Genes

11 pages, 1798 KiB

Open AccessArticle

Arabidopsis thaliana MLK3, a Plant-Specific Casein Kinase 1, Negatively Regulates Flowering and Phosphorylates Histone H3 In Vitro

by Junmei Kang, Huiting Cui, Shangang Jia, Wenwen Liu, Renjie Yu, Zhihai Wu and Zhen Wang

Genes 2020, 11(3), 345; https://doi.org/10.3390/genes11030345 - 24 Mar 2020

Cited by 13 | Viewed by 3763

Abstract

Arabidopsis thaliana MUT9-LIKE KINASES (MLKs), a family of the plant-specific casein kinase 1 (CK1), have been implicated collectively in multiple biological processes including flowering. Three of the four MLKs (MLK1/2/4) have been characterized, however, little is known about MLK3 [...] Read more.

Arabidopsis thaliana MUT9-LIKE KINASES (MLKs), a family of the plant-specific casein kinase 1 (CK1), have been implicated collectively in multiple biological processes including flowering. Three of the four MLKs (MLK1/2/4) have been characterized, however, little is known about MLK3, the most divergent member of MLKs. Here, we demonstrated that disruption of MLK3 transcript in mlk3 caused early flowering with retarded leaf growth under long-day conditions. In vitro kinase assay showed the nuclear protein MLK3 phosphorylated histone 3 at threonine 3 (H3T3) and mutation of a conserved residue (K146R) abolished the catalytic activity. Ectopic expression of MLK3 but not MLK3(K146R) rescued the morphological defects of mlk3, indicating that an intact MLK3 is critical for maintaining proper flowering time. Transcriptomic analysis revealed that the floral repressor FLOWERING LOCUS C (FLC) was down-regulated significantly in mlk3, suggesting that MLK3 negatively regulates flowering. Hence, MLK3 plays a role in repressing the transition from vegetative to reproductive phase in A. thaliana. This study sheds light on the delicate control of flowering time by A. thaliana CK1 specific to the plant kingdom. Full article

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

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16 pages, 1293 KiB

Open AccessArticle

A Novel WAC Loss of Function Mutation in an Individual Presenting with Encephalopathy Related to Status Epilepticus during Sleep (ESES)

by Emanuela Leonardi, Mariagrazia Bellini, Maria C. Aspromonte, Roberta Polli, Anna Mercante, Claudia Ciaccio, Elisa Granocchio, Elisa Bettella, Ilaria Donati, Elisa Cainelli, Stefania Boni, Stefano Sartori, Chiara Pantaleoni, Clementina Boniver and Alessandra Murgia

Genes 2020, 11(3), 344; https://doi.org/10.3390/genes11030344 - 24 Mar 2020

Cited by 13 | Viewed by 4040

Abstract

WAC (WW Domain Containing Adaptor With Coiled-Coil) mutations have been reported in only 20 individuals presenting a neurodevelopmental disorder characterized by intellectual disability, neonatal hypotonia, behavioral problems, and mildly dysmorphic features. Using targeted deep sequencing, we screened a cohort of 630 individuals with [...] Read more.

WAC (WW Domain Containing Adaptor With Coiled-Coil) mutations have been reported in only 20 individuals presenting a neurodevelopmental disorder characterized by intellectual disability, neonatal hypotonia, behavioral problems, and mildly dysmorphic features. Using targeted deep sequencing, we screened a cohort of 630 individuals with variable degrees of intellectual disability and identified five WAC rare variants: two variants were inherited from healthy parents; two previously reported de novo mutations, c.1661_1664del (p.Ser554*) and c.374C>A (p.Ser125*); and a novel c.381+2T>C variant causing the skipping of exon 4 of the gene, inherited from a reportedly asymptomatic father with somatic mosaicism. A phenotypic evaluation of this individual evidenced areas of cognitive and behavioral deficits. The patient carrying the novel splicing mutation had a clinical history of encephalopathy related to status epilepticus during slow sleep (ESES), recently reported in another WAC individual. This first report of a WAC somatic mosaic remarks the contribution of mosaicism in the etiology of neurodevelopmental and neuropsychiatric disorders. We summarized the clinical data of reported individuals with WAC pathogenic mutations, which together with our findings, allowed for the expansion of the phenotypic spectrum of WAC-related disorders. Full article

(This article belongs to the Special Issue Selected Papers from the International Workshop on Fragile X and Other Neurodevelopmental Disorders)

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24 pages, 4175 KiB

Open AccessArticle

Ectopic Expression of AhGLK1b (GOLDEN2-like Transcription Factor) in Arabidopsis Confers Dual Resistance to Fungal and Bacterial Pathogens

by Niaz Ali, Hua Chen, Chong Zhang, Shahid Ali Khan, Mamadou Gandeka, Dongyang Xie and Weijian Zhuang

Genes 2020, 11(3), 343; https://doi.org/10.3390/genes11030343 - 24 Mar 2020

Cited by 19 | Viewed by 5307

Abstract

GOLDEN2-LIKE (GLK) is a member of the myeloblastosis (MYB) family transcription factor and it plays an important role in the regulation of plastid development and stress tolerance. In this study, a gene named AhGLK1b was identified from a cultivated peanut showing down-regulation in [...] Read more.

GOLDEN2-LIKE (GLK) is a member of the myeloblastosis (MYB) family transcription factor and it plays an important role in the regulation of plastid development and stress tolerance. In this study, a gene named AhGLK1b was identified from a cultivated peanut showing down-regulation in response to low calcium with a complete open reading frame (ORF) of 1212 bp. The AhGLK1b has 99.26% and 96.28% sequence similarities with its orthologs in Arachis ipaensis and A. duranensis, respectively. In the peanut, the AhGLK1b was localized in the nucleus and demonstrated the highest expression in the leaf, followed by the embryo. Furthermore, the expression of AhGLK1b was induced significantly in response to a bacterial pathogen, Ralstonia solanacearum infection. Ectopic expression of AhGLK1b in Arabidopsis showed stronger resistance against important phytopathogenic fungi S. sclerotiorum. It also exhibited high resistance to infection of the bacterial pathogen Pst DC3000. AhGLK1b-expressing Arabidopsis induced defense-related genes including PR10 and Phox/Bem 1 (PBI), which are involved in multiple disease resistance. Taken together, the results suggest that AhGLK1b might be useful in providing dual resistance to fungal and bacterial pathogens as well as tolerance to abiotic stresses. Full article

(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)

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14 pages, 648 KiB

Open AccessReview

CRISPR-Generated Animal Models of Duchenne Muscular Dystrophy

by Kenji Rowel Q. Lim, Quynh Nguyen, Kasia Dzierlega, Yiqing Huang and Toshifumi Yokota

Genes 2020, 11(3), 342; https://doi.org/10.3390/genes11030342 - 24 Mar 2020

Cited by 16 | Viewed by 8737

Abstract

Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive neuromuscular disorder most commonly caused by mutations disrupting the reading frame of the dystrophin (DMD) gene. DMD codes for dystrophin, which is critical for maintaining the integrity of muscle cell membranes. Without [...] Read more.

Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive neuromuscular disorder most commonly caused by mutations disrupting the reading frame of the dystrophin (DMD) gene. DMD codes for dystrophin, which is critical for maintaining the integrity of muscle cell membranes. Without dystrophin, muscle cells receive heightened mechanical stress, becoming more susceptible to damage. An active body of research continues to explore therapeutic treatments for DMD as well as to further our understanding of the disease. These efforts rely on having reliable animal models that accurately recapitulate disease presentation in humans. While current animal models of DMD have served this purpose well to some extent, each has its own limitations. To help overcome this, clustered regularly interspaced short palindromic repeat (CRISPR)-based technology has been extremely useful in creating novel animal models for DMD. This review focuses on animal models developed for DMD that have been created using CRISPR, their advantages and disadvantages as well as their applications in the DMD field. Full article

(This article belongs to the Special Issue Genetic Advances in Neuromuscular Disorders: From Gene Identification to Gene Therapy)

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16 pages, 1213 KiB

Open AccessReview

Intracellular Communication among Morphogen Signaling Pathways during Vertebrate Body Plan Formation

by Kimiko Takebayashi-Suzuki and Atsushi Suzuki

Genes 2020, 11(3), 341; https://doi.org/10.3390/genes11030341 - 24 Mar 2020

Cited by 10 | Viewed by 5935

Abstract

During embryonic development in vertebrates, morphogens play an important role in cell fate determination and morphogenesis. Bone morphogenetic proteins (BMPs) belonging to the transforming growth factor-β (TGF-β) family control the dorsal–ventral (DV) patterning of embryos, whereas other morphogens such as fibroblast growth factor [...] Read more.

During embryonic development in vertebrates, morphogens play an important role in cell fate determination and morphogenesis. Bone morphogenetic proteins (BMPs) belonging to the transforming growth factor-β (TGF-β) family control the dorsal–ventral (DV) patterning of embryos, whereas other morphogens such as fibroblast growth factor (FGF), Wnt family members, and retinoic acid (RA) regulate the formation of the anterior–posterior (AP) axis. Activation of morphogen signaling results in changes in the expression of target genes including transcription factors that direct cell fate along the body axes. To ensure the correct establishment of the body plan, the processes of DV and AP axis formation must be linked and coordinately regulated by a fine-tuning of morphogen signaling. In this review, we focus on the interplay of various intracellular regulatory mechanisms and discuss how communication among morphogen signaling pathways modulates body axis formation in vertebrate embryos. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Early Embryogenesis)

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16 pages, 5076 KiB

Open AccessArticle

Functional Annotation and Curation of Hypothetical Proteins Present in A Newly Emerged Serotype 1c of Shigella flexneri: Emphasis on Selecting Targets for Virulence and Vaccine Design Studies

by Tanuka Sen and Naresh K. Verma

Genes 2020, 11(3), 340; https://doi.org/10.3390/genes11030340 - 23 Mar 2020

Cited by 18 | Viewed by 4402

Abstract

Shigella flexneri is the principal cause of bacillary dysentery, contributing significantly to the global burden of diarrheal disease. The appearance and increase in the multi-drug resistance among Shigella strains, necessitates further genetic studies and development of improved/new drugs against the pathogen. The presence [...] Read more.

Shigella flexneri is the principal cause of bacillary dysentery, contributing significantly to the global burden of diarrheal disease. The appearance and increase in the multi-drug resistance among Shigella strains, necessitates further genetic studies and development of improved/new drugs against the pathogen. The presence of an abundance of hypothetical proteins in the genome and how little is known about them, make them interesting genetic targets. The present study aims to carry out characterization of the hypothetical proteins present in the genome of a newly emerged serotype of S. flexneri (strain Y394), toward their novel regulatory functions using various bioinformatics databases/tools. Analysis of the genome sequence rendered 4170 proteins, out of which 721 proteins were annotated as hypothetical proteins (HPs) with no known function. The amino acid sequences of these HPs were evaluated using a combination of latest bioinformatics tools based on homology search against functionally identified proteins. Functional domains were considered as the basis to infer the biological functions of HPs in this case and the annotation helped in assigning various classes to the proteins such as signal transducers, lipoproteins, enzymes, membrane proteins, transporters, virulence, and binding proteins. This study contributes to a better understanding of growth, survival, and disease mechanism at molecular level and provides potential new targets for designing drugs against Shigella infection. Full article

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

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20 pages, 2116 KiB

Open AccessReview

Experimental Evolution of Legume Symbionts: What Have We Learnt?

by Ginaini Grazielli Doin de Moura, Philippe Remigi, Catherine Masson-Boivin and Delphine Capela

Genes 2020, 11(3), 339; https://doi.org/10.3390/genes11030339 - 23 Mar 2020

Cited by 16 | Viewed by 6179

Abstract

Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. They likely emerged and diversified through independent horizontal transfers of key symbiotic genes. To replay the evolution of a new rhizobium genus under laboratory conditions, the symbiotic [...] Read more.

Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. They likely emerged and diversified through independent horizontal transfers of key symbiotic genes. To replay the evolution of a new rhizobium genus under laboratory conditions, the symbiotic plasmid of Cupriavidus taiwanensis was introduced in the plant pathogen Ralstonia solanacearum, and the generated proto-rhizobium was submitted to repeated inoculations to the C. taiwanensis host, Mimosa pudica L. This experiment validated a two-step evolutionary scenario of key symbiotic gene acquisition followed by genome remodeling under plant selection. Nodulation and nodule cell infection were obtained and optimized mainly via the rewiring of regulatory circuits of the recipient bacterium. Symbiotic adaptation was shown to be accelerated by the activity of a mutagenesis cassette conserved in most rhizobia. Investigating mutated genes led us to identify new components of R. solanacearum virulence and C. taiwanensis symbiosis. Nitrogen fixation was not acquired in our short experiment. However, we showed that post-infection sanctions allowed the increase in frequency of nitrogen-fixing variants among a non-fixing population in the M. pudica–C. taiwanensis system and likely allowed the spread of this trait in natura. Experimental evolution thus provided new insights into rhizobium biology and evolution. Full article

(This article belongs to the Special Issue Genetic Evolution of Root Nodule Symbioses)

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10 pages, 496 KiB

Open AccessArticle

Diversity of KIR/HLA Genotypes and Their Association with Psoriasis Vulgaris in the Western Mexican Population

by Omar Graciano-Machuca, Anabell Alvarado-Navarro, María Guadalupe Ramírez-Dueñas, Delfina Guadalupe Villanueva-Quintero, Erandi Enif Velarde-de la Cruz, Andrea Carolina Machado-Sulbarán, Margarita Montoya-Buelna and Pedro Ernesto Sánchez-Hernández

Genes 2020, 11(3), 338; https://doi.org/10.3390/genes11030338 - 22 Mar 2020

Cited by 3 | Viewed by 3338

Abstract

NK and some T cell functions are regulated by the interaction between KIR and HLA molecules. Several studies have shown an association between activating KIR genes and the development of autoimmune diseases, including psoriasis vulgaris (PsV). Our objective was to determine the association [...] Read more.

