avian MHCIIB lineages, except in the Charadriidae family). Additionally, sites under diversifying selection revealed a better match with peptide-binding sites inferred in birds than those described in humans. Despite the negative anthropogenic activity reported on Isla Rasa, Heermann’s Gull showed MHCIIB variability consistent with population expansion, possibly due to a sudden growth following conservation efforts. Duplication must play an essential role in shaping Charadriiformes MHCIIB variability, buffering selective pressures through balancing selection. These findings suggest that MHC copy number and protected islands can contribute to seabird conservation. Full article

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

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14 pages, 2555 KiB

Open AccessArticle

Identification of Pathogenicity Loci in Magnaporthe oryzae Using GWAS with Neck Blast Phenotypic Data

by Nyein Nyein Aye Myint, Siripar Korinsak, Cattleya Chutteang, Kularb Laosatit, Burin Thunnom, Theerayut Toojinda and Jonaliza L. Siangliw

Genes 2022, 13(5), 916; https://doi.org/10.3390/genes13050916 - 20 May 2022

Viewed by 2071

Abstract

Magnaporthae oryzae (M. oryzae) is the most destructive disease of rice worldwide. In this study, one hundred and two isolates of M. oryzae were collected from rice (Oryzae sativa L.) from 2001 to 2017, and six rice varieties with resistance genes [...] Read more.

Magnaporthae oryzae (M. oryzae) is the most destructive disease of rice worldwide. In this study, one hundred and two isolates of M. oryzae were collected from rice (Oryzae sativa L.) from 2001 to 2017, and six rice varieties with resistance genes Pizt, Pish, Pik, Pib, and Pi2 were used in a genome-wide association study to identify pathogenicity loci in M. oryzae. Genome-wide association analysis was performed using 5338 single nucleotide polymorphism (SNPs) and phenotypic data of neck blast screening by TASSEL software together with haplotype block and SNP effect analysis. Twenty-seven significant SNPs were identified on chromosomes 1, 2, 3, 4, 5, 6, and 7. Many predicted genes (820 genes) were found in the target regions of six rice varieties. Most of these genes are described as putative uncharacterized proteins, however, some genes were reported related to virulence in M. oryzae. Moreover, this study revealed that R genes, Pik, Pish, and Pi2, were broad-spectrum resistant against neck blast disease caused by Thai blast isolate. Haplotype analysis revealed that the combination of the favorable alleles causing reduced virulence of isolates against IRBLz5-CA carrying Pi2 gene contributes 69% of the phenotypic variation in pathogenicity. The target regions and information are useful to develop marker-specific genes to classify blast fungal isolates and select appropriate resistance genes for rice cultivation and improvement. Full article

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

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13 pages, 2144 KiB

Open AccessFeature PaperReview

Recent Advances in Understanding the Structures of Translesion Synthesis DNA Polymerases

by Justin A. Ling, Zach Frevert and M. Todd Washington

Genes 2022, 13(5), 915; https://doi.org/10.3390/genes13050915 - 20 May 2022

Cited by 3 | Viewed by 2037

Abstract

DNA damage in the template strand causes replication forks to stall because replicative DNA polymerases are unable to efficiently incorporate nucleotides opposite template DNA lesions. To overcome these replication blocks, cells are equipped with multiple translesion synthesis polymerases that have evolved specifically to [...] Read more.

DNA damage in the template strand causes replication forks to stall because replicative DNA polymerases are unable to efficiently incorporate nucleotides opposite template DNA lesions. To overcome these replication blocks, cells are equipped with multiple translesion synthesis polymerases that have evolved specifically to incorporate nucleotides opposite DNA lesions. Over the past two decades, X-ray crystallography has provided a wealth of information about the structures and mechanisms of translesion synthesis polymerases. This approach, however, has been limited to ground state structures of these polymerases bound to DNA and nucleotide substrates. Three recent methodological developments have extended our understanding of the structures and mechanisms of these polymerases. These include time-lapse X-ray crystallography, which allows one to identify novel reaction intermediates; full-ensemble hybrid methods, which allow one to examine the conformational flexibility of the intrinsically disordered regions of proteins; and cryo-electron microscopy, which allows one to determine the high-resolution structures of larger protein complexes. In this article, we will discuss how these three methodological developments have added to our understanding of the structures and mechanisms of translesion synthesis polymerases. Full article

