tetano
Editor, Senior Moderator
Gene Rep
. 2021 Jan 26;23:101020.
doi: 10.1016/j.genrep.2021.101020. Online ahead of print.
Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes
Rasel Siddiqe[SUP] 1 [/SUP], Ajit Ghosh[SUP] 1 [/SUP]
Affiliations
Abstract
Simple sequence repeats (SSR) or, Microsatellites are short repeat sequences that have been extensively studied in eukaryotic (plants) and prokaryotic (bacteria) organisms. Compared to other organisms, studies the presence and incidence of SSR on viral genomes are less numerous. 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 was no tetra- or pent-nucleotide repeats in the analyzed SARS-CoV-2 genomes. The discovery of microsatellites in SARS-CoV-2 genomes may become useful for the population genetic, evolutionary analysis, strain identification and genetic variation.
Keywords: (COVID-19), Coronavirus disease 2019; (HCV), Hepatitis C virus; (RA), Relative Abundance; (RD), Relative Density; (SARS-CoV-2), severe acute respiratory syndrome coronavirus 2; (SSR), Simple sequence repeats; (SpliMNPV), Spodoptera littoralis multiple nucleopolyhedrovirus; Comparative genomics; Microsatellite; SARS-CoV-2 virus; Simple sequence repeat; genome sequence.
. 2021 Jan 26;23:101020.
doi: 10.1016/j.genrep.2021.101020. Online ahead of print.
Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes
Rasel Siddiqe[SUP] 1 [/SUP], Ajit Ghosh[SUP] 1 [/SUP]
Affiliations
- PMID: 33521382
- PMCID: PMC7835092
- DOI: 10.1016/j.genrep.2021.101020
Abstract
Simple sequence repeats (SSR) or, Microsatellites are short repeat sequences that have been extensively studied in eukaryotic (plants) and prokaryotic (bacteria) organisms. Compared to other organisms, studies the presence and incidence of SSR on viral genomes are less numerous. 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 was no tetra- or pent-nucleotide repeats in the analyzed SARS-CoV-2 genomes. The discovery of microsatellites in SARS-CoV-2 genomes may become useful for the population genetic, evolutionary analysis, strain identification and genetic variation.
Keywords: (COVID-19), Coronavirus disease 2019; (HCV), Hepatitis C virus; (RA), Relative Abundance; (RD), Relative Density; (SARS-CoV-2), severe acute respiratory syndrome coronavirus 2; (SSR), Simple sequence repeats; (SpliMNPV), Spodoptera littoralis multiple nucleopolyhedrovirus; Comparative genomics; Microsatellite; SARS-CoV-2 virus; Simple sequence repeat; genome sequence.