NK and some T cell functions are regulated by the interaction between KIR and HLA molecules. Several studies have shown an association between activating KIR genes and the development of autoimmune diseases, including psoriasis vulgaris (PsV). Our objective was to determine the association between KIR/HLA genes and genotypes with PsV in the Western mestizo Mexican population. One hundred subjects diagnosed with PsV (SP) and 108 healthy subjects (HS) were genotyped for 14 KIR genes, HLA-Bw4, HLA-C1, and HLA-C2 by PCR-single specific primer (SSP). Positive associations of the KIR3DS1 gene (odds ratio (OR) 1.959, p = 0.021), G11 genotype (OR 19.940, p = 0.008), and KIR3DS1/HLA-A^Bw4 (OR 2.265, p = 0.009) were found with susceptibility to PsV. In contrast, the G1 genotype (OR 0.448, p = 0.031) and KIR3DL1/HLA-Bw4^Ile80 (OR 0.522, p = 0.022) were negatively associated with susceptibility to this disease. These results suggest an implication of the KIR3DS1/HLA-A^Bw4 genotype in PsV pathology. Full article

(This article belongs to the Special Issue Genetic Basis of Psoriasis)

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17 pages, 2634 KiB

Open AccessArticle

Quantitative Trait Loci (QTLs) Associated with Microspore Culture in Raphanus sativus L. (Radish)

by Kyeongmin Kim, Yuna Kang, Sol-Ji Lee, Se-Hyun Choi, Dong-Hyun Jeon, Min-Young Park, Suhyoung Park, Yong Pyo Lim and Changsoo Kim

Genes 2020, 11(3), 337; https://doi.org/10.3390/genes11030337 - 21 Mar 2020

Cited by 4 | Viewed by 3488

Abstract

The radish is a highly self-incompatible plant, and consequently it is difficult to produce homozygous lines. Bud pollination in cross-fertilization plants should be done by opening immature pollen and attaching pollen to mature flowers. It accordingly takes a lot of time and effort [...] Read more.

The radish is a highly self-incompatible plant, and consequently it is difficult to produce homozygous lines. Bud pollination in cross-fertilization plants should be done by opening immature pollen and attaching pollen to mature flowers. It accordingly takes a lot of time and effort to develop lines with fixed alleles. In the current study, a haploid breeding method has been applied to obtain homozygous plants in a short period of time by doubling chromosomes through the induction of a plant body in the haploid cells, in order to shorten the time to breed inbred lines. We constructed genetic maps with an F1 population derived by crossing parents that show a superior and inferior ability to regenerate microspores, respectively. Genetic maps were constructed from the maternal and parental maps, separately, using the two-way pseudo-testcross model. The phenotype of the regeneration rate was examined by microspore cultures and a quantitative trait loci (QTL) analysis was performed based on the regeneration rate. From the results of the culture of microspores in the F1 population, more than half of the group did not regenerate, and only a few showed a high regeneration rate. A total of five significant QTLs were detected in the F1 population, and five candidate genes were found based on the results. These candidate genes are divided into two classes, and appear to be related to either PRC2 subunits or auxin synthesis. Full article

(This article belongs to the Special Issue Recent Advances in Genetics and Breeding of Major Staple Food Crops)

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11 pages, 1165 KiB

Open AccessArticle

Prolactin-Responsive Circular RNA circHIPK3 Promotes Proliferation of Mammary Epithelial Cells from Dairy Cow

by Jia Liu, MoLan Zhang, DeWei Li, MengLu Li, LingHao Kong, MengWen Cao, YanHong Wang, ChengChuang Song, XingTang Fang, Hong Chen, Hu Xu and ChunLei Zhang

Genes 2020, 11(3), 336; https://doi.org/10.3390/genes11030336 - 20 Mar 2020

Cited by 14 | Viewed by 3137

Abstract

The highly expressed circHIPK3 is a circular RNA that has been previously reported to regulate the growth of human cells. In this study, we found an increased expression of circHIPK3 in bovine mammary epithelial cells treated with prolactin (PRL) in high-throughput sequencing data. [...] Read more.

The highly expressed circHIPK3 is a circular RNA that has been previously reported to regulate the growth of human cells. In this study, we found an increased expression of circHIPK3 in bovine mammary epithelial cells treated with prolactin (PRL) in high-throughput sequencing data. Thus, we further investigated the effect of circHIPK3 on the proliferation and differentiation of mammary epithelial cells. We used qRT-PCR/Cell Counting Kit-8 (CCK-8) and a Western blotting analysis to evaluate the effects on cell proliferation. We found that circHIPK3 promotes the proliferation of mammary epithelial cells. The STAT5 signaling pathway was previously associated with the prolactin response and when the STAT5 was suppressed, the expression of circHIPK3 decreased. The results suggest that the response to prolactin and the associated STAT5 signaling pathway affect the expression of circHIPK3, which subsequently affects the proliferation of mammary epithelial cells in dairy cows. Full article

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

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15 pages, 3936 KiB

Open AccessArticle

Ohr and OhrR Are Critical for Organic Peroxide Resistance and Symbiosis in Azorhizobium caulinodans ORS571

by Yang Si, Dongsen Guo, Shuoxue Deng, Xiuming Lu, Juanjuan Zhu, Bei Rao, Yajun Cao, Gaofei Jiang, Daogeng Yu, Zengtao Zhong and Jun Zhu

Genes 2020, 11(3), 335; https://doi.org/10.3390/genes11030335 - 20 Mar 2020

Cited by 14 | Viewed by 3243

Abstract

Azorhizobium caulinodans is a symbiotic nitrogen-fixing bacterium that forms both root and stem nodules on Sesbania rostrata. During nodule formation, bacteria have to withstand organic peroxides that are produced by plant. Previous studies have elaborated on resistance to these oxygen radicals in [...] Read more.

Azorhizobium caulinodans is a symbiotic nitrogen-fixing bacterium that forms both root and stem nodules on Sesbania rostrata. During nodule formation, bacteria have to withstand organic peroxides that are produced by plant. Previous studies have elaborated on resistance to these oxygen radicals in several bacteria; however, to the best of our knowledge, none have investigated this process in A. caulinodans. In this study, we identified and characterised the organic hydroperoxide resistance gene ohr (AZC_2977) and its regulator ohrR (AZC_3555) in A. caulinodans ORS571. Hypersensitivity to organic hydroperoxide was observed in an ohr mutant. While using a lacZ-based reporter system, we revealed that OhrR repressed the expression of ohr. Moreover, electrophoretic mobility shift assays demonstrated that OhrR regulated ohr by direct binding to its promoter region. We showed that this binding was prevented by OhrR oxidation under aerobic conditions, which promoted OhrR dimerization and the activation of ohr. Furthermore, we showed that one of the two conserved cysteine residues in OhrR, Cys₁₁, was critical for the sensitivity to organic hydroperoxides. Plant assays revealed that the inactivation of Ohr decreased the number of stem nodules and nitrogenase activity. Our data demonstrated that Ohr and OhrR are required for protecting A. caulinodans from organic hydroperoxide stress and play an important role in the interaction of the bacterium with plants. The results that were obtained in our study suggested that a thiol-based switch in A. caulinodans might sense host organic peroxide signals and enhance symbiosis. Full article

(This article belongs to the Special Issue Genetic Evolution of Root Nodule Symbioses)

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18 pages, 2990 KiB

Open AccessArticle

Effect of Transgenesis on mRNA and miRNA Profiles in Cucumber Fruits Expressing Thaumatin II

by Magdalena Ewa Pawełkowicz, Agnieszka Skarzyńska, Małgorzata Sroka, Maria Szwacka, Tomasz Pniewski and Wojciech Pląder

Genes 2020, 11(3), 334; https://doi.org/10.3390/genes11030334 - 20 Mar 2020

Cited by 8 | Viewed by 3589

Abstract

Transgenic plants are commonly used in breeding programs because of the various features that can be introduced. However, unintended effects caused by genetic transformation are still a topic of concern. This makes research on the nutritional safety of transgenic crop plants extremely interesting. [...] Read more.