(This article belongs to the Special Issue Mechanisms of Replication of Damaged DNA)

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9 pages, 2345 KiB

Open AccessArticle

Novel Gene Rearrangements in the Mitochondrial Genomes of Cynipoid Wasps (Hymenoptera: Cynipoidea)

by Xiaohan Shu, Zekai Li, Ruizhong Yuan, Pu Tang and Xuexin Chen

Genes 2022, 13(5), 914; https://doi.org/10.3390/genes13050914 - 20 May 2022

Cited by 4 | Viewed by 1704

Abstract

Cynipoidea is a medium-sized superfamily of Hymenoptera with diverse lifestyles. In this study, 16 mitochondrial genomes were newly sequenced, 11 of which were the first obtained mitochondrial genomes in the family Liopteridae and four subfamilies (Anacharitinae, Aspicerinae, Figitinae, and Parnipinae) of Figitidae. All [...] Read more.

Cynipoidea is a medium-sized superfamily of Hymenoptera with diverse lifestyles. In this study, 16 mitochondrial genomes were newly sequenced, 11 of which were the first obtained mitochondrial genomes in the family Liopteridae and four subfamilies (Anacharitinae, Aspicerinae, Figitinae, and Parnipinae) of Figitidae. All of the newly sequenced mitogenomes have unique rearrangement types within Cynipoidea, whereas some gene patterns are conserved in several groups. nad5-nad4-nad4L-nad6-cytb was remotely inverted and two rRNA genes were translocated to nad3 downstream in Ibaliidae and three subfamilies (Anacharitinae, Eucoilinae, and Parnipinae within Figitidae); two rRNA genes in Aspicerinae, Figitinae, and Liopteridae were remotely inverted to the cytb-nad1 junction; rrnL-rrnS was translocated to the cytb-nad1 junction in Cynipidae. Phylogenetic inference suggested that Figitidae was a polyphyletic group, while the Ibaliidae nested deep within Cynipoidea and was a sister-group to the Figitidae. These results will improve our understanding of the gene rearrangement of the mitogenomes and the phylogenetic relationships in the Cynipoidea. Full article

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

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16 pages, 3617 KiB

Open AccessArticle

RADseq Data Suggest Occasional Hybridization between Microcebus murinus and M. ravelobensis in Northwestern Madagascar

by Helena Teixeira, Tobias van Elst, Malcolm S. Ramsay, Romule Rakotondravony, Jordi Salmona, Anne D. Yoder and Ute Radespiel

Genes 2022, 13(5), 913; https://doi.org/10.3390/genes13050913 - 19 May 2022

Cited by 1 | Viewed by 2159 | Retraction

Abstract

The occurrence of natural hybridization has been reported in a wide range of organisms, including primates. The present study focuses on the endemic lemurs of Madagascar, primates for which only a few species occur in sympatry or parapatry with congeners, thereby creating limited [...] Read more.

The occurrence of natural hybridization has been reported in a wide range of organisms, including primates. The present study focuses on the endemic lemurs of Madagascar, primates for which only a few species occur in sympatry or parapatry with congeners, thereby creating limited opportunity for natural hybridization. This study examines RADseq data from 480 individuals to investigate whether the recent expansion of Microcebus murinus towards the northwest and subsequent secondary contact with Microcebus ravelobensis has resulted in the occurrence of hybridization between the two species. Admixture analysis identified one individual with 26% of nuclear admixture, which may correspond to an F2- or F3-hybrid. A composite-likelihood approach was subsequently used to test the fit of alternative phylogeographic scenarios to the genomic data and to date introgression. The simulations yielded support for low levels of gene flow (2Nm0 = 0.063) between the two species starting before the Last Glacial Maximum (between 54 and 142 kyr). Since M. murinus most likely colonized northwestern Madagascar during the Late Pleistocene, the rather recent secondary contact with M. ravelobensis has likely created the opportunity for occasional hybridization. Although reproductive isolation between these distantly related congeners is not complete, it is effective in maintaining species boundaries. Full article

(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)

