Utilization of Microsatellite Polymorphism for Differentiating Herpes Simplex Virus Type 1 Strains

Deback, Claire; Boutolleau, David; Depienne, Christel; Luyt, Charles‐Édouard; Bonnafous, Pascale; Gautheret‐Dejean, Agnès; Garrigue, Isabelle; Agut, Henri

doi:10.1128/jcm.01565-08

Cited by 58 publications

(56 citation statements)

References 53 publications

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“…Also, repeat sequences are known to account for genome evolution and adaptation. This is accomplished through their ability to act as hot spots for mutation and association with strand slippage inducing copy number variations and polymorphisms (12,27,28).…”

Section: Motif Types and Iterationsmentioning

confidence: 99%

Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

Alam

Iqbal²,

Tripathi

et al. 2017

Gene Cell Tissue

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The present study focused on Staphylococcus phage genomes, which have been classified to 3 categories on the basis of their size. Overall, 18 classes of II Staphylococcus phage genomes with genome size around 40 kbp were investigated to elucidate the presence, distribution, and complexity of SSRs therein. The full length genome sequences from NCBI were analyzed using the IMEx software. A total of 3656 simple sequence repeats (SSRs) and 213 compound SSRs (cSSR) were present in the studied genomes. The incident frequency of SSR and cSSR per genome ranged from 183 to 308 and 8 to 19, respectively. The SSRs distribution across genomes was non-linear and so was its conversion to cSSR (the range of cSSR percentage was from 4.15 to 9.13) implicating a non-uniform incidence and clustering in genomes. The AT rich content of genomes was reflected in the prevalence of repeats with A, AT/TA, and AAG/GAA being the highest represented mono-, di-, and tri-nucleotide repeat motifs, respectively. An increase in dMAX was accompanied by greater cSSRs in the genomes yet the increase was neither uniform across genomes nor linear. The SSRs and cSSRs are predominantly localized on the coding region. The non-coding region accounts for~19% in SSR and~30% in cSSR while a hypothetical protein accounted for~30% in SSRs as well as cSSR. The relative frequencies and distribution of different classes of simple and compound microsatellites within and across genomes are suggestive of these sequences being involved in genome evolution and adaptation.

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Section: Motif Types and Iterationsmentioning

confidence: 99%

Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

Alam

Iqbal²,

Tripathi

et al. 2017

Gene Cell Tissue

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“…In prokaryotic genomes, a mononucleotide repeat of eight nucleotides in length was found to be polymorphic (Gur-Arie et al, 2000). Polymorphic microsatellites have been observed in virus genomes such as those of HIV, HCV (Chen et al, 2011), human cytomegalovirus (Davis et al, 1999), and herpes simplex virus type 1 strains (Deback et al, 2009). In CaMV the CT-rich motif located downstream of the transcription start site of the CaMV 35S promoter is involved in enhancing gene expression and in interaction with plant nuclear proteins (Pauli et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

“…However, such small microsatellite repeats have been previously shown to be useful as polymorphic markers (Deback et al, 2009). In this report we analyzed simple and complex SSRs from 36 completely sequenced genomes belonging to the family Closteroviridae, representing at least one member from each of the three genera.…”

Section: Discussionmentioning

confidence: 99%

“…Strand slippage and unequal recombination leads to variation in the number of copies of microsatellites (Toth et al, 2000), thereby making them an important source of genetic diversity and critical players in genome evolution (Kashi and King, 2006;Deback et al, 2009). Indeed, polymorphic microsatellites have been used to identify relationships between virus isolates (Deback et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

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In silico genome-wide identification and analysis of microsatelliterepeats in the largest RNA virus family (Closteroviridae)

George¹,

George²,

Awasthi³

et al. 2016

Turk J Biol

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Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life, including viruses. Members of the family Closteroviridae are the largest RNA viruses and severely affect different agricultural crops worldwide, including citrus, grapevine, and vegetables. Here we identified and systematically analyzed the nature and distribution of both simple and complex microsatellites present in the complete genome of 36 species belonging to Closteroviridae. Our results showed, in all analyzed genomes, that neither genome size nor GC content had any influence on number, relative abundance, or relative density of microsatellites. For each genome, dinucleotide repeats were found to be highly predominant and AT/TA and AG/GA were the two most abundant dinucleotide repeat motifs. Repeats larger than trinucleotide were relatively rare in these viral genomes. Comparative study of occurrence, abundance, and density of microsatellites among available RNA and DNA viral genomes indicated that simple repeats were less abundant in genomes of Closteroviridae. To our knowledge, this is the first analysis of microsatellites occurring in the largest viral genome that infects plants. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.

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“…For instance, the more the number of repeats, the higher the mutability (7). Moreover, variations in copy number due to strand slippage and unequal recombination highlight the instability of the microsatellites (5); which in turn makes them a predominant source of genetic diversity and a crucial player in viral genome evolution (8,9). Variable length of microsatellites may affect local DNA structure or the encoded proteins (6) and hence influence the expression profile of the corresponding genes.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

2015

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Background:Microsatellites have evoked the interest of researchers owing to their applications in different fields such as DNA fingerprinting, genetic mapping, population genetics, forensics, paternity studies and evolution. Objectives: The present study focused on the analysis of simple sequence repeats (SSRs) in genomes of seven species from three genera of the Filoviridae family. Materials and Methods: Genome sequences of seven species from the Filoviridae family were assessed by the National Center for Biotechnology Information (NCBI), microsatellites were extracted using the IMEx software, and statistical analysis was performed Microsoft Office Excel 2007. Results: A total of 516 microsatellites and 14 Compound Simple Sequence Repeats (cSSR) (also known as compound microsatellites) were extracted. Evidently, the conversion of SSRs to cSSR was low. Mononucleotide A/T was the most prevalent followed by dinucleotide AC/CA and trinucleotide AAC/CAA. Highest incidence of SSRs (mon-/di-nucleotide motif) was observed in RNA Dependent RNA Polymerase (RDRP) gene whereas tri-nucleotide motif was maximally localized in nucleoproteins (NP). Conclusions:The salient features of simple and compound microsatellites in Filoviridae family have been highlighted herein. Microsatellite regions with higher mutation rates compared to the rest of the genome play a crucial role in genome evolution by acting as a source of quantitative genetic variation. The SSR mutation rate is known to be affected by motif length, motif sequence, and number of repeats and purity of repetition. The functional role of tandem repeats in viruses, remains to be fully elucidated. However, with the repetitive sequence allegedly acting as a hot spot for recombination, we postulate their involvement in genetic events such as recombination, replication, and repair mechanisms that drive sequence diversity leading to the formation of the genetic basis of adaptation.

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Utilization of Microsatellite Polymorphism for Differentiating Herpes Simplex Virus Type 1 Strains

Cited by 58 publications

References 53 publications

Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

In silico genome-wide identification and analysis of microsatelliterepeats in the largest RNA virus family (Closteroviridae)

Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

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