scholarly journals Genetic Analysis of Clinical VZV Isolates Collected in China Reveals a More Homologous Profile

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Longfeng Jiang ◽  
Lin Gan ◽  
Jason Chen ◽  
Mingli Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Open Reading Frames ◽  
Polymorphic Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Varicella Zoster ◽  
Clade B ◽  
The Us ◽  
The World ◽  
Reading Frames

Forty-four varicella-zoster virus (VZV) isolates from China were genotyped by using a scattered single nucleotide polymorphism (SNP) method, including open reading frames (ORFs) 1, 22, 31, 37, 60, 62, 67, and 68. Based on the analysis of the polymorphic markers in the 8 ORFs, all of the 44 isolates can be placed in genotype J defined by the SNP profiles in ORF22 or clade B defined by the SNP profiles in ORFs 31, 37, 60, 62, 67, and 68. The three consecutive nucleotide (CGG) in-frame insertions in ORF 1 were found in 8 (18.2%) isolates, which has not been described in VZV strains from any other part of the world. A novel synonymous A>G substitution in ORF60 was revealed in 4 (9.1%) of the isolates. In addition, a previously described three consecutive nucleotide (ATC) insertion in ORF 60 was found in all the Chinese isolates but not in the US isolate MLS. The results showed all the 44 strains that belong to genotype J/clade B with significantly high homogeneity, and phylogenetic analysis suggested that the 44 Chinese isolates consist of 4 clusters, but interstrain variations also exist. Overall, VZV isolates obtained in China showed significantly higher genetic homogeneity than isolates reported from other countries.

scholarly journals Pangaea and the Out-of-Africa Model of Varicella-Zoster Virus Evolution and Phylogeography

2012 ◽  
Vol 86 (18) ◽  
pp. 9558-9565 ◽  
Author(s):  
Charles Grose
Keyword(s):  
Varicella Zoster Virus ◽  
Open Reading Frames ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type ◽  
Varicella Zoster ◽  
Building Models ◽  
Anatomically Modern Humans ◽  
Tree Building ◽  
Reading Frames

The goal of this minireview is to provide an overview of varicella-zoster virus (VZV) phylogenetics and phylogeography when placed in the broad context of geologic time. Planet Earth was formed over 4 billion years ago, and the supercontinent Pangaea coalesced around 400 million years ago (mya). Based on detailed tree-building models, the base of the phylogenetic tree of theHerpesviridaefamily has been estimated at 400 mya. Subsequently, Pangaea split into Laurasia and Gondwanaland; in turn, Africa rifted from Gondwanaland. Based on available data, the hypothesis of this minireview is that the ancestral alphaherpesvirus VZV coevolved in simians, apes, and hominins in Africa. When anatomically modern humans first crossed over the Red Sea 60,000 years ago, VZV was carried along in their dorsal root ganglia. Currently, there are five VZV clades, distinguishable by single nucleotide polymorphisms. These clades likely represent continued VZV coevolution, as humans with latent VZV infection left Arabia and dispersed into Asia (clades 2 and 5) and Europe (clades 1, 3, and 4). The prototype VZV sequence contains nearly 125,000 bp, divided into 70 open reading frames. Generally, isolates within a clade display >99.9% identity to one another, while members of one clade compared to a second clade show 99.8% identity to one another. Recently, four different VZV genotypes that do not segregate into the previously defined five clades have been identified, a result indicating a wider than anticipated diversity among newly collected VZV strains around the world.

Phylogenetic analysis of wheat cultivars in Kazakhstan based on the wheat 90 K single nucleotide polymorphism array

2015 ◽  
Vol 15 (1) ◽  
pp. 29-35 ◽  
Author(s):  
Yerlan Turuspekov ◽  
Joerg Plieske ◽  
Martin Ganal ◽  
Eduard Akhunov ◽  
Saule Abugalieva
Keyword(s):  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphism ◽  
Single Nucleotide Polymorphism Array ◽  
Genetic Relationships ◽  
Snp Array ◽  
Geographic Origin ◽  
Wheat Cultivars ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The World

The recent introduction of Illumina single nucleotide polymorphism (SNP) arrays is an important step towards comprehensive genome-wide studies of genetic diversity in wheat. In this study, 90 cultivars of hexaploid spring wheat growing in Kazakhstan were genotyped using the high-density wheat 90 K Illumina SNP array. The analysis allowed the identification of 30,288 polymorphic SNPs. A subset of 3541 high-quality SNPs were used for a comparison of 690 wheat accessions representing landraces and varieties, including those from Asia, Australia, Canada, Europe, Kazakhstan, USA and other parts of the world. Phylogenetic analysis showed a clear separation of wheat cultivars according to their geographic origin. In the phylogenetic tree, accessions from Kazakhstan and the USA formed two neighbouring clusters with a common node, and they were distinct from accessions from other regions of the world, including Europe. The results provide important new insights into the genetic relationships between diverse wheat accessions.