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13 pages, 2491 KiB

Open AccessArticle

An Inexpensive CRISPR-Based Point-of-Care Test for the Identification of Meat Species and Meat Products

by Dagang Tao, Xiao Xiao, Xiaochen Lan, Bingrong Xu, Yuan Wang, Emmanuel Mulaya Khazalwa, Wenya Pan, Jinxue Ruan, Yu Jiang, Xiangdong Liu, Changchun Li, Ruizhen Ye, Xinyun Li, Jing Xu, Shuhong Zhao and Shengsong Xie

Genes 2022, 13(5), 912; https://doi.org/10.3390/genes13050912 - 19 May 2022

Cited by 8 | Viewed by 2409

Abstract

The growing demand for and supply of meat and meat products has led to a proportional increase in cases of meat adulteration. Adulterated meat poses serious economic and health consequences globally. Current laboratory methods for meat species identification require specialized equipment with limited [...] Read more.

The growing demand for and supply of meat and meat products has led to a proportional increase in cases of meat adulteration. Adulterated meat poses serious economic and health consequences globally. Current laboratory methods for meat species identification require specialized equipment with limited field applications. This study developed an inexpensive, point-of-care Loop-Mediated Isothermal Amplification (LAMP)-CRISPR/Cas12a colorimetric assay to detect meat species using a Texas Red-labelled single-strand (ssDNA) reporter. As low as 1.0 pg/µL of the porcine NADH4, the chicken NADH dehydrogenase subunit 2 (ND2) and the duck D-loop genes was detectable under white, blue and ultraviolet light. The test turnaround time from DNA extraction to visualization was approximately 40 min. The assay accurately detected pure and mixed-meat products in the laboratory (n = 15) and during a pilot point-of-care test (n = 8) in a food processing factory. The results are 100% reproducible using lateral flow detection strips and the real-time PCR detection instrument. This technology is fully deployable and usable in any standard room. Thus, our study demonstrates that this method is a straightforward, specific, sensitive, point-of-care test (POCT) adaptable to various outlets such as customs, quarantine units and meat import/export departments. Full article

(This article belongs to the Special Issue Application of New Gene Editing Techniques in Pig Breeding)

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11 pages, 1380 KiB

Open AccessArticle

Complete Mitochondrial Genome of Malenka flexura (Plecoptera: Nemouridae) and Phylogenetic Analysis

by Jinjun Cao, Xuan Guo, Caiyue Guo, Xuan Wang, Ying Wang and Fengming Yan

Genes 2022, 13(5), 911; https://doi.org/10.3390/genes13050911 - 19 May 2022

Cited by 5 | Viewed by 1505

Abstract

The genus-level relationships within the subfamily Amphinemurinae have been controversial, although attempts have been made based on morphology and limited molecular data. With the establishment of two new genera, the phylogenetic relationships within Amphinemurinae should be re-examined. In this study, the complete mitochondrial [...] Read more.

The genus-level relationships within the subfamily Amphinemurinae have been controversial, although attempts have been made based on morphology and limited molecular data. With the establishment of two new genera, the phylogenetic relationships within Amphinemurinae should be re-examined. In this study, the complete mitochondrial genome (mitogenome) of Malenka flexura of the genus Malenka was firstly sequenced and analyzed. The phylogeny of Amphinemurinae was also reconstructed using 13 proteincoding genes (PCGs) from previously published stoneflies. This mitogenome was 15,744 bp long and encoded the typical 37 genes, as well as a putative control region. The gene arrangement of M. flexura mitogenome is identical with the putative ancestral mitogenome in Drosophila yakuba. Most PCGs used standard ATN as start codons and TAA/TAG as termination codons. All tRNA genes exhibited the typical cloverleaf secondary structure, except for tRNA^Ser(AGN), whose dihydrouridine (DHU) arm was lacking. Some structural elements in the control region were founded, such as tandem repeat regions, stemloop structures, polyN stretch and microsatellite structure, etc. Phylogenetic analyses of sequenced Amphinemurinae mitogenomes unsupported the sister relationship of Amphinemura and Malenka. Finally, the phylogenetic analyses inferred a relationship within Amphinemurinae: Amphinemura + (Malenka + (Protonemura + (Indonemoura + (Sphaeronemoura + Mesonemoura)))). Full article

