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Deciphering the SSR incidences across viral members of Coronaviridae family
Presence of Simple Sequence Repeats (SSRs), both in genic and intergenic regions, have been widely studied in eukaryotes, prokaryotes, and viruses. In the current study, we undertook a survey to analyze the frequency and distribution of microsatellites or SSRs in multiple genomes of Coronaviridae me...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier B.V.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7505113/ https://www.ncbi.nlm.nih.gov/pubmed/32971122 http://dx.doi.org/10.1016/j.cbi.2020.109226 |
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author | Satyam, Rohit Jha, Niraj Kumar Kar, Rohan Jha, Saurabh Kumar Sharma, Ankur Kumar, Dhruv Nand, Parma Ruokolainen, Janne Kesari, Kavindra Kumar Kamal, Mohammad Amjad |
author_facet | Satyam, Rohit Jha, Niraj Kumar Kar, Rohan Jha, Saurabh Kumar Sharma, Ankur Kumar, Dhruv Nand, Parma Ruokolainen, Janne Kesari, Kavindra Kumar Kamal, Mohammad Amjad |
author_sort | Satyam, Rohit |
collection | PubMed |
description | Presence of Simple Sequence Repeats (SSRs), both in genic and intergenic regions, have been widely studied in eukaryotes, prokaryotes, and viruses. In the current study, we undertook a survey to analyze the frequency and distribution of microsatellites or SSRs in multiple genomes of Coronaviridae members. We successfully identified 919 SSRs with length ≥12 bp across 55 reference genomes majority of which (838 SSRs) were found abundant in genic regions. The in-silico analysis further identified the preferential abundance of hexameric SSRs than any other size-based motif class. Our analysis shows that the genome size and GC content of the genome had a weak influence on SSR frequency and density. However, we find a positive correlation of SSRs GC content with genomic GC content. We also report relatively low abundances of all theoretically possible 501 repeat motif classes in all the genomes of Coronaviridae. The majority of SSRs were AT-rich. Overall, we see an underrepresentation of SSRs across the genomes of Coronaviridae. Besides, our integrative study highlights the presence of SSRs in ORF1ab (nsp3, nsp4, nsp5A_3CLpro and nsp5B_3CLpro, nsp6, nsp10, nsp12, nsp13, & nsp15 domains), S, ORF3a, ORF7a, N & 3′ UTR regions of SARS-CoV-2 and harbours multiple mutations (3′UTR and ORF1ab SSRs serving as major mutational hotspots). This indicates the genic SSRs are under selection pressure against mutations that might alter the reading frame and at the same time responsible for rapid protein evolution. Our preliminary results indicate the significance of the limited repertoire of SSRs in the genomes of Coronaviridae. |
format | Online Article Text |
id | pubmed-7505113 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Elsevier B.V. |
record_format | MEDLINE/PubMed |
spelling | pubmed-75051132020-09-23 Deciphering the SSR incidences across viral members of Coronaviridae family Satyam, Rohit Jha, Niraj Kumar Kar, Rohan Jha, Saurabh Kumar Sharma, Ankur Kumar, Dhruv Nand, Parma Ruokolainen, Janne Kesari, Kavindra Kumar Kamal, Mohammad Amjad Chem Biol Interact Research Article Presence of Simple Sequence Repeats (SSRs), both in genic and intergenic regions, have been widely studied in eukaryotes, prokaryotes, and viruses. In the current study, we undertook a survey to analyze the frequency and distribution of microsatellites or SSRs in multiple genomes of Coronaviridae members. We successfully identified 919 SSRs with length ≥12 bp across 55 reference genomes majority of which (838 SSRs) were found abundant in genic regions. The in-silico analysis further identified the preferential abundance of hexameric SSRs than any other size-based motif class. Our analysis shows that the genome size and GC content of the genome had a weak influence on SSR frequency and density. However, we find a positive correlation of SSRs GC content with genomic GC content. We also report relatively low abundances of all theoretically possible 501 repeat motif classes in all the genomes of Coronaviridae. The majority of SSRs were AT-rich. Overall, we see an underrepresentation of SSRs across the genomes of Coronaviridae. Besides, our integrative study highlights the presence of SSRs in ORF1ab (nsp3, nsp4, nsp5A_3CLpro and nsp5B_3CLpro, nsp6, nsp10, nsp12, nsp13, & nsp15 domains), S, ORF3a, ORF7a, N & 3′ UTR regions of SARS-CoV-2 and harbours multiple mutations (3′UTR and ORF1ab SSRs serving as major mutational hotspots). This indicates the genic SSRs are under selection pressure against mutations that might alter the reading frame and at the same time responsible for rapid protein evolution. Our preliminary results indicate the significance of the limited repertoire of SSRs in the genomes of Coronaviridae. Elsevier B.V. 2020-11-01 2020-09-21 /pmc/articles/PMC7505113/ /pubmed/32971122 http://dx.doi.org/10.1016/j.cbi.2020.109226 Text en © 2020 Elsevier B.V. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Research Article Satyam, Rohit Jha, Niraj Kumar Kar, Rohan Jha, Saurabh Kumar Sharma, Ankur Kumar, Dhruv Nand, Parma Ruokolainen, Janne Kesari, Kavindra Kumar Kamal, Mohammad Amjad Deciphering the SSR incidences across viral members of Coronaviridae family |
title | Deciphering the SSR incidences across viral members of Coronaviridae family |
title_full | Deciphering the SSR incidences across viral members of Coronaviridae family |
title_fullStr | Deciphering the SSR incidences across viral members of Coronaviridae family |
title_full_unstemmed | Deciphering the SSR incidences across viral members of Coronaviridae family |
title_short | Deciphering the SSR incidences across viral members of Coronaviridae family |
title_sort | deciphering the ssr incidences across viral members of coronaviridae family |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7505113/ https://www.ncbi.nlm.nih.gov/pubmed/32971122 http://dx.doi.org/10.1016/j.cbi.2020.109226 |
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