Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes.
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.
COVID-19, coronavirus disease 2019; Comparative genomics; Genome sequence; HCV, hepatitis C virus; Microsatellite; RA, relative abundance; RD, relative density; SARS-CoV-2 virus; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SSR, simple sequence repeats; Simple sequence repeat; SpliMNPV, Spodoptera littoralis multiple nucleopolyhedrovirus
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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