(This article belongs to the Special Issue Phylogeny and Genetic Diversity of Insects)

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10 pages, 2329 KiB

Open AccessEditor’s ChoiceReview

m¹A RNA Modification in Gene Expression Regulation

by Hao Jin, Chunxiao Huo, Tianhua Zhou and Shanshan Xie

Genes 2022, 13(5), 910; https://doi.org/10.3390/genes13050910 - 19 May 2022

Cited by 25 | Viewed by 3600

Abstract

N¹-methyladenosine (m¹A) is a prevalent and reversible post-transcriptional RNA modification that decorates tRNA, rRNA and mRNA. Recent studies based on technical advances in analytical chemistry and high-throughput sequencing methods have revealed the crucial roles of m¹A RNA [...] Read more.

N¹-methyladenosine (m¹A) is a prevalent and reversible post-transcriptional RNA modification that decorates tRNA, rRNA and mRNA. Recent studies based on technical advances in analytical chemistry and high-throughput sequencing methods have revealed the crucial roles of m¹A RNA modification in gene regulation and biological processes. In this review, we focus on progress in the study of m¹A methyltransferases, m¹A demethylases and m¹A-dependent RNA-binding proteins and highlight the biological mechanisms and functions of m¹A RNA modification, as well as its association with human disease. We also summarize the current understanding of detection approaches for m¹A RNA modification. Full article

(This article belongs to the Special Issue Regulation of Gene Expression: RNA Modification of Genes)

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17 pages, 1247 KiB

Open AccessArticle

Mutation in Hemagglutinin Antigenic Sites in Influenza A pH1N1 Viruses from 2015–2019 in the United States Mountain West, Europe, and the Northern Hemisphere

by Craig H. Decker, Naomi Rapier-Sharman and Brett E. Pickett

Genes 2022, 13(5), 909; https://doi.org/10.3390/genes13050909 - 19 May 2022

Cited by 1 | Viewed by 1948

Abstract

H1N1 influenza A virus is a respiratory pathogen that undergoes antigenic shift and antigenic drift to improve viral fitness. Tracking the evolutionary trends of H1N1 aids with the current detection and the future response to new viral strains as they emerge. Here, we [...] Read more.

H1N1 influenza A virus is a respiratory pathogen that undergoes antigenic shift and antigenic drift to improve viral fitness. Tracking the evolutionary trends of H1N1 aids with the current detection and the future response to new viral strains as they emerge. Here, we characterize antigenic drift events observed in the hemagglutinin (HA) sequence of the pandemic H1N1 lineage from 2015–2019. We observed the substitutions S200P, K147N, and P154S, together with other mutations in structural, functional, and/or epitope regions in 2015–2019 HA protein sequences from the Mountain West region of the United States, the larger United States, Europe, and other Northern Hemisphere countries. We reconstructed multiple phylogenetic trees to track the relationships and spread of these mutations and tested for evidence of selection pressure on HA. We found that the prevalence of amino acid substitutions at positions 147, 154, 159, 200, and 233 significantly changed throughout the studied geographical regions between 2015 and 2019. We also found evidence of coevolution among a subset of these amino acid substitutions. The results from this study could be relevant for future epidemiological tracking and vaccine prediction efforts. Similar analyses in the future could identify additional sequence changes that could affect the pathogenicity and/or infectivity of this virus in its human host. Full article

(This article belongs to the Special Issue Comparative Genomics of Human Pathogens)

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13 pages, 1256 KiB

Open AccessArticle

Novel Loss-of-Function Variants in CHD2 Cause Childhood-Onset Epileptic Encephalopathy in Chinese Patients

by Xu Wang, Di Cui, Changhong Ding, Chunhong Chen, Xiaohui Wang, Fang Fang, Hong Jin and Xiaotun Ren

Genes 2022, 13(5), 908; https://doi.org/10.3390/genes13050908 - 19 May 2022

Cited by 1 | Viewed by 2093

Abstract

Developmental and epileptic encephalopathy-94 (DEE94) is a severe form of epilepsy characterized by a broad spectrum of neurodevelopmental disorders. It is caused by pathogenic CHD2 variants. While only a few pathogenic CHD2 variants have been reported with detailed clinical phenotypes, most of which [...] Read more.

