Structure and Temporal Dynamics of Populations within Wheat Streak Mosaic Virus Isolates

ABSTRACT Variation within the Type and Sidney 81 strains of wheat streak mosaic virus was assessed by single-strand conformation polymorphism (SSCP) analysis and confirmed by nucleotide sequencing. Limiting-dilution subisolates (LDSIs) of each strain were evaluated for polymorphism in the P1, P3, NIa, and CP cistrons. Different SSCP patterns among LDSIs of a strain were associated with single-nucleotide substitutions. Sidney 81 LDSI-S10 was used as founding inoculum to establish three lineages each in wheat, corn, and barley. The P1, HC-Pro, P3, CI, NIa, NIb, and CP cistrons of LDSI-S10 and each lineage at passages 1, 3, 6, and 9 were evaluated for polymorphism. By passage 9, each lineage differed in consensus sequence from LDSI-S10. The majority of substitutions occurred within NIa and CP, although at least one change occurred in each cistron except HC-Pro and P3. Most consensus sequence changes among lineages were independent, with substitutions accumulating over time. However, LDSI-S10 bore a variant nucleotide (G6016) in NIa that was restored to A6016 in eight of nine lineages by passage 6. This near-global reversion is most easily explained by selection. Examination of nonconsensus variation revealed a pool of unique substitutions (singletons) that remained constant in frequency during passage, regardless of the host species examined. These results suggest that mutations arising by viral polymerase error are generated at a constant rate but that most newly generated mutants are sequestered in virions and do not serve as replication templates. Thus, a substantial fraction of variation generated is static and has yet to be tested for relative fitness. In contrast, nonsingleton variation increased upon passage, suggesting that some mutants do serve as replication templates and may become established in a population. Replicated mutants may or may not rise to prominence to become the consensus sequence in a lineage, with the fate of any particular mutant subject to selection and stochastic processes such as genetic drift and population growth factors.

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Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus

Investigative Genetics ◽

10.1186/2041-2223-3-10 ◽

2012 ◽

Vol 3 (1) ◽

pp. 10 ◽

Cited By ~ 2

Author(s):

Stephanie M Rogers ◽

Mark Payton ◽

Robert W Allen ◽

Ulrich Melcher ◽

Jesse Carver ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Mosaic Virus ◽

Wheat Streak Mosaic Virus ◽

Single Nucleotide Polymorphism Genotyping ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genotyping Method

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Distribution of Fitness and Virulence Effects Caused by Single-Nucleotide Substitutions in Tobacco Etch Virus

Journal of Virology ◽

10.1128/jvi.00524-07 ◽

2007 ◽

Vol 81 (23) ◽

pp. 12979-12984 ◽

Cited By ~ 136

Author(s):

Purificación Carrasco ◽

Francisca de la Iglesia ◽

Santiago F. Elena

Keyword(s):

Single Case ◽

Site Directed Mutagenesis ◽

Relative Fitness ◽

In Planta ◽

Nucleotide Substitutions ◽

Phenotypic Effect ◽

Single Nucleotide ◽

Mutant Genotype

ABSTRACT Little is known about the fitness and virulence consequences of single-nucleotide substitutions in RNA viral genomes, and most information comes from the analysis of nonrandom sets of mutations with strong phenotypic effect or which have been assessed in vitro, with their relevance in vivo being unclear. Here we used site-directed mutagenesis to create a collection of 66 clones of Tobacco etch potyvirus, each carrying a different, randomly chosen, single-nucleotide substitution. Competition experiments between each mutant and the ancestral nonmutated clone were performed in planta to quantitatively assess the relative fitness of each mutant genotype. Among all mutations, 40.9% were lethal, and among the viable ones, 36.4% were significantly deleterious and 22.7% neutral. Not a single case of beneficial effects was observed within the level of resolution of our measures. On average, the fitness of a genotype carrying a deleterious but viable mutation was 49% smaller than that for its unmutated progenitor. Deleterious mutational effects conformed to a beta probability distribution. The virulence of a subset of viable mutants was assessed as the reduction in the number of viable seeds produced by infected plants. Mutational effects on virulence ranged between 17% reductions and 24.4% increases. Interestingly, the only mutations showing a significant effect on virulence were hypervirulent. Competitive fitness and virulence were uncorrelated traits.