Transgenic plants are commonly used in breeding programs because of the various features that can be introduced. However, unintended effects caused by genetic transformation are still a topic of concern. This makes research on the nutritional safety of transgenic crop plants extremely interesting. Cucumber (Cucumis sativus L.) is a crop that is grown worldwide. The aim of this study was to identify and characterize differentially expressed genes and regulatory miRNAs in transgenic cucumber fruits that contain the thaumatin II gene, which encodes the sweet-tasting protein thaumatin II, by NGS sequencing. We compared the fruit transcriptomes and miRNomes of three transgenic cucumber lines with wild-type cucumber. In total, we found 47 differentially expressed genes between control and all three transgenic lines. We performed the bioinformatic functional analysis and gene ontology classification. We also identified 12 differentially regulated miRNAs, from which three can influence the two targets (assigned as DEGs) in one of the studied transgenic lines (line 224). We found that the transformation of cucumber with thaumatin II and expression of the transgene had minimal impact on gene expression and epigenetic regulation by miRNA, in the cucumber fruits. Full article

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

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5 pages, 215 KiB

Open AccessCommunication

NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification

by Nicholas Toda, Camille Rustenholz, Agnès Baud, Marie-Christine Le Paslier, Joelle Amselem, Didier Merdinoglu and Patricia Faivre-Rampant

Genes 2020, 11(3), 333; https://doi.org/10.3390/genes11030333 - 20 Mar 2020

Cited by 23 | Viewed by 5201

Abstract

Although there are a number of bioinformatic tools to identify plant nucleotide-binding leucine-rich repeat (NLR) disease resistance genes based on conserved protein sequences, only a few of these tools have attempted to identify disease resistance genes that have not been annotated in the [...] Read more.

Although there are a number of bioinformatic tools to identify plant nucleotide-binding leucine-rich repeat (NLR) disease resistance genes based on conserved protein sequences, only a few of these tools have attempted to identify disease resistance genes that have not been annotated in the genome. The overall goal of the NLGenomeSweeper pipeline is to annotate NLR disease resistance genes, including RPW8, in the genome assembly with high specificity and a focus on complete functional genes. This is based on the identification of the complete NB-ARC domain, the most conserved domain of NLR genes, using the BLAST suite. In this way, the tool has a high specificity for complete genes and relatively intact pseudogenes. The tool returns all candidate NLR gene locations as well as InterProScan ORF and domain annotations for manual curation of the gene structure. Full article

(This article belongs to the Special Issue NLR Gene Evolution in Plants)

10 pages, 725 KiB

Open AccessCommunication

A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

by Krishnamoorthy Srikanth, Jong-Eun Park, Dajeong Lim, Jihye Cha, Sang-Rae Cho, In-Cheol Cho and Woncheoul Park

Genes 2020, 11(3), 332; https://doi.org/10.3390/genes11030332 - 20 Mar 2020

Cited by 2 | Viewed by 3557

Abstract

Until recently, genome-scale phasing was limited due to the short read sizes of sequence data. Though the use of long-read sequencing can overcome this limitation, they require extensive error correction. The emergence of technologies such as 10X genomics linked read sequencing and Hi-C [...] Read more.

Until recently, genome-scale phasing was limited due to the short read sizes of sequence data. Though the use of long-read sequencing can overcome this limitation, they require extensive error correction. The emergence of technologies such as 10X genomics linked read sequencing and Hi-C which uses short-read sequencers along with library preparation protocols that facilitates long-read assemblies have greatly reduced the complexities of genome scale phasing. Moreover, it is possible to accurately assemble phased genome of individual samples using these methods. Therefore, in this study, we compared three phasing strategies which included two sample preparation methods along with the Long Ranger pipeline of 10X genomics and HapCut2 software, namely 10X-LG, 10X-HapCut2, and HiC-HapCut2 and assessed their performance and accuracy. We found that the 10X-LG had the best phasing performance amongst the method analyzed. They had the highest phasing rate (89.6%), longest adjusted N50 (1.24 Mb), and lowest switch error rate (0.07%). Moreover, the phasing accuracy and yield of the 10X-LG stayed over 90% for distances up to 4 Mb and 550 Kb respectively, which were considerably higher than 10X-HapCut2 and Hi-C Hapcut2. The results of this study will serve as a good reference for future benchmarking studies and also for reference-based imputation in Hanwoo. Full article

(This article belongs to the Section Technologies and Resources for Genetics)

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20 pages, 5474 KiB

Open AccessArticle

Kinome Profiling of NF1-Related MPNSTs in Response to Kinase Inhibition and Doxorubicin Reveals Therapeutic Vulnerabilities

by Jamie L. Grit, Matt G. Pridgeon, Curt J. Essenburg, Emily Wolfrum, Zachary B. Madaj, Lisa Turner, Julia Wulfkuhle, Emanuel F. Petricoin III, Carrie R. Graveel and Matthew R. Steensma

Genes 2020, 11(3), 331; https://doi.org/10.3390/genes11030331 - 20 Mar 2020

Cited by 8 | Viewed by 4177

Abstract

Neurofibromatosis Type 1 (NF1)-related Malignant Peripheral Nerve Sheath Tumors (MPNST) are highly resistant sarcomas that account for significant mortality. The mechanisms of therapy resistance are not well-understood in MPNSTs, particularly with respect to kinase inhibition strategies. In this study, we aimed to quantify [...] Read more.

