scholarly journals Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of Vinca minor and Wisteria sinensis in Iran: with Implications for the Genetic Structure of the Virus

2021 ◽  
Vol 37 (6) ◽  
pp. 619-631
Author(s):  
Zohreh Moradi ◽  
Mohsen Mehrvar
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Mosaic Virus ◽  
De Novo ◽  
Alfalfa Mosaic Virus ◽  
Dominant Negative ◽  
Chinese Isolate ◽  
Vinca Minor ◽  
Canadian Isolate ◽  
Wisteria Sinensis

Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.

scholarly journals Metagenomic Analysis Reveals a Nearly Complete Genome Sequence of Alfalfa Mosaic Virus from a Field Pea in Australia

2019 ◽  
Vol 8 (31) ◽  
Author(s):  
S. Maina ◽  
L. Zheng ◽  
W. M. Kinoti ◽  
M. Aftab ◽  
N. Nancarrow ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Alfalfa Mosaic Virus ◽  
Field Pea ◽  
Metagenomic Analysis ◽  
Chinese Isolate

Here, we report the first nearly complete genome sequence of Alfalfa mosaic virus (AMV) obtained from a symptomatic field pea sample (Aus295) in Australia. Its genome RNA1 and RNA2 segments resembled those of the Argentinian isolate Manfredi, with 99.4% and 96.7% nucleotide (nt) identity, respectively; its RNA3 segment resembled that of Chinese isolate AMV-Gyn, with 99.6% nt identity.

Microsatellite loci and the complete mitochondrial DNA sequence characterised through next-generation sequencing and de novo genome assembly, and a preliminary assessment of population genetic structure for the Australian crane, Antigone rubicunda

2019 ◽  
Vol 12 (2) ◽  
pp. 49-58
Author(s):  
Adam D Miller ◽  
Inka Veltheim ◽  
Timothy Nevard ◽  
Han Ming Gan ◽  
Martin Haase
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Genetic Structure ◽  
Mitochondrial Genome ◽  
Microsatellite Markers ◽  
Genome Sequence ◽  
Population Genetic ◽  
De Novo ◽  
South Eastern ◽  
Generation Sequencing

The Brolga ( Antigone rubicunda) is a large Australian crane species with a broad distribution spanning from the tropical north to the south-eastern regions of the continent. Brolga populations throughout New South Wales, Victoria and South Australia have been in decline since the early twentieth century, with the species being listed as vulnerable in each state. To aid future conservation of the species, its taxonomic status needs to be validated, and patterns of gene flow and population connectivity across the species distribution need to be understood. To assist future genetic studies, we developed a suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence by next-generation sequencing. A total of 18 polymorphic loci were characterised using DNA extractions from 47 individuals, comprising 30 and 17 individuals from Victoria and northern Australia, respectively. We observed moderate genetic variation across loci with only a single locus deviating significantly from Hardy–Weinberg equilibrium. De novo and reference-based genome assemblies were used to assemble the A. rubicunda mitochondrial genome sequence, which consists of 16,700 base pairs, and a typical metazoan mitochondrial gene content and arrangement. We test these new markers by conducting a preliminary analysis of genetic structure between south-eastern and northern Australian Brolga populations. Mitochondrial analyses provided evidence of shared haplotypes across the species range supporting the conspecific status of extant populations, while microsatellite markers indicated weak but significant genetic differentiation suggesting gene flow is limited. We discuss the implications of these findings and the benefits that these genetic markers will provide for future population genetic research on this iconic Australian bird species.

scholarly journals Cowpea Mosaic Virus Infection Induces a Massive Proliferation of Endoplasmic Reticulum but Not Golgi Membranes and Is Dependent on De Novo Membrane Synthesis