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Different Mutations in the Genome-Linked Protein VPg of Potato virus Y Confer Virulence on the pvr23 Resistance in Pepper

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-19-0557 ◽

2006 ◽

Vol 19 (5) ◽

pp. 557-563 ◽

Cited By ~ 86

Author(s):

Valérie Ayme ◽

Sylvie Souche ◽

Carole Caranta ◽

Mireille Jacquemond ◽

Joël Chadœuf ◽

...

Keyword(s):

Amino Acid ◽

Genetic Drift ◽

Potato Virus ◽

High Frequency ◽

Potato Virus Y ◽

Relative Fitness ◽

Amino Acid Substitutions ◽

Nucleotide Substitutions ◽

Single Nucleotide ◽

Pepper Plants

Five different amino acid substitutions in the VPg of Potato virus Y were shown to be independently responsible for virulence toward pvr23 resistance gene of pepper. A consequence of these multiple mutations toward virulence involving single nucleotide substitutions is a particularly high frequency of resistance breaking (37% of inoculated plants from the first inoculation) and suggests a potentially low durability of pvr23 resistance. These five mutants were observed with significantly different frequencies, one of them being overrepresented. Genetic drift alone could not explain the observed distribution of virulent mutants. More plausible scenarios were obtained by taking into account either the relative substitution rates, the relative fitness of the mutants in pvr23 pepper plants, or both.

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High-Throughput Mutation Detection Method to Scan BRCA1 and BRCA2 Based on Heteroduplex Analysis by Capillary Array Electrophoresis

Clinical Chemistry ◽

10.1373/clinchem.2003.023614 ◽

2004 ◽

Vol 50 (2) ◽

pp. 313-320 ◽

Cited By ~ 20

Author(s):

Eva Esteban-Cardeñosa ◽

Mercedes Duran ◽

Mar Infante ◽

Eladio Velasco ◽

Cristina Miner

Keyword(s):

Single Strand Conformation Polymorphism ◽

Heteroduplex Analysis ◽

Breast Cancer Patients ◽

Brca1 And Brca2 ◽

Nucleotide Substitutions ◽

Single Nucleotide ◽

Coding Regions ◽

Hands On ◽

Dna Sequence Variants ◽

Capillary Array

Abstract Background: Scanning for mutations in BRCA1 and BRCA2 in a large number of samples is hampered by the large sizes of these genes and the scattering of mutations throughout their coding sequences. Automated capillary electrophoresis has been shown to be a powerful system to detect mutations by either single-strand conformation polymorphism or heteroduplex analysis (HA). Methods: We investigated the adaptation of gel-based HA of BRCA1 and BRCA2 to a fluorescent multicapillary platform to increase the throughput of this technique. We combined multiplex PCR, three different fluorescent labels, and HA in a 16-capillary DNA sequencer and tested 57 DNA sequence variants (11 insertions/deletions and 46 single-nucleotide changes) of BRCA1 and BRCA2. Results: We detected all 57 DNA changes in a blinded assay, and 2 additional single-nucleotide substitutions (1186 A>G of BRCA1 and 3624 A>G of BRCA2), previously unresolved by conformation-sensitive gel electrophoresis. Furthermore, different DNA changes in the same PCR fragment could be distinguished by their peak patterns. Conclusions: Capillary-based HA is a fast, efficient, and sensitive method that considerably reduces the amount of “hands-on” time for each sample. By this approach, the entire coding regions of BRCA1 and BRCA2 from two breast cancer patients can be scanned in a single run of 90 min.