Developmental and epileptic encephalopathy-94 (DEE94) is a severe form of epilepsy characterized by a broad spectrum of neurodevelopmental disorders. It is caused by pathogenic CHD2 variants. While only a few pathogenic CHD2 variants have been reported with detailed clinical phenotypes, most of which lack molecular analysis. In this study, next-generation sequencing (NGS) was performed to identify likely pathogenic CHD2 variants in patients with epilepsy. Three likely pathogenic variants were finally identified in different patients. The seizure onset ages were from two years to six years. Patients 1 and 2 had developmental delays before epilepsy, while patient 3 had intellectual regression after the first seizure onset. The observed seizures were myoclonic, febrile, and generalized tonic-clonic, which had been controlled by different combinations of antiepileptic drugs. Two de novo (c.1809_1809+1delGGinsTT, p.? and c.3455+2_3455+3insTG, p.?) and one maternal (c.3783G>A, p.W1261*) variant were identified, which were all predicted to be pathogenic/likely pathogenic. Molecular analysis was performed in patient 1, and we detected aberrantly spliced products, proving the pathogenicity of this CHD2 variant. New cases with novel variants, along with a detailed clinical and molecular analysis, are important for a better understanding of CHD2-related epileptic encephalopathy. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Correlation: Gene-Disease Validation)

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13 pages, 339 KiB

Open AccessArticle

Deep Splicer: A CNN Model for Splice Site Prediction in Genetic Sequences

by Elisa Fernandez-Castillo, Liliana Ibeth Barbosa-Santillán, Luis Falcon-Morales and Juan Jaime Sánchez-Escobar

Genes 2022, 13(5), 907; https://doi.org/10.3390/genes13050907 - 19 May 2022

Cited by 6 | Viewed by 2596

Abstract

Many living organisms have DNA in their cells that is responsible for their biological features. DNA is an organic molecule of two complementary strands of four different nucleotides wound up in a double helix. These nucleotides are adenine (A), thymine (T), guanine (G), [...] Read more.

Many living organisms have DNA in their cells that is responsible for their biological features. DNA is an organic molecule of two complementary strands of four different nucleotides wound up in a double helix. These nucleotides are adenine (A), thymine (T), guanine (G), and cytosine (C). Genes are DNA sequences containing the information to synthesize proteins. The genes of higher eukaryotic organisms contain coding sequences, known as exons and non-coding sequences, known as introns, which are removed on splice sites after the DNA is transcribed into RNA. Genome annotation is the process of identifying the location of coding regions and determining their function. This process is fundamental for understanding gene structure; however, it is time-consuming and expensive when done by biochemical methods. With technological advances, splice site detection can be done computationally. Although various software tools have been developed to predict splice sites, they need to improve accuracy and reduce false-positive rates. The main goal of this research was to generate Deep Splicer, a deep learning model to identify splice sites in the genomes of humans and other species. This model has good performance metrics and a lower false-positive rate than the currently existing tools. Deep Splicer achieved an accuracy between 93.55% and 99.66% on the genetic sequences of different organisms, while Splice2Deep, another splice site detection tool, had an accuracy between 90.52% and 98.08%. Splice2Deep surpassed Deep Splicer on the accuracy obtained after evaluating C. elegans genomic sequences (97.88% vs. 93.62%) and A. thaliana (95.40% vs. 94.93%); however, Deep Splicer’s accuracy was better for H. sapiens (98.94% vs. 97.15%) and D. melanogaster (97.14% vs. 92.30%). The rate of false positives was 0.11% for human genetic sequences and 0.25% for other species’ genetic sequences. Another splice prediction tool, Splice Finder, had between 1% and 3% of false positives for human sequences, while other species’ sequences had around 4% and 10%. Full article

(This article belongs to the Topic Big Data in Healthcare, Bioinformatics and Precision Medicine)