Neurofibromatosis Type 1 (NF1)-related Malignant Peripheral Nerve Sheath Tumors (MPNST) are highly resistant sarcomas that account for significant mortality. The mechanisms of therapy resistance are not well-understood in MPNSTs, particularly with respect to kinase inhibition strategies. In this study, we aimed to quantify the impact of both the genomic context and targeted therapy on MPNST resistance using reverse phase phosphoproteome array (RPPA) analysis. We treated tumorgrafts from three genetically engineered mouse models using MET (capmatinib) and MEK (trametinib) inhibitors and doxorubicin, and assessed phosphosignaling at 4 h, 2 days, and 21 days. Baseline kinase signaling in our mouse models recapitulated an MET-addicted state (NF1-MET), P53 mutation (NF1-P53), and HGF overexpression (NF1). Following perturbation with the drug, we observed broad and redundant kinome adaptations that extended well beyond canonical RAS/ERK or PI3K/AKT/mTOR signaling. MET and MEK inhibition were both associated with an initial inflammatory response mediated by kinases in the JAK/STAT pathway and NFkB. Growth signaling predominated at the 2-day and 21-day time points as a result of broad RTK and intracellular kinase activation. Interestingly, AXL and NFkB were strongly activated at the 2-day and 21-day time points, and tightly correlated, regardless of the treatment type or genomic context. The degree of kinome adaptation observed in innately resistant tumors was significantly less than the surviving fractions of responsive tumors that exhibited a latency period before reinitiating growth. Lastly, doxorubicin resistance was associated with kinome adaptations that strongly favored growth and survival signaling. These observations confirm that MPNSTs are capable of profound signaling plasticity in the face of kinase inhibition or DNA damaging agent administration. It is possible that by targeting AXL or NFkB, therapy resistance can be mitigated. Full article

(This article belongs to the Special Issue Genomics and Models of Nerve Sheath Tumors)

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17 pages, 751 KiB

Open AccessReview

The Spectrum of Mutations of Homocystinuria in the MENA Region

by Duaa W. Al-Sadeq and Gheyath K. Nasrallah

Genes 2020, 11(3), 330; https://doi.org/10.3390/genes11030330 - 20 Mar 2020

Cited by 24 | Viewed by 11776

Abstract

Homocystinuria is an inborn error of metabolism due to the deficiency in cystathionine beta-synthase (CBS) enzyme activity. It leads to the elevation of both homocysteine and methionine levels in the blood and urine. Consequently, this build-up could lead to several complications such as [...] Read more.

Homocystinuria is an inborn error of metabolism due to the deficiency in cystathionine beta-synthase (CBS) enzyme activity. It leads to the elevation of both homocysteine and methionine levels in the blood and urine. Consequently, this build-up could lead to several complications such as nearsightedness, dislocated eye lenses, a variety of psychiatric and behavioral disorders, as well as vascular system complications. The prevalence of homocystinuria is around 1/200,000 births worldwide. However, its prevalence in the Gulf region, notably Qatar, is exceptionally high and reached 1:1800. To date, more than 191 pathogenic CBS mutations have been documented. The majority of these mutations were identified in Caucasians of European ancestry, whereas only a few mutations from African-Americans or Asians were reported. Approximately 87% of all CBS mutations are missense and do not target the CBS catalytic site, but rather result in unstable misfolded proteins lacking the normal biological function, designating them for degradation. The early detection of homocystinuria along with low protein and methionine-restricted diet is the best treatment approach for all types of homocystinuria patients. Yet, less than 50% of affected individuals show a significant reduction in plasma homocysteine levels after treatment. Patients who fail to lower the elevated homocysteine levels, through high protein-restricted diet or by B6 and folic acid supplements, are at higher risk for cardiovascular diseases, neurodegenerative diseases, neural tube defects, and other severe clinical complications. This review aims to examine the mutations spectrum of the CBS gene, the disease management, as well as the current and potential treatment approaches with a greater emphasis on studies reported in the Middle East and North Africa (MENA) region. Full article

(This article belongs to the Special Issue The Value of Genetics in the Identification of Treatable Rare Diseases. The Paradigm of Inborn Errors of Metabolism)

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29 pages, 1115 KiB

Open AccessReview

Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation

by Anja Schmidt

Genes 2020, 11(3), 329; https://doi.org/10.3390/genes11030329 - 20 Mar 2020

Cited by 57 | Viewed by 9772

Abstract

In higher plants, sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. As apomixis leads to the formation of clonal offspring, its great potential for agricultural applications has long been recognized. However, the genetic basis and the molecular control underlying [...] Read more.

In higher plants, sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. As apomixis leads to the formation of clonal offspring, its great potential for agricultural applications has long been recognized. However, the genetic basis and the molecular control underlying apomixis and its evolutionary origin are to date not fully understood. Both in sexual and apomictic plants, reproduction is tightly controlled by versatile mechanisms regulating gene expression, translation, and protein abundance and activity. Increasing evidence suggests that interrelated pathways including epigenetic regulation, cell-cycle control, hormonal pathways, and signal transduction processes are relevant for apomixis. Additional molecular mechanisms are being identified that involve the activity of DNA- and RNA-binding proteins, such as RNA helicases which are increasingly recognized as important regulators of reproduction. Together with other factors including non-coding RNAs, their association with ribosomes is likely to be relevant for the formation and specification of the apomictic reproductive lineage. Subsequent seed formation appears to involve an interplay of transcriptional activation and repression of developmental programs by epigenetic regulatory mechanisms. In this review, insights into the genetic basis and molecular control of apomixis are presented, also taking into account potential relations to environmental stress, and considering aspects of evolution. Full article

(This article belongs to the Special Issue Molecular Basis of Apomixis in Plants)

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14 pages, 1682 KiB

Open AccessArticle

Fetal Hypoxia Impacts on Proliferation and Differentiation of Sca-1⁺ Cardiac Progenitor Cells and Maturation of Cardiomyocytes: A Role of MicroRNA-210

by Xianmei Meng, Peng Zhang and Lubo Zhang

Genes 2020, 11(3), 328; https://doi.org/10.3390/genes11030328 - 20 Mar 2020

Cited by 12 | Viewed by 3052

Abstract

Hypoxia is one of the most frequent and severe stresses to an organism’s homeostatic mechanisms, and hypoxia during gestation has profound adverse effects on the heart development increasing the occurrence of congenital heart defects (CHDs). Cardiac progenitor cells (CPCs) are responsible for early [...] Read more.

Hypoxia is one of the most frequent and severe stresses to an organism’s homeostatic mechanisms, and hypoxia during gestation has profound adverse effects on the heart development increasing the occurrence of congenital heart defects (CHDs). Cardiac progenitor cells (CPCs) are responsible for early heart development and the later occurrence of heart disease. However, the mechanism of how hypoxic stress affects CPC fate decisions and contributes to CHDs remains a topic of debate. Here we examined the effect of hypoxic stress on the regulations of CPC fate decisions and the potential mechanism. We found that experimental induction of hypoxic responses compromised CPC function by regulating CPC proliferation and differentiation and restraining cardiomyocyte maturation. In addition, echocardiography indicated that fetal hypoxia reduced interventricular septum thickness at diastole and the ejection time, but increased the heart rate, in mouse young adult offspring with a gender-related difference. Further study revealed that hypoxia upregulated microRNA-210 expression in Sca-1⁺ CPCs and impeded the cell differentiation. Blockage of microRNA-210 with LNA-anti-microRNA-210 significantly promoted differentiation of Sca-1⁺ CPCs into cardiomyocytes. Thus, the present findings provide clear evidence that hypoxia alters CPC fate decisions and reveal a novel mechanism of microRNA-210 in the hypoxic effect, raising the possibility of microRNA-210 as a potential therapeutic target for heart disease. Full article

(This article belongs to the Special Issue Genes at Ten)

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20 pages, 4117 KiB

Open AccessArticle

Structural Variation of the X Chromosome Heterochromatin in the Anopheles gambiae Complex

by Atashi Sharma, Nicholas A. Kinney, Vladimir A. Timoshevskiy, Maria V. Sharakhova and Igor V. Sharakhov

Genes 2020, 11(3), 327; https://doi.org/10.3390/genes11030327 - 19 Mar 2020

Cited by 16 | Viewed by 4447

Abstract

Heterochromatin is identified as a potential factor driving diversification of species. To understand the magnitude of heterochromatin variation within the Anopheles gambiae complex of malaria mosquitoes, we analyzed metaphase chromosomes in An. arabiensis, An. coluzzii, An. gambiae, An. merus, [...] Read more.

