J Bacteriol Virol.  2013 Dec;43(4):317-327. 10.4167/jbv.2013.43.4.317.

Codon Usage Bias of Human Cytomegalovirus Genes with Different Evolutionary Conservancy

• Kim YY
• Lee CH

• KMID: 1502000
• DOI: http://doi.org/10.4167/jbv.2013.43.4.317

Abstract

Human cytomegalovirus (HCMV) is a member of beta-herpesvirus and contains a double-stranded genome with longer than 230 Kbp. HCMV infection of human is mostly asymptomatic, but often causes fatal diseases in immunocompromised people. In this study, codon usages of HCMV genes were analyzed and attempted to correlate with evolutionary conservancy. Core genes are the most conserved genes common among herpesvirus family, beta-herpes genes are common to beta-herpesviruses, and CMV genes are the least conserved found only in CMVs. Core genes had higher codon adaptation index (CAI) and GC content of silent 3rd codon position (GC3s) values and lower effective number of codons (Nc) and Nc/GC3s values than CMV genes. The average length of core genes was statistically longer than CMV genes, and core genes were found to be less varied than CMV genes. beta-herpes genes could be placed between core and CMV genes. Higher CAI and GC3s values along with lower Nc and Nc/GC3s values are suggestive of higher codon usage bias and more adaptation to host cells. Thus it is concluded that core genes of HCMV are more biased in codon usage and adapted to host cells compared to CMV genes.

Keyword

Human cytomegalovirus; Codon usage bias

MeSH Terms

Base Composition
Bias (Epidemiology)*
Codon*
Cytomegalovirus*
Genome
Humans*
Codon

Figure

• 

  Figure 1. Codon usage bias index (CUI) values of HCMV genes. These graphs represent the distribution of CUI values of 3 groups. Each graph shows (A) CAI, (B) GC3s, (C) Nc, and (D) Nc/GC3s values. CORE genes are indicated by black circles, β-HERPES genes by white circles, and CMV genes by black triangles. Black bars indicate the standard error of the mean. Statistical significance of the difference in mean values was examined by student's t-test.

• 

  Figure 2. Nc versus GC3s plots for HCMV gene groups. (A) Scatter plot for all HCMV ORFs. (B) plot for CORE genes. (C) plot for β-HERPES genes. (D) plot for CMV genes. The continuous curve represents the expected Nc values by Wright's formula.

• 

  Figure 3. Genetic characteristics of HCMV genes. (A) Distribution of length of HCMV genes. (B) Genetic distance values of HCMV genes. (C) Relative amount of mRNA of HCMV genes. CORE genes are indicated by black circles, β-HERPES genes by white circles, and CMV genes by black triangles. Black bars indicate the standard error of the mean. Statistical significance of the difference in mean values was examined by student's t-test.

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