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26 pages, 1740 KiB

Open AccessArticle

Combining Ability and Gene Action Controlling Agronomic Traits for Cytoplasmic Male Sterile Line, Restorer Lines, and New Hybrids for Developing of New Drought-Tolerant Rice Hybrids

by Mamdouh M. A. Awad-Allah, Kotb A. Attia, Ahmad Alsayed Omar, Azza H. Mohamed, Rehab M. Habiba, Fahad Mohammed Alzuaibr, Mohammed Ali Alshehri, Mohammed Alqurashi, Salman Aloufi, Eldessoky S. Dessoky and Mohamed A. Abdein

Genes 2022, 13(5), 906; https://doi.org/10.3390/genes13050906 - 19 May 2022

Cited by 2 | Viewed by 1826

Abstract

This study aimed to identify new rice lines and hybrids that are tolerant to water deficit and produce high yields under water stress conditions. A line × tester mating design was used to study the lines and testers’ general combining ability (GCA) effects. [...] Read more.

This study aimed to identify new rice lines and hybrids that are tolerant to water deficit and produce high yields under water stress conditions. A line × tester mating design was used to study the lines and testers’ general combining ability (GCA) effects. The specific combining ability (SCA) of the hybrid rice combinations was measured under three different irrigation regimes; 6, 9, and 12 days. The study was carried out at the experimental farm of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the 2018 and 2019 rice growing seasons. Due to the genotypes and their partitions to the parents and the crosses, the mean squares were highly significant for all studied traits under the three irrigation regimes. The additive gene effects play an important role in expressing most of the studied traits. Therefore, the selection procedures based on the accumulation of the additive effect would be successful at improving these traits and the grain yield. The cytoplasmic male sterile (CMS) line G46A (L1) was the best combiner for most yield component traits in the three irrigation regimes. The newly devolved restorer lines T11, T1, T2, T5, T4, and T3, as well as the new hybrids L2 × T10, L2 × T6, L1 × T7, L1 × T5, L1 × T3, L2 × T7, L2 × T9, L2 × T8, L2 × T4, L1 × T4, L2 × T2, L1 × T8, L1 × T9, and L2 × NRL 10, showed good, desirable values of the studied traits such as earliness of flowering, short plant height, number of panicles/plant, panicle length, number of spikelets/panicle, number of filled grains/panicle, panicle weight, 1000-grain weight, hulling percentage, milling percentage, head rice percentage, and grain yield under the irrigation regimes of 6, 9, and 12 days. The hybrids L2 × T10, L2 × T6, L1 × T7, and L1 × T5, showed significant positive SCA effects for grain yield, under all three irrigation regimes. Full article

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

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13 pages, 793 KiB

Open AccessArticle

Array Comparative Genomic Hybridisation and Droplet Digital PCR Uncover Recurrent Copy Number Variation of the TTN Segmental Duplication Region

by Lydia Sagath, Vilma-Lotta Lehtokari, Katarina Pelin and Kirsi Kiiski

Genes 2022, 13(5), 905; https://doi.org/10.3390/genes13050905 - 19 May 2022

Viewed by 1687

Abstract

Intragenic segmental duplication regions are potential hotspots for recurrent copy number variation and possible pathogenic aberrations. Two large sarcomeric genes, nebulin and titin, both contain such segmental duplication regions. Using our custom Comparative Genomic Hybridisation array, we have previously shown that a gain [...] Read more.

Intragenic segmental duplication regions are potential hotspots for recurrent copy number variation and possible pathogenic aberrations. Two large sarcomeric genes, nebulin and titin, both contain such segmental duplication regions. Using our custom Comparative Genomic Hybridisation array, we have previously shown that a gain or loss of more than one copy of the repeated block of the nebulin triplicate region constitutes a recessive pathogenic mutation. Using targeted array-CGH, similar copy number variants can be detected in the segmental duplication region of titin. Due to the limitations of the array-CGH methodology and the repetitiveness of the region, the exact copy numbers of the blocks could not be determined. Therefore, we developed complementary custom Droplet Digital PCR assays for the titin segmental duplication region to confirm true variation. Our combined methods show that the titin segmental duplication region is subject to recurrent copy number variation. Gains and losses were detected in samples from healthy individuals as well as in samples from patients with different muscle disorders. The copy number variation observed in our cohort is likely benign, but pathogenic copy number variants in the segmental duplication region of titin cannot be excluded. Further investigations are needed, however, this region should no longer be neglected in genetic analyses. Full article

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

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