An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

2021 ◽  
Author(s):  
Juan F Cornejo-Franco ◽  
Francisco Flores ◽  
Dimitre Mollov ◽  
diego fernando quito-avila
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Genomic Features ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

scholarly journals Epigenetic Regulation of Varicella-Zoster Virus Open Reading Frames 62 and 63 in Latently Infected Human Trigeminal Ganglia

2006 ◽  
Vol 80 (10) ◽  
pp. 4921-4926 ◽  
Author(s):  
Lee Gary ◽  
Donald H. Gilden ◽  
Randall J. Cohrs
Keyword(s):  
Varicella Zoster Virus ◽  
Chromatin Immunoprecipitation ◽  
Latent Infection ◽  
Open Reading Frames ◽  
Trigeminal Ganglia ◽  
Varicella Zoster ◽  
Glycoprotein C ◽  
Latently Infected ◽  
Human Chromosome 4 ◽  
Reading Frames

ABSTRACT Open reading frames (ORFs) 21, 29, 62, 63, and 66 of varicella-zoster virus (VZV) are transcribed during latency in human ganglia. ORF 63 is the most frequently expressed gene, and ORF 62 encodes a transcriptional activator. The mechanisms regulating the expression of these genes are not well understood, although analyses of other alphaherpesviruses indicate a role for chromatin in virus gene regulation during latent infection. Using chromatin immunoprecipitation (ChIP) assays to analyze the euchromatic state of ORFs 62 and 63 compared to the centromere from human chromosome 4 (heterochromatic) and the human glyceraldehyde-3-phosphate dehydrogenase promoter (euchromatic), we show that the promoters of ORFs 62 and 63 are associated with the histone protein H3K9(Ac) and thus maintained in a euchromatic state during latency. Conversely, the promoters of ORF 36 (thymidine kinase) and ORF 14 (glycoprotein C), genes expressed during lytic but not latent infection, were not enriched in the fraction of latently infected ganglia that bound to anti-H3K9(Ac) antibody. A ChIP assay using productively infected MeWo cells revealed that VZV ORFs 62, 63, 36, and 14 are all euchromatic. Together, these data indicate that the expression of the two latency-related VZV genes, ORFs 62 and 63, is regulated epigenetically through chromatin structure.

Genetic diversity of limonene synthase genes in Rongan kumquat (Fortunella crassifolia)

2020 ◽  
Vol 47 (5) ◽  
pp. 425
Author(s):  
Mengyu Liu ◽  
Xiaofeng Liu ◽  
Junhua Hu ◽  
Yang Xue ◽  
Xiaochun Zhao
Keyword(s):  
Large Family ◽  
Open Reading Frames ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Geranyl Diphosphate ◽  
Limonene Synthase ◽  
High Amino Acid ◽  
Main Component ◽  
Reading Frames

D-limonene is the main component of citrus essential oils. In the monoterpene biosynthetic pathway, geranyl diphosphate reacts with monoterpenes to form the prenyl-carbocation intermediate to produce d-limonene. In this study, d-limonene synthase (FcLS) genes were first isolated from Rongan kumquat (Fortunella crassifolia Swingle). Sequencing analysis revealed that the open reading frames of 18 FcLS genes contain 12 single nucleotide polymorphisms, which resulted in the variation of FcLS proteins, indicating that the limonene synthase genes are a large family in F. crassifolia. This phenomenon has not been reported in Citrus. The predicted FcLS proteins showed a high amino acid sequence identity with other Citrus limonene synthases and also had the typical structures of limonene synthase protein. FcLS1 was validated to be a functional d-limonene synthase by prokaryotic expression.

scholarly journals SNPs in miRNAs and Target Sequences: Role in Cancer and Diabetes

2021 ◽  
Vol 12 ◽  
Author(s):  
Yogita Chhichholiya ◽  
Aman Kumar Suryan ◽  
Prabhat Suman ◽  
Anjana Munshi ◽  
Sandeep Singh
Keyword(s):  
Gene Expression ◽  
Single Nucleotide Polymorphism ◽  
Human Diseases ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Present Evidence ◽  
Single Target ◽  
The World ◽  
Target Sequences ◽  
Regulated Gene Expression

miRNAs are fascinating molecular players for gene regulation as individual miRNA can control multiple targets and a single target can be regulated by multiple miRNAs. Loss of miRNA regulated gene expression is often reported to be implicated in various human diseases like diabetes and cancer. Recently, geneticists across the world started reporting single nucleotide polymorphism (SNPs) in seed sequences of miRNAs. Similarly, SNPs are also reported in various target sequences of these miRNAs. Both the scenarios lead to dysregulated gene expression which may result in the progression of diseases. In the present paper, we explore SNPs in various miRNAs and their target sequences reported in various human cancers as well as diabetes. Similarly, we also present evidence of these mutations in various other human diseases.

scholarly journals Genomic Characterization of a New Enamovirus Infecting Common Bean

2021 ◽  
Author(s):  
Ruo-bin Lu ◽  
Ping-xiu Lan ◽  
Ru-jing Kang ◽  
Guan-lin Tan ◽  
Xiao-jiao Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Novel Species ◽  
Open Reading Frames ◽  
Amino Acid Sequence Level ◽  
Disease Symptoms ◽  
Bean Plants ◽  
Genomic Characterization ◽  
Pea Enation Mosaic Virus ◽  
Reading Frames