Heterochromatin is identified as a potential factor driving diversification of species. To understand the magnitude of heterochromatin variation within the Anopheles gambiae complex of malaria mosquitoes, we analyzed metaphase chromosomes in An. arabiensis, An. coluzzii, An. gambiae, An. merus, and An. quadriannulatus. Using fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA), a highly repetitive fraction of DNA, and heterochromatic Bacterial Artificial Chromosome (BAC) clones, we established the correspondence of pericentric heterochromatin between the metaphase and polytene X chromosomes of An. gambiae. We then developed chromosome idiograms and demonstrated that the X chromosomes exhibit qualitative differences in their pattern of heterochromatic bands and position of satellite DNA (satDNA) repeats among the sibling species with postzygotic isolation, An. arabiensis, An. merus, An. quadriannulatus, and An. coluzzii or An. gambiae. The identified differences in the size and structure of the X chromosome heterochromatin point to a possible role of repetitive DNA in speciation of mosquitoes. We found that An. coluzzii and An. gambiae, incipient species with prezygotic isolation, share variations in the relative positions of the satDNA repeats and the proximal heterochromatin band on the X chromosomes. This previously unknown genetic polymorphism in malaria mosquitoes may be caused by a differential amplification of DNA repeats or an inversion in the sex chromosome heterochromatin. Full article

(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)

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24 pages, 3288 KiB

Open AccessArticle

Impaired Replication Timing Promotes Tissue-Specific Expression of Common Fragile Sites

by Klizia Maccaroni, Elisa Balzano, Federica Mirimao, Simona Giunta and Franca Pelliccia

Genes 2020, 11(3), 326; https://doi.org/10.3390/genes11030326 - 19 Mar 2020

Cited by 17 | Viewed by 4013

Abstract

Common fragile sites (CFSs) are particularly vulnerable regions of the genome that become visible as breaks, gaps, or constrictions on metaphase chromosomes when cells are under replicative stress. Impairment in DNA replication, late replication timing, enrichment of A/T nucleotides that tend to form [...] Read more.

Common fragile sites (CFSs) are particularly vulnerable regions of the genome that become visible as breaks, gaps, or constrictions on metaphase chromosomes when cells are under replicative stress. Impairment in DNA replication, late replication timing, enrichment of A/T nucleotides that tend to form secondary structures, the paucity of active or inducible replication origins, the generation of R-loops, and the collision between replication and transcription machineries on particularly long genes are some of the reported characteristics of CFSs that may contribute to their tissue-specific fragility. Here, we validated the induction of two CFSs previously found in the human fetal lung fibroblast line, Medical Research Council cell strain 5 (MRC-5), in another cell line derived from the same fetal tissue, Institute for Medical Research-90 cells (IMR-90). After induction of CFSs through aphidicolin, we confirmed the expression of the CFS 1p31.1 on chromosome 1 and CFS 3q13.3 on chromosome 3 in both fetal lines. Interestingly, these sites were found to not be fragile in lymphocytes, suggesting a role for epigenetic or transcriptional programs for this tissue specificity. Both these sites contained late-replicating genes NEGR1 (neuronal growth regulator 1) at 1p31.1 and LSAMP (limbic system-associated membrane protein) at 3q13.3, which are much longer, 0.880 and 1.4 Mb, respectively, than the average gene length. Given the established connection between long genes and CFS, we compiled information from the literature on all previously identified CFSs expressed in fibroblasts and lymphocytes in response to aphidicolin, including the size of the genes contained in each fragile region. Our comprehensive analysis confirmed that the genes found within CFSs are longer than the average human gene; interestingly, the two longest genes in the human genome are found within CFSs: Contactin Associated Protein 2 gene (CNTNAP2) in a lymphocytes’ CFS, and Duchenne muscular dystrophy gene (DMD) in a CFS expressed in both lymphocytes and fibroblasts. This indicates that the presence of very long genes is a unifying feature of all CFSs. We also obtained replication profiles of the 1p31.1 and 3q13.3 sites under both perturbed and unperturbed conditions using a combination of fluorescent in situ hybridization (FISH) and immunofluorescence against bromodeoxyuridine (BrdU) on interphase nuclei. Our analysis of the replication dynamics of these CFSs showed that, compared to lymphocytes where these regions are non-fragile, fibroblasts display incomplete replication of the fragile alleles, even in the absence of exogenous replication stress. Our data point to the existence of intrinsic features, in addition to the presence of long genes, which affect DNA replication of the CFSs in fibroblasts, thus promoting chromosomal instability in a tissue-specific manner. Full article

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

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15 pages, 4603 KiB

Open AccessArticle

A Novel Germline MLH1 In-Frame Deletion in a Slovenian Lynch Syndrome Family Associated with Uncommon Isolated PMS2 Loss in Tumor Tissue

by Gašper Klančar, Ana Blatnik, Vita Šetrajčič Dragoš, Vesna Vogrič, Vida Stegel, Olga Blatnik, Primož Drev, Barbara Gazič, Mateja Krajc and Srdjan Novaković

Genes 2020, 11(3), 325; https://doi.org/10.3390/genes11030325 - 18 Mar 2020

Cited by 10 | Viewed by 3525

Abstract

The diagnostics of Lynch syndrome (LS) is focused on the detection of DNA mismatch repair (MMR) system deficiency. MMR deficiency can be detected on tumor tissue by microsatellite instability (MSI) using molecular genetic test or by loss of expression of one of the [...] Read more.

