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Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes.
Siddiqe, Rasel; Ghosh, Ajit.
  • Siddiqe R; Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
  • Ghosh A; Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
Gene Rep ; 23: 101020, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1051645
ABSTRACT
Simple sequence repeats (SSRs) or, Microsatellites are short repeat sequences that have been extensively studied in eukaryotic (plants) and prokaryotic (bacteria) organisms. Compared to other organisms, the presence and incidence of SSR on viral genomes are less studied. With the emergence of novel infectious viruses over the past few decades, it is imperative to study the genetic diversity in such viruses to predict their evolutionary and functional changes over time. Following the emergence of SARS-CoV-2, we have assembled 121 complete genomes reported from 31 countries across the six continents for the identification and characterization of SSR repeats. Using two independent SSR identification tools, we have found remarkable consistency in the diversity of microsatellites pattern (38-42 per genome) found in the 121 analyzed SARS-CoV-2 genomes indication their important role for genome stability. Among the identified motifs, trinucleotide and hexanucleotide repeats were found to be the most abundant form followed by mono- and di-nucleotide. There were no tetra- or penta-nucleotide repeats in the analyzed SARS-CoV-2 genomes. The discovery of microsatellites in SARS-CoV-2 genomes may become useful for the population genetics, evolutionary analysis, strain identification and genetic variation.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study / Prognostic study Language: English Journal: Gene Rep Year: 2021 Document Type: Article Affiliation country: J.genrep.2021.101020

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study / Prognostic study Language: English Journal: Gene Rep Year: 2021 Document Type: Article Affiliation country: J.genrep.2021.101020