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Rapid evolutionary dynamics of the Pepino mosaic virus – status and future perspectives

Journal of Plant Protection Research ◽

10.1515/jppr-2016-0054 ◽

2016 ◽

Vol 56 (4) ◽

pp. 337-345 ◽

Cited By ~ 3

Author(s):

Julia Minicka ◽

Beata Hasiów-Jaroszewska ◽

Natasza Borodynko-Filas ◽

Henryk Pospieszny ◽

Inge Maria Hanssen

Keyword(s):

Mosaic Virus ◽

Evolutionary Dynamics ◽

Current Knowledge ◽

Plant Protection ◽

Diagnostic Tools ◽

Nucleotide Substitutions ◽

Single Nucleotide ◽

Pepino Mosaic Virus ◽

Worldwide Population ◽

Protection Strategies

AbstractPepino mosaic virus (PepMV) has emerged as an important pathogen of greenhouse tomato crops and is currently distributed worldwide. Population genetic studies have revealed a shift in the dominant PepMV genotype from European (EU) to Chilean 2 (CH2) in North America and several European countries. New genetic variants are constantly being created by mutation and recombination events. Single nucleotide substitutions in different parts of the genome were found to affect on development of symptoms resulting in new pathotypes and accumulation of viral RNA. The variability of the PepMV population has a great impact on designing specific diagnostic tools and developing efficient and durable strategies of disease control. In this paper we review the current knowledge about the PepMV population, the evolutionary dynamics of this highly infective virus, methods for its detection and plant protection strategies.

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Nucleotide substitutions in the Candida albicans ERG11 gene of azole-susceptible and azole-resistant clinical isolates.

Acta Biochimica Polonica ◽

10.18388/abp.2013_2019 ◽

2013 ◽

Vol 60 (4) ◽

Cited By ~ 8

Author(s):

Joanna Katarzyna Strzelczyk ◽

Anna Slemp-Migiel ◽

Magdalena Rother ◽

Karolina Gołąbek ◽

Andrzej Wiczkowski

Keyword(s):

Candida Albicans ◽

Sequence Analysis ◽

Point Mutations ◽

Single Strand Conformation Polymorphism ◽

Clinical Isolates ◽

Primary Target ◽

Nucleotide Substitutions ◽

Single Nucleotide ◽

Conformation Polymorphism

One of the mechanisms of Candida albicans resistance to azole drugs used in antifungal therapy relies on increased expression and presence of point mutations in the ERG11 gene that encodes sterol 14α demethylase (14DM), an enzyme which is the primary target for the azole class of antifungals. The aim of the study was to analyze nucleotide substitutions in the Candida albicans ERG11 gene of azole-susceptible and azole-resistant clinical isolates. The Candida albicans isolates represented a collection of 122 strains selected from 658 strains isolated from different biological materials. Samples were obtained from hospitalized patients. Fluconazole susceptibility was tested in vitro using a microdilution assay. Candida albicans strains used in this study consisted of two groups: 61 of the isolates were susceptible to azoles and the 61 were resistant to azoles. Four overlapping regions of the ERG11 gene of the isolates of Candida albicans strains were amplified and sequenced. The MSSCP (multitemperature single strand conformation polymorphism) method was performed to select Candida albicans samples presenting genetic differences in the ERG11 gene fragments for subsequent sequence analysis. Based on the sequencing results we managed to detect 19 substitutions of nucleotides in the ERG11 gene fragments. Sequencing revealed 4 different alterations: T495A, A530C, G622A and A945C leading to changes in the corresponding amino acid sequence: D116E, K128T, V159I and E266D. The single nucleotide changes in the ERG11 gene did not affect the sensitivity of Candida albicans strains, whereas multiple nucleotide substitutions in the ERG11 gene fragments indicated a possible relation with the increase in resistance to azole drugs.

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