The diagnostics of Lynch syndrome (LS) is focused on the detection of DNA mismatch repair (MMR) system deficiency. MMR deficiency can be detected on tumor tissue by microsatellite instability (MSI) using molecular genetic test or by loss of expression of one of the four proteins (MLH1, MSH2, MSH6, and PMS2) involved in the MMR system using immunohistochemistry (IHC) staining. According to the National Comprehensive Cancer Network (NCCN) guidelines, definitive diagnosis of LS requires the identification of the germline pathogenic variant in one of the MMR genes. In the report, we are presenting interesting novel MLH1 in-frame deletion LRG_216t1:c.2236_2247delCTGCCTGATCTA p.(Leu746_Leu749del) associated with LS. The variant appears to be associated with uncommon isolated loss of PMS2 immunohistochemistry protein staining (expression) in tumor tissue instead of MLH1 and PMS2 protein loss, which is commonly seen with pathogenic variants in MLH1. The variant was classified as likely pathogenic, based on segregation analysis and molecular characterization of blood and tumor samples. According to the American College of Medical Genetics (ACMG) guidelines, the following evidence categories of PM1, PM2, PM4, and PP1 moderate have been used for classification of the novel variant. By detecting and classifying the novel MLH1 variant as likely pathogenic, we confirmed the LS in this family. Full article

(This article belongs to the Special Issue Colorectal Cancer Genetics, Epigenetics, and Emerging Therapies)

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16 pages, 5868 KiB

Open AccessArticle

Genome-Wide Transcriptomic Analysis Reveals a Regulatory Network of Oxidative Stress-Induced Flowering Signals Produced in Litchi Leaves

by Xingyu Lu, Sheng Yu, Peitao Lü, Houbin Chen, Silin Zhong and Biyan Zhou

Genes 2020, 11(3), 324; https://doi.org/10.3390/genes11030324 - 18 Mar 2020

Cited by 12 | Viewed by 3287

Abstract

Litchi is an important subtropical fruit tree that requires an appropriately low temperature to trigger floral initiation. Our previous studies have shown that reactive oxygen species (ROS) are involved in litchi flowering. To identify oxidative stress-induced flowering related genes in leaves, ‘Nuomici’ potted [...] Read more.

Litchi is an important subtropical fruit tree that requires an appropriately low temperature to trigger floral initiation. Our previous studies have shown that reactive oxygen species (ROS) are involved in litchi flowering. To identify oxidative stress-induced flowering related genes in leaves, ‘Nuomici’ potted trees were grown at medium low-temperature conditions (18/13 °C for day/night, medium-temperature). The trees were treated with the ROS generator methyl viologen dichloride hydrate (MV) as the MV-generated ROS treatment (MM, medium-temperature plus MV) and water as the control treatment (M, medium-temperature plus water). Sixteen RNA-sequencing libraries were constructed, and each library generated more than 5,000,000 clean reads. A total of 517 differentially expressed genes (DEGs) were obtained. Among those DEGs, plant hormone biosynthesis and signal transduction genes, ROS-specific transcription factors, such as AP2/ERF and WRKY genes, stress response genes, and flowering-related genes FLOWERING LOCUS T1 (FT1) and FLOWERING LOCUS T2 (FT2) were significantly enriched. Then, as a confirmatory experiment, the potted trees were uniformly sprayed with MV, N,N’-dimethylthiourea (DMTU, ROS scavenger) plus MV, and water at medium-temperature. The results showed that the MV-generated ROS promoted flowering and changed related gene expression, but these effects were repressed by DMTU treatment. The results of our studies indicate that ROS could promote flowering and partly bypass chilling for litchi flowering. Full article

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

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15 pages, 683 KiB

Open AccessReview

Crosstalk between Dendritic Cells and Immune Modulatory Agents against Sepsis

by Guoying Wang, Xianghui Li, Lei Zhang, Abualgasim Elgaili Abdalla, Tieshan Teng and Yanzhang Li

Genes 2020, 11(3), 323; https://doi.org/10.3390/genes11030323 - 18 Mar 2020

Cited by 9 | Viewed by 4002

Abstract

Dendritic cells (DCs) play a critical role in the immune system which sense pathogens and present their antigens to prime the adaptive immune responses. As the progression of sepsis occurs, DCs are capable of orchestrating the aberrant innate immune response by sustaining the [...] Read more.

Dendritic cells (DCs) play a critical role in the immune system which sense pathogens and present their antigens to prime the adaptive immune responses. As the progression of sepsis occurs, DCs are capable of orchestrating the aberrant innate immune response by sustaining the Th1/Th2 responses that are essential for host survival. Hence, an in-depth understanding of the characteristics of DCs would have a beneficial effect in overcoming the obstacle occurring in sepsis. This paper focuses on the role of DCs in the progression of sepsis and we also discuss the reverse sepsis-induced immunosuppression through manipulating the DC function. In addition, we highlight some potent immunotherapies that could be used as a novel strategy in the early treatment of sepsis. Full article

(This article belongs to the Special Issue Shared Mechanisms and Multimorbidity for Immune-Mediated Diseases)

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13 pages, 1823 KiB

Open AccessArticle

Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica

by Zhenhua Dang, Lei Huang, Yuanyuan Jia, Peter J. Lockhart, Yang Fong and Yunyun Tian

Genes 2020, 11(3), 322; https://doi.org/10.3390/genes11030322 - 18 Mar 2020

Cited by 8 | Viewed by 3029

Abstract

Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast [...] Read more.

Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast adaptation to environmental change. Thus, identifying SSRs and their possible effects on gene behavior has the potential to provide valuable information for studies of adaptation. In this study, we sequenced six individual transcriptomes of T. mongolica from heterogeneous habitats, focused on SSRs located in genes, and identified 811 polymorphic SSRs. Of the identified SSRs, 172, 470, and 76 were located in 5′ UTRs, CDSs, and 3′ UTRs in 591 transcripts; and AG/CT, AAC/GTT, and AT/AT were the most abundant repeats in each gene region. Functional annotation showed that many of the identified polymorphic SSRs were in genes that were enriched in several GO terms and KEGG pathways, suggesting the functional significance of these genes in the environmental adaptation process. The identification of polymorphic genic SSRs in our study lays a foundation for future studies investigating the contribution of SSRs to regulation of genes in natural populations of T. mongolica and their importance for adaptive evolution of this species. Full article

(This article belongs to the Special Issue Rapid Evolution)

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15 pages, 1153 KiB

Open AccessArticle

Comparative Transcriptomics Reveals Clues for Differences in Pathogenicity between Hysterothylacium aduncum, Anisakis simplex sensu stricto and Anisakis pegreffii

by Serena Cavallero, Fabrizio Lombardo, Marco Salvemini, Antonella Pizzarelli, Cinzia Cantacessi and Stefano D’Amelio

Genes 2020, 11(3), 321; https://doi.org/10.3390/genes11030321 - 18 Mar 2020

Cited by 25 | Viewed by 3892

Abstract

Ascaridoid nematodes are widespread in marine fishes. Despite their major socioeconomic importance, mechanisms associated to the fish-borne zoonotic disease anisakiasis are still obscure. RNA-Seq and de-novo assembly were herein applied to RNA extracted from larvae and dissected pharynx of Hysterothylacium aduncum (HA), a [...] Read more.

