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Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses

Using the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using ei...

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Autores principales: Woo, Patrick C.Y., Wong, Beatrice H.L., Huang, Yi, Lau, Susanna K.P., Yuen, Kwok-Yung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Inc. 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103290/
https://www.ncbi.nlm.nih.gov/pubmed/17881030
http://dx.doi.org/10.1016/j.virol.2007.08.010
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author Woo, Patrick C.Y.
Wong, Beatrice H.L.
Huang, Yi
Lau, Susanna K.P.
Yuen, Kwok-Yung
author_facet Woo, Patrick C.Y.
Wong, Beatrice H.L.
Huang, Yi
Lau, Susanna K.P.
Yuen, Kwok-Yung
author_sort Woo, Patrick C.Y.
collection PubMed
description Using the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G + C content in CoV-HKU1 warrants further studies.
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spelling pubmed-71032902020-03-31 Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses Woo, Patrick C.Y. Wong, Beatrice H.L. Huang, Yi Lau, Susanna K.P. Yuen, Kwok-Yung Virology Article Using the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G + C content in CoV-HKU1 warrants further studies. Elsevier Inc. 2007-12-20 2007-09-19 /pmc/articles/PMC7103290/ /pubmed/17881030 http://dx.doi.org/10.1016/j.virol.2007.08.010 Text en Copyright © 2007 Elsevier Inc. 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 Article
Woo, Patrick C.Y.
Wong, Beatrice H.L.
Huang, Yi
Lau, Susanna K.P.
Yuen, Kwok-Yung
Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
title Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
title_full Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
title_fullStr Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
title_full_unstemmed Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
title_short Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
title_sort cytosine deamination and selection of cpg suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103290/
https://www.ncbi.nlm.nih.gov/pubmed/17881030
http://dx.doi.org/10.1016/j.virol.2007.08.010
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