In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes

Alam, Chaudhary Mashhood; Singh, Avadhesh Kumar; Sharfuddin, Choudhary; Ali, Safdar

doi:10.1016/j.gene.2013.08.046

Cited by 27 publications

(21 citation statements)

References 45 publications

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“…For our analysis, we used 11 proteins present in most number of species (Figure 6). Coding regions accounting for over 80% of the total SSRs has been observed in earlier studies [17][18][19][20][21][22] across a diverse set of viruses suggestive of their role in gene expression, regulation and evolution. In the present study, interestingly, there was no cSSR present in the non-coding region ( Figure 6).…”

Section: Ssrs/cssrs In Coding Regionsmentioning

confidence: 99%

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Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus

Alam¹

2016

J Data Mining Genomics Proteomics

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Simple sequence repeats (SSRs), also known as microsatellites, are 1-6 nucleotides repeat motif, present in varying number of iterations, across coding and non-coding regions of prokaryotes, eukaryotes and viruses. Present study focuses on simple sequence repeats (SSRs) in 27 Flavivirus genomes, which includes dengue virus. The comparative viral genomics in the light of SSRs would help us understand the diversity and adaptability to new hosts. A total of 1164 SSRs and 53 cSSRs were uncovered from the 27studied genomes. Mononucleotide A was the most prevalent repeat motif with an average distribution of around 6. This was followed by G (average distribution of 2). Amongst the dinucleotides AG/GA repeat motif was the most prevalent with an average distribution of 14 across studied genomes. The Flavivirus genomes lacked two essential features responsible for genome evolution, dinucleotide repeat motif AT/TA (least represented with average distribution of ~0.5) and cSSR in non-coding regions, suggesting a stable genome or evolution by hitherto unexplained mechanisms. The unveiling of conserved sequences in the isolates of Dengue virus suggests a basis for biomarker development for viral diagnostics.

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Section: Ssrs/cssrs In Coding Regionsmentioning

confidence: 99%

“…IMEx has been widely used to obtain the SSRs in a genome [17][18][19][20][21][22]. However, for subsequent analysis we developed two MATLAB based tools namely Identification of Gene Location from NCBI Nucleotide File (IGLNNF) and In-corporation of Gene Location in SSR File (IGLSF).…”

Section: Matlab Based Tools For Ssr Analysismentioning

confidence: 99%

Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus

Alam¹

2016

J Data Mining Genomics Proteomics

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“…The analysis was done using the 'Advance-Mode' of IMEx with parameters as reported earlier (17)(18)(19)(20)(21)(22)(23). Two SSRs separated by a distance of ≤ dMAX were treated as compound SSR (cSSR).…”

Section: Microsatellite Extractionmentioning

confidence: 99%

“…The use of IMEx to extract SSRs in a genome is welldocumented (17)(18)(19)(20)(21)(22)(23). However, subsequent to SSR extraction, obtaining the gene locations as well as incorporation of SSRs in the genome is still a manual process.…”

Section: Matlab-based Ssr Analysismentioning

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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“…Earlier studies on eukaryotes and E. coli genomes have focused on microsatellites with lengths of 12 bp or more (5), yet due to the smaller size of the Filoviridae family genome, simple and compound microsatellite search using these parameters did not yield any results. Therefore, the search for simple and compound microsatellites was accomplished with the 'Advance-Mode' of IMEx using the parameters used for HIV (15), potexvirus, carlavirus, tobamovirus and potyvirus (25)(26)(27)(28). The parameters were set as follows: type of repeat: perfect; repeat size: all; minimum repeat number: 6, 3, 3, 3, 3, 3; and maximum distance allowed between any two SSRs (dMAX) was 10.…”

Section: Microsatellite Identification and Investigationmentioning

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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In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes

Cited by 27 publications

References 45 publications

Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus

Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus

Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

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

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