Ascaridoid nematodes are widespread in marine fishes. Despite their major socioeconomic importance, mechanisms associated to the fish-borne zoonotic disease anisakiasis are still obscure. RNA-Seq and de-novo assembly were herein applied to RNA extracted from larvae and dissected pharynx of Hysterothylacium aduncum (HA), a non-pathogenic nematode. Assembled transcripts in HA were annotated and compared to the transcriptomes of the zoonotic species Anisakis simplex sensu stricto (AS) and Anisakis pegreffii (AP). Approximately 60,000,000 single-end reads were generated for HA, AS and AP. Transcripts in HA encoded for 30,254 putative peptides while AS and AP encoded for 20,574 and 20,840 putative peptides, respectively. Differential gene expression analyses yielded 471, 612 and 526 transcripts up regulated in the pharynx of HA, AS and AP. The transcriptomes of larvae and pharynx of HA were enriched in transcripts encoding collagen, peptidases, ribosomal proteins and in heat-shock motifs. Transcripts encoding proteolytic enzymes, anesthetics, inhibitors of primary hemostasis and virulence factors, anticoagulants and immunomodulatory peptides were up-regulated in AS and AP pharynx. This study represents the first transcriptomic characterization of a marine parasitic nematode commonly recovered in fish and probably of negligible concern for public health. Full article

(This article belongs to the Special Issue Novel Omics Studies on Anisakid Nematodes)

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17 pages, 3180 KiB

Open AccessArticle

Genome-Wide Analysis and Function Prediction of Long Noncoding RNAs in Sheep Pituitary Gland Associated with Sexual Maturation

by Hua Yang, Jianyu Ma, Zhibo Wang, Xiaolei Yao, Jie Zhao, Xinyue Zhao, Feng Wang and Yanli Zhang

Genes 2020, 11(3), 320; https://doi.org/10.3390/genes11030320 - 17 Mar 2020

Cited by 17 | Viewed by 3437

Abstract

Long noncoding RNA (lncRNA) plays a crucial role in the hypothalamic-pituitary-testis (HPT) axis associated with sheep reproduction. The pituitary plays a connecting role in the HPT axis. However, little is known of their expression pattern and potential roles in the pituitary gland. To [...] Read more.

Long noncoding RNA (lncRNA) plays a crucial role in the hypothalamic-pituitary-testis (HPT) axis associated with sheep reproduction. The pituitary plays a connecting role in the HPT axis. However, little is known of their expression pattern and potential roles in the pituitary gland. To explore the potential lncRNAs that regulate the male sheep pituitary development and sexual maturation, we constructed immature and mature sheep pituitary cDNA libraries (three-month-old, TM, and nine-month-old, NM, respectively, n = 3) for lncRNA and mRNA high-throughput sequencing. Firstly, the expression of lncRNA and mRNA were comparatively analyzed. 2417 known lncRNAs and 1256 new lncRNAs were identified. Then, 193 differentially expressed (DE) lncRNAs and 1407 DE mRNAs were found in the pituitary between the two groups. Moreover, mRNA-lncRNA interaction network was constructed according to the target gene prediction of lncRNA and functional enrichment analysis. Five candidate lncRNAs and their targeted genes HSD17B12, DCBLD2, PDPK1, GPX3 and DLL1 that enriched in growth and reproduction related pathways were further filtered. Lastly, the interaction of candidate lncRNA TCONS_00066406 and its targeted gene HSD17B12 were validated in in vitro of sheep pituitary cells. Our study provided a systematic presentation of lncRNAs and mRNAs in male sheep pituitary, which revealed the potential role of lncRNA in male reproduction. Full article

(This article belongs to the Special Issue Genomics of Sexual Development and Reproduction in Mammals)

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24 pages, 1598 KiB

Open AccessReview

The Critical Role of miRNAs in Regulation of Flowering Time and Flower Development

by Saquib Waheed and Lihui Zeng

Genes 2020, 11(3), 319; https://doi.org/10.3390/genes11030319 - 17 Mar 2020

Cited by 70 | Viewed by 8614

Abstract

Flowering is an important biological process for plants that ensures reproductive success. The onset of flowering needs to be coordinated with an appropriate time of year, which requires tight control of gene expression acting in concert to form a regulatory network. MicroRNAs (miRNAs) [...] Read more.

Flowering is an important biological process for plants that ensures reproductive success. The onset of flowering needs to be coordinated with an appropriate time of year, which requires tight control of gene expression acting in concert to form a regulatory network. MicroRNAs (miRNAs) are non-coding RNAs known as master modulators of gene expression at the post-transcriptional level. Many different miRNA families are involved in flowering-related processes such as the induction of floral competence, floral patterning, and the development of floral organs. This review highlights the diverse roles of miRNAs in controlling the flowering process and flower development, in combination with potential biotechnological applications for miRNAs implicated in flower regulation. Full article

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

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2 pages, 153 KiB

Open AccessEditorial

Conservation Genetics and Genomics

by Michael Russello, George Amato, Robert DeSalle and Michael Knapp

Genes 2020, 11(3), 318; https://doi.org/10.3390/genes11030318 - 17 Mar 2020

Cited by 9 | Viewed by 3524

Abstract

For more than thirty years, methods and theories from evolutionary biology, phylogenetics, population genetics and molecular biology have been used by conservation biologists to better understand threats to endangered species due to anthropogenic changes [...] Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

17 pages, 1378 KiB

Open AccessReview

Genes, Pathways, and Mechanisms Involved in the Virulence of Mucorales

by Carlos Lax, Carlos Pérez-Arques, María Isabel Navarro-Mendoza, José Tomás Cánovas-Márquez, Ghizlane Tahiri, José Antonio Pérez-Ruiz, Macario Osorio-Concepción, Laura Murcia-Flores, Eusebio Navarro, Victoriano Garre and Francisco Esteban Nicolás

Genes 2020, 11(3), 317; https://doi.org/10.3390/genes11030317 - 16 Mar 2020

Cited by 49 | Viewed by 6420

Abstract

The order Mucorales is a group of ancient fungi with limited tools for gene manipulation. The main consequence of this manipulation unwillingness is the limited knowledge about its biology compared to other fungal groups. However, the emerging of mucormycosis, a fungal infection caused [...] Read more.

The order Mucorales is a group of ancient fungi with limited tools for gene manipulation. The main consequence of this manipulation unwillingness is the limited knowledge about its biology compared to other fungal groups. However, the emerging of mucormycosis, a fungal infection caused by Mucorales, is attracting the medical spotlight in recent years because the treatments available are not efficient in reducing the high mortality associated with this disease. The result of this renewed interest in Mucorales and mucormycosis is an extraordinarily productive effort to unveil their secrets during the last decade. In this review, we describe the most compelling advances related to the genetic study of virulence factors, pathways, and molecular mechanisms developed in these years. The use of a few genetic study models has allowed the characterization of virulence factors in Mucorales that were previously described in other pathogens, such as the uptake iron systems, the mechanisms of dimorphism, and azole resistances. More importantly, recent studies are identifying new genes and mechanisms controlling the pathogenic potential of Mucorales and their interactions with the host, offering new alternatives to develop specific strategies against mucormycosis. Full article

(This article belongs to the Special Issue Human Fungal Pathogens and Emerging Antifungal Resistance—A Global Public Health Problem?)

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22 pages, 2701 KiB

Open AccessArticle

A Gene-Set Enrichment and Protein–Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

by Krishnamoorthy Srikanth, Seung-Hwan Lee, Ki-Yong Chung, Jong-Eun Park, Gul-Won Jang, Mi-Rim Park, Na Yeon Kim, Tae-Hun Kim, Han-Ha Chai, Won Cheoul Park and Dajeong Lim

Genes 2020, 11(3), 316; https://doi.org/10.3390/genes11030316 - 16 Mar 2020

Cited by 44 | Viewed by 6310

Abstract

Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in [...] Read more.

Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10⁻⁷) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein–protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits. Full article

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

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