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. 2014 Mar 4;9(3):e90905. doi: 10.1371/journal.pone.0090905

Table 2. The synonymous codon usage patterns of CHIKV, its hosts and transmission vectors.

RSCU RSCU
AA Codon CHIKV Hosts & Vectors AA Codon CHIKV Hosts & Vectors
Overall ECSA Asian WA HS PT AG AB Overall ECSA Asian WA HS PT AG AB
Pheb , c UUU 0.76 0.74 0.81 0.98 0.92 0.78 0.56 0.48 Sera , c UCU 0.95 0.95 0.89 1.07 1.14 1.20 0.66 0.54
UUC 1.24 1.26 1.19 1.02 1.08 1.22 1.44 1.52 UCC 1.00 0.99 1.07 1.00 1.32 1.44 1.20 1.38
Leub , d UUA 0.60 0.60 0.69 0.43 0.48 0.36 0.36 0.24 UCA 1.32 1.35 1.27 1.17 0.90 0.78 0.66 0.48
UUG 0.88 0.84 0.93 1.24 0.78 0.66 1.32 1.14 UCG 0.86 0.86 0.88 0.87 0.30 0.30 1.44 1.68
CUU 0.59 0.57 0.62 0.68 0.78 0.72 0.66 0.48 AGU 0.62 0.64 0.59 0.51 0.90 0.78 0.96 0.78
CUC 0.57 0.58 0.49 0.55 1.20 1.38 0.84 0.84 AGC 1.25 1.22 1.31 1.39 1.44 1.44 1.08 1.08
CUA 1.39 1.43 1.34 1.04 0.42 0.42 0.54 0.54 Arga , c AGA 2.11 2.10 2.20 2.04 1.26 1.26 0.66 0.60
CUG 1.98 1.98 1.92 2.06 2.40 2.58 2.28 2.76 CGU 0.38 0.38 0.39 0.48 0.48 0.42 1.38 1.50
Ileb , c AUU 0.70 0.70 0.68 0.74 1.08 0.96 0.99 0.75 CGC 1.03 1.04 0.99 0.91 1.08 1.20 1.26 1.32
AUC 1.31 1.31 1.30 1.26 1.41 1.56 1.59 1.86 CGA 0.63 0.63 0.66 0.59 0.66 0.60 1.20 0.96
AUA 0.99 0.99 1.02 0.99 0.51 0.48 0.39 0.39 CGG 0.46 0.45 0.49 0.46 1.20 1.14 1.02 1.20
Valb , c GUU 0.51 0.51 0.51 0.41 0.72 0.60 1.04 0.88 AGG 1.38 1.39 1.28 1.53 1.26 1.32 0.54 0.42
GUC 1.12 1.14 1.05 1.10 0.96 1.00 1.08 1.32 Cysb , c UGU 0.67 0.69 0.71 0.44 0.92 0.84 0.84 0.70
GUA 0.97 0.95 1.02 0.99 0.48 0.36 0.60 0.52 UGC 1.33 1.31 1.29 1.56 1.08 1.16 1.16 1.30
GUG 1.41 1.40 1.42 1.51 1.84 2.04 1.28 1.32 Hisb , c CAU 0.65 0.61 0.75 0.89 0.84 2.40 0.84 0.76
Prob , d CCU 0.84 0.84 0.88 0.69 1.16 1.08 0.68 0.36 CAC 1.35 1.39 1.25 1.11 1.16 1.20 1.16 1.24
CCC 0.71 0.71 0.64 0.80 1.28 1.40 0.84 1.12 Glnb , c CAA 0.89 0.90 0.89 0.80 0.54 0.46 0.82 0.60
CCA 1.20 1.19 1.15 1.37 1.12 0.96 1.20 1.08 CAG 1.11 1.10 1.11 1.20 1.46 1.54 1.18 1.40
CCG 1.26 1.26 1.33 1.14 0.44 0.52 1.32 1.44 Asnb , c AAU 0.74 0.73 0.84 0.66 0.94 0.84 0.80 0.64
Thra , c ACU 0.79 0.80 0.76 0.77 1.00 0.84 0.80 0.64 AAC 1.26 1.27 1.16 1.34 1.06 1.16 1.20 1.36
ACC 0.98 0.99 0.97 0.93 1.44 1.68 1.48 1.80 Lysa , d AAA 1.00 1.02 0.96 0.97 0.86 0.80 0.80 0.58
ACA 1.33 1.34 1.28 1.36 1.12 1.00 0.72 0.60 AAG 1.00 0.98 1.04 1.03 1.14 1.20 1.20 1.42
ACG 0.90 0.88 0.99 0.93 0.44 0.44 1.00 1.00 Aspb , c GAU 0.61 0.59 0.71 0.66 0.92 0.80 1.12 0.96
Alaa , c GCU 0.66 0.66 0.67 0.65 1.08 1.08 1.08 1.00 GAC 1.39 1.41 1.29 1.34 1.08 1.20 0.88 1.04
GCC 1.11 1.10 1.13 1.18 1.60 1.56 1.48 1.80 Glua , d GAA 1.09 1.09 1.11 1.06 0.84 0.68 1.16 1.10
GCA 1.43 1.44 1.37 1.49 0.92 0.80 0.76 0.60 GAG 0.91 0.91 0.89 0.94 1.16 1.32 0.84 0.90
GCG 0.80 0.80 0.84 0.67 0.44 0.56 0.68 0.60 Glya , c GGU 0.72 0.69 0.83 0.70 0.64 0.56 1.12 1.24
Tyrb , c UAU 0.73 0.75 0.72 0.55 0.88 0.78 0.64 0.56 GGC 0.95 0.96 0.87 0.99 1.36 1.40 1.04 1.08
UAC 1.27 1.25 1.28 1.45 1.12 1.22 1.36 1.44 GGA 1.27 1.26 1.27 1.34 1.00 0.92 1.48 1.20
GGG 1.07 1.08 1.04 0.97 1.00 1.16 0.36 0.48

AA: amino acid, HS: H. sapiens, AG: A. aegypti, AB: A. albopictus, PT: P. troglodytes. Preferred codons of CHIKV, H. sapiens, A. aegypti, A. albopictus and P. troglodytes are shown in bold.

a

Amino acids with A/U-ended preferred codons in CHIKV.

b

Amino acids with G/C-ended preferred codons in CHIKV.

c

Amino acids with A/U-ended preferred codons in CHIKV.

d

Amino acids with G/C-ended preferred codons in CHIKV.