2000 ◽  
Vol 74 (14) ◽  
pp. 6556-6563 ◽  
Author(s):  
Jan E. Carette ◽  
Marchel Stuiver ◽  
Jan Van Lent ◽  
Joan Wellink ◽  
Ab Van Kammen
Keyword(s):  
Endoplasmic Reticulum ◽  
Mosaic Virus ◽  
Fluorescent Protein ◽  
De Novo ◽  
Alfalfa Mosaic Virus ◽  
Lipid Synthesis ◽  
Cowpea Mosaic Virus ◽  
Living Plant ◽  
Fluorescence Confocal Microscopy ◽  
Golgi Membranes

ABSTRACT Replication of cowpea mosaic virus (CPMV) is associated with small membranous vesicles that are induced upon infection. The effect of CPMV replication on the morphology and distribution of the endomembrane system in living plant cells was studied by expressing green fluorescent protein (GFP) targeted to the endoplasmic reticulum (ER) and the Golgi membranes. CPMV infection was found to induce an extensive proliferation of the ER, whereas the distribution and morphology of the Golgi stacks remained unaffected. Immunolocalization experiments using fluorescence confocal microscopy showed that the proliferated ER membranes were closely associated with the electron-dense structures that contain the replicative proteins encoded by RNA1. Replication of CPMV was strongly inhibited by cerulenin, an inhibitor of de novo lipid synthesis, at concentrations where the replication of the two unrelated viruses alfalfa mosaic virus and tobacco mosaic virus was largely unaffected. These results suggest that proliferating ER membranes produce the membranous vesicles formed during CPMV infection and that this process requires continuous lipid biosynthesis.

THESIS SUMMARY STUDIES OF ALFALFA MOSAIC VIRUS AND SUBTERRANEAN CLOVER RED LEAF VIRUS

1979 ◽  
pp. 163-164
Author(s):  
P.B. Teh
Keyword(s):  
Mosaic Virus ◽  
Alfalfa Mosaic Virus ◽  
Subterranean Clover ◽  
Test Plant ◽  
Transmission Frequency ◽  
Virus Source ◽  
Leaf Virus

AMV was shown to be transmitted by sap, aphids and through lucerne seed, but not by Cuscuta. Virus source and test plant influenced transmission frequency. Sap-inoculation tests showed that 20 species of plants were susceptible to this virus. Thirteen species of plants from the fields where AMV had been detected were tested but only three were found to be infected with the virus.

scholarly journals A Novel Intronic Pathogenic Variant in STAR With a Dominant Negative Mechanism Causes Attenuated Lipoid Congenital Adrenal Hyperplasia

2021 ◽  
Vol 9 ◽  
pp. 232470962110146
Author(s):  
Erin Finn ◽  
Kimberly Kripps ◽  
Christina Chambers ◽  
Michele Rapp ◽  
Naomi J. L. Meeks ◽  
...  
Keyword(s):  
Congenital Adrenal Hyperplasia ◽  
Autosomal Recessive ◽  
De Novo ◽  
Dominant Negative ◽  
Adrenal Hyperplasia ◽  
Primary Adrenal Insufficiency ◽  
Heterozygous Variant ◽  
Novel Variant ◽  
Autosomal Recessive Condition ◽  
Clinically Significant

Lipoid congenital adrenal hyperplasia (LCAH) is typically inherited as an autosomal recessive condition. There are 3 reports of individuals with a dominantly acting heterozygous variant leading to a clinically significant phenotype. We report a 46,XY child with a novel heterozygous intronic variant in STAR resulting in LCAH with an attenuated genital phenotype. The patient presented with neonatal hypoglycemia and had descended testes with a fused scrotum and small phallus. Evaluation revealed primary adrenal insufficiency with deficiencies of cortisol, aldosterone, and androgens. He was found to have a de novo heterozygous novel variant in STAR: c.65-2A>C. We report a case of a novel variant and review of other dominant mutations at the same position in the literature. Clinicians should be aware of the possibility of attenuated genital phenotypes of LCAH and the contribution of de novo variants in STAR at c.65-2 to the pathogenesis of that phenotype.

scholarly journals Hierarchical Analysis of Genetic Structure in Native Fire Ant Populations: Results From Three Classes of Molecular Markers

