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Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51

Xiaochun Tan

Xiaochun Tan

Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing UniversityJiaxing, China
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Tan, Xiaochun
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Siwen Bao

Siwen Bao

Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing UniversityJiaxing, China
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Bao, Siwen
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Xiaolei Lu

Xiaolei Lu

Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing UniversityJiaxing, China
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Lu, Xiaolei
, 
Binbin Lu

Binbin Lu

Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing UniversityJiaxing, China
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Lu, Binbin
, 
Weifeng Shen

Weifeng Shen

Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing UniversityJiaxing, China
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Shen, Weifeng
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Chaoyue Jiang

Chaoyue Jiang

Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing UniversityJiaxing, China
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Jiang, Chaoyue
  
28 ott 2024
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Categoria dell'articolo: ORIGINAL PAPER
Pubblicato online: 28 ott 2024
Pagine: 455 - 465
Ricevuto: 14 mag 2024
Accettato: 03 set 2024
DOI: https://doi.org/10.33073/pjm-2024-036
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© 2024 Xiaochun Tan et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1.

Analysis of dinucleotide frequencies in the complete coding sequences of HPV-51. Dashed lines represent overrepresented values (Pxy > 1.23) or underrepresented values (Pxy < 0.78). The error bars are minimal due to the proximity of the data points.
Analysis of dinucleotide frequencies in the complete coding sequences of HPV-51. Dashed lines represent overrepresented values (Pxy > 1.23) or underrepresented values (Pxy < 0.78). The error bars are minimal due to the proximity of the data points.

Fig. 2.

Analysis of Relative Synonymous Codon Usage (RSCU) in the complete coding sequences of HPV-51. Codon values less than 0.6, between 0.6 and 1.6, and greater than 1.6 indicate low, normal, and excessive codon usage, respectively.
Analysis of Relative Synonymous Codon Usage (RSCU) in the complete coding sequences of HPV-51. Codon values less than 0.6, between 0.6 and 1.6, and greater than 1.6 indicate low, normal, and excessive codon usage, respectively.

Fig. 3.

Analysis of Parity Rule 2 (PR2) constructed from the complete coding sequences of HPV-51. The central point of the plot, represented by coordinates (0.5, 0.5), indicates a balance between mutation and selection rates.
Analysis of Parity Rule 2 (PR2) constructed from the complete coding sequences of HPV-51. The central point of the plot, represented by coordinates (0.5, 0.5), indicates a balance between mutation and selection rates.

Fig. 4.

Analysis of the Effective Number of Codons (ENC) plot for the complete coding sequences of HPV-51. ENC values are plotted against the GC3s content. The black line represents the standard curve based on codon usage bias deter-mined solely by GC3s composition. This standard curve illus-trates the expected relationship between ENC and GC3s without selective pressures. The deviation of actual ENC values below this curve indicates a more significant influence of natural selection on codon bias.
Analysis of the Effective Number of Codons (ENC) plot for the complete coding sequences of HPV-51. ENC values are plotted against the GC3s content. The black line represents the standard curve based on codon usage bias deter-mined solely by GC3s composition. This standard curve illus-trates the expected relationship between ENC and GC3s without selective pressures. The deviation of actual ENC values below this curve indicates a more significant influence of natural selection on codon bias.

Fig. 5.

Neutrality analysis of the complete coding sequencesof HPV-51. The relationship between GC content at the first and second positions of the codon (GC12s) and the third position of the codon (GC3s) was analyzed. The dashed line depicts the correlation between GC12s and GC3s in HPV-51. A slope approaching 1 indicates that mutation pressure predominantly shapes the codon usage pattern, while a slope closer to 0 suggests a more substantial influence of natural selection.
Neutrality analysis of the complete coding sequencesof HPV-51. The relationship between GC content at the first and second positions of the codon (GC12s) and the third position of the codon (GC3s) was analyzed. The dashed line depicts the correlation between GC12s and GC3s in HPV-51. A slope approaching 1 indicates that mutation pressure predominantly shapes the codon usage pattern, while a slope closer to 0 suggests a more substantial influence of natural selection.

Correlation analysis between GC3s, CAI, GRAVY, and AROMO_

GC3s CAI GRAVY
CAI –0.036
GRAVY 0.143 0.168
Aromo 0.818*** –0.135 –0.122

Frequency of tRNA genes in human cells corresponding to the most preferentially used codons in HPV-51_

Amino acid Most preferred codons in HPV-51 tRNA isotypes in human cells Total count
Ala (A) GCG AGC (22), GGC (0), CGC (4), TGC (8) 34
Gly (G) GGC ACC (0), GCC (14), CCC (5), TCC (9) 28
Pro (P) CCG AGG (9), GGG (0), CGG (4), TGG (7) 20
Thr (T) ACG AGT (9), GGT (0), CGT (5), TGT (6) 20
Val (V) GTG AAC (9), GAC (0), CAC (11), TAC (5) 25
Ser (S) TCG AGA (9), GGA (0), CGA (4), TGA (4), ACT (0), GCT (8) 25
Arg (R) AGG ACG (7), GCG (0), CCG (4), TCG (6), CCT (5), TCT (6) 28
Leu (L) CTG AAG (9), GAG (0), CAG (9), TAG (3), CAA (6), TAA (4) 31
Phe (F) TTC AAA (0), GAA (10) 10
Asn (N) AAT ATT (0), GTT (20) 20
Lys (K) AAG CTT (15), TTT (12) 27
Asp (D) GAC ATC (0), GTC (13) 13
Glu (E) GAG CTC (8), TTC (7) 15
His (H) CAC ATG (0), GTG (10) 10
Gln (Q) CAG CTG (13), TTG (6) 19
Ile (I) ATC AAT (14), GAT (3), TAT (5) 22
Tyr (Y) TAT ATA (0), GTA (13) 13
Cys (C) TGC ACA (0), GCA (29) 29
Trp (W) TGG CCA (7) 7
Met (M) ATG CAT (9/10) 19

Nucleotide composition of complete genomes in HPV-51_

Genotype GC1s* GC2s GC3s T3s C3s A3s G3s
HPV-51 46.23 ± 0.27 43.26 ± 0.22 31.03 ± 0.24 43.36 ± 5.56 17.08 ± 2.19 44.32 ± 5.68 19.59 ± 2.51

The Effective Number of Codons (ENC), Codon Adaptation Index (CAI), and Relative Codon Deoptimization Index (RCDI) values of complete genomes in HPV-51_

Genotype ENC* CAI RCDI
HPV-51 48.25 ± 0.20 0.72 ± 0.00 ± 0.01
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