Abstract A novel enamovirus was identified from bean plants with disease symptoms. Its genome of 5,781 nucleotides (nt) encodes five open reading frames. The virus and other species of the genus Enamovirus share identities of 50.4%-68.4% at the complete genome, and 19.9%-51.9% of P0, 24.9%-52.5% of P1, 33.4%-62.9% of P1-P2, 30.6%-81.1% of P3, 32.3%-74.2% of P3-P5 at amino acid sequence level, respectively. Phylogenetic analysis showed that the virus is most closely related to Alfalfa enamovirus 1 and Pea enation mosaic virus 1 in the genus Enamovirus within family Solemoviridae. These results suggest that the virus should be considered as a novel species in the genus Enamovirus and tentatively named as “bean enamovirus 1”.

scholarly journals Reverse transcriptase-related enzymes are associated with horizontal chromosome transfer in an asexual pathogen

2015 ◽  
Author(s):  
Xiaoqiu Huang ◽  
Anindya Das ◽  
Binod B Sahu ◽  
Subodh K Srivastava ◽  
Leonor F Leandro ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Root Rot ◽  
Supernumerary Chromosome ◽  
Open Reading Frames ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Chromosome Transfer ◽  
Supernumerary Chromosomes ◽  
The Mean ◽  
Reading Frames

Supernumerary chromosomes have been shown to transfer horizontally from one isolate to another. However, the mechanism by which horizontal chromosome transfer (HCT) occurs is unknown. In this study, we compared the genomes of 11 isolates comprising six Fusarium species that cause soybean sudden death syndrome (SDS) or bean root rot (BRR), and detected numerous instances of HCT in supernumerary chromosomes. We also identified a statistically significant number (21 standard deviations above the mean) of single nucleotide polymorphisms (SNPs) in the supernumerary chromosomes between isolates of the asexual pathogen F. virguliforme. Supernumerary chromosomes carried reverse transcriptase-related genes (RVT); the presence of long RVT open reading frames (ORFs) in the supernumerary chromosome was correlated with the presence of two or more chromosome copies with a significant number of SNPs between them. Our results suggest that supernumerary chromosomes transfer horizontally via an RNA intermediate. Understanding the mechanism by which HCT occurs will have a profound impact on understanding evolution and applying biotechnology as well as accepting HCT as a natural source of genetic variation.

scholarly journals Polymorphism Study on SLC30A8 and Its Association with Type 2 Diabetes

2016 ◽  
Vol 02 ◽  
pp. 118
Author(s):  
M Vignesh ◽  
T Sangeetha ◽  
T Varsha ◽  
◽  
◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Tryptophan Residue ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The World ◽  
Hereditary Factors ◽  
The Common

Type 2 diabetes mellitus (T2DM) is one of the threatening disorders in the world. It affects people of all ages. Type 2 diabetes mellitus is a condition in which the glucose level in the blood is elevated due to improper function of the secretion of insulin from beta cells of the pancreas. It is a multifactorial disease because it is caused by both environmental and hereditary factors. One of the genes which play an important role in type 2 diabetes mellitus is SLC30A8 which encodes for zinc transporter ZnT8. The common polymorphic site for SLC30A8 is rs13266634. This single-nucleotide polymorphism leads to type 2 diabetes mellitus by replacing the arginine residue with tryptophan residue. This review mainly focuses on the polymorphic studies in the gene SLC30A8 and its association with type 2 diabetes mellitus.

scholarly journals Abundant Small Genetic Alterations after Upland Cotton Domestication

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Ying Bao ◽  
Xia Zhang ◽  
Xin Xu
Keyword(s):  
Upland Cotton ◽  
Genetic Alterations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genetic Changes ◽  
Noncoding Regions ◽  
Insertion And Deletion ◽  
Short Period ◽  
Wild Cotton ◽  
Reading Frames

Domestication has long been recognized as the most direct and effective way to intentionally influence morphological and physiological phenotypes in plants and animals. Consequently, understanding how small genetic alterations contribute to domestication is of considerable importance. In this study, we resequenced the genome of the wild upland cotton variety Gossypium hirsutum var. yucatanense, the putative wild ancestor of cultivated upland cotton, and then compared single nucleotide polymorphism (SNP) and short insertion and deletion (InDel) variations of the genome with the cultivated accession (TM-1) of G. hirsutum. We found approximately 6.6 million SNPs and 0.7 million InDels between the two genomes. Most of the small genetic variations were anchored in the noncoding regions. With regard to potential coding genes, we found 24,035 genes with nonsynonymous SNPs. Interestingly, 2603 genes in domesticated cotton are found that have changed the positions of stop codons or shifted reading frames from that in G. hirsutum var. yucatanense. This suggests that domestication may have been selected for mutations that restored gene function or that wild cotton has undergone a number of gene inactivation events since its divergence from cultivated cotton. The former scenario seems most likely due to the intense selective pressure applied during the domestication process. These results demonstrate that, within a relatively short period of time, the cotton genome has been readjusted through small genetic changes. The current study provides useful clues for seeking interesting genes for cotton improvement.

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