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 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.
Woo
Patrick C Y
PC
State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; Department of Microbiology, The University of Hong Kong, Hong Kong.
Wong
Beatrice H L
BH
Huang
Yi
Y
Lau
Susanna K P
SK
Yuen
Kwok-Yung
KY
D000818:Animals; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D003332:Coronaviridae / Q000145:classification / Q000235:genetics*; D018899:CpG Islands; D003596:Cytosine / Q000737:chemistry; D016679:Genome, Viral; D006801:Humans; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D013045:Species Specificity
D003062:Codon; D012367:RNA, Viral; D003596:Cytosine