Genetics ◽  
1997 ◽  
Vol 147 (2) ◽  
pp. 643-655 ◽  
Author(s):  
Kenneth G Ross ◽  
Michael J B Krieger ◽  
D DeWayne Shoemaker ◽  
Edward L Vargo ◽  
Laurent Keller
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Solenopsis Invicta ◽  
Large Scale ◽  
Fire Ant ◽  
Nuclear Markers ◽  
Social Forms ◽  
Native Populations ◽  
Nest Level ◽  
Nuclear Differentiation

We describe genetic structure at various scales in native populations of the fire ant Solenopsis invicta using two classes of nuclear markers, allozymes and microsatellites, and markers of the mitochondrial genome. Strong structure was found at the nest level in both the monogyne (single queen) and polygyne (multiple queen) social forms using allozymes. Weak but significant microgeographic structure was detected above the nest level in polygyne populations but not in monogyne populations using both classes of nuclear markers. Pronounced mitochondrial DNA (mtDNA) differentiation was evident also at this level in the polygyne form only. These microgeographic patterns are expected because polygyny in ants is associated with restricted local gene flow due mainly to limited vagility of queens. Weak but significant nuclear differentiation was detected between sympatric social forms, and strong mtDNA differentiation also was found at this level. Thus, queens of each form seem unable to establish themselves in nests of the alternate type, and some degree of assortative mating by form may exist as well. Strong differentiation was found between the two study regions usinga all three sets of markers. Phylogeographic analyses of the mtDNA suggest that recent limitations on gene flow rather than longstanding barriers to dispersal are responsible for this large-scale structure.

scholarly journals Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

Genetics ◽  
1997 ◽  
Vol 147 (4) ◽  
pp. 1843-1854 ◽  
Author(s):  
Nancy N FitzSimmons ◽  
Craig Moritz ◽  
Colin J Limpus ◽  
Lisa Pope ◽  
Robert Prince
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Green Turtle ◽  
Nuclear Dna ◽  
Nuclear Gene ◽  
Chelonia Mydas ◽  
Single Copy ◽  
Microsatellite Data ◽  
Ecological Data ◽  
Infinite Allele Model

Abstract The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

Osmotic stress-induced remodeling of the cortical cytoskeleton

2002 ◽  
Vol 283 (3) ◽  
pp. C850-C865 ◽  
Author(s):  
Caterina Di Ciano ◽  
Zilin Nie ◽  
Katalin Szászi ◽  
Alison Lewis ◽  
Takehito Uruno ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
De Novo ◽  
Small Gtpases ◽  
Dominant Negative ◽  
Actin Binding ◽  
Cell Cortex ◽  
Actin Assembly ◽  
Signaling Mechanism ◽  
Actin Binding Domain ◽  
Cytoskeleton Remodeling

Osmotic stress is known to affect the cytoskeleton; however, this adaptive response has remained poorly characterized, and the underlying signaling pathways are unexplored. Here we show that hypertonicity induces submembranous de novo F-actin assembly concomitant with the peripheral translocation and colocalization of cortactin and the actin-related protein 2/3 (Arp2/3) complex, which are key components of the actin nucleation machinery. Additionally, hyperosmolarity promotes the association of cortactin with Arp2/3 as revealed by coimmunoprecipitation. Using various truncation or phosphorylation-incompetent mutants, we show that cortactin translocation requires the Arp2/3- or the F-actin binding domain, but the process is independent of the shrinkage-induced tyrosine phosphorylation of cortactin. Looking for an alternative signaling mechanism, we found that hypertonicity stimulates Rac and Cdc42. This appears to be a key event in the osmotically triggered cytoskeletal reorganization, because 1) constitutively active small GTPases translocate cortactin, 2) Rac and cortactin colocalize at the periphery of hypertonically challenged cells, and 3) dominant-negative Rac and Cdc42 inhibit the hypertonicity-provoked cortactin and Arp3 translocation. The Rho family-dependent cytoskeleton remodeling may be an important osmoprotective response that reinforces the cell cortex.

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