Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias
Table 1
Relative synonymous codon usage patterns of RABV in comparison with its host.
AA
Codon
Virus
Host
All-sequences
Bat-related
Dog-related
RAC&SK-related
Myotis lucifugus
Mustela putorius furo
Canis
Homo sapiens
ALA
GCA
1.34
1.31
1.31
1.39
1.16
1.1
1.05
1.18
GCC
1.12
1.11
1.12
1.11
1.23
1.22
1.32
1.22
GCG
0.34
0.49
0.33
0.35
0.48
0.55
0.48
0.44
GCU
1.2
1.09
1.24
1.15
1.13
1.12
1.15
1.16
ARG
AGA
2.76
2.63
2.78
2.73
1.9
1.81
1.86
1.99
AGG
1.73
1.89
1.67
1.81
1.57
1.36
1.28
1.59
CGA
0.62
0.53
0.66
0.56
0.61
0.71
0.71
0.6
CGC
0.27
0.29
0.27
0.28
0.64
0.73
0.77
0.61
CGG
0.38
0.44
0.39
0.37
0.82
0.87
0.88
0.76
CGU
0.24
0.22
0.23
0.25
0.46
0.53
0.51
0.45
ASN
AAC
1.06
1.1
1.11
0.99
1.01
1.01
0.98
0.98
AAU
0.94
0.9
0.89
1.01
0.99
0.99
1.02
1.02
ASP
GAC
1.03
0.97
1.01
1.09
1
1.04
1
0.97
GAU
0.97
1.03
0.99
0.91
1
0.96
1
1.03
CYS
UGC
0.77
0.81
0.78
0.75
1.12
1.12
1.05
1.11
UGU
1.23
1.19
1.22
1.25
0.88
0.88
0.95
0.89
GLN
CAA
0.97
0.97
0.97
0.96
0.78
0.84
0.79
0.78
CAG
1.03
1.03
1.03
1.04
1.22
1.16
1.21
1.22
GLU
GAA
0.8
0.79
0.81
0.8
1.04
1.05
1.02
1.06
GAG
1.2
1.21
1.19
1.2
0.96
0.95
0.98
0.94
GLY
GGA
1.34
1.38
1.36
1.3
1.36
1.41
1.35
1.38
GGC
0.58
0.58
0.59
0.56
1.06
1.08
1.12
1.06
GGG
1.46
1.41
1.45
1.48
0.93
0.89
0.87
0.91
GGU
0.62
0.64
0.6
0.65
0.65
0.63
0.66
0.65
HIS
CAC
0.87
0.78
0.89
0.85
1.04
1.03
1.01
1.03
CAU
1.13
1.22
1.11
1.15
0.96
0.97
0.99
0.97
ILE
AUA
1.03
1.03
1.03
1.02
0.77
0.72
0.61
0.76
AUC
1.16
1.11
1.17
1.14
1.14
1.2
1.25
1.13
AUU
0.81
0.85
0.79
0.84
1.09
1.07
1.14
1.11
LEU
CUA
0.87
0.77
0.92
0.81
0.59
0.62
0.59
0.61
CUC
0.92
0.92
0.87
1.01
1.13
1.25
1.23
1.12
CUG
1.22
1.32
1.22
1.22
1.77
1.72
1.85
1.76
CUU
0.94
0.98
0.91
0.97
0.99
1.1
1.09
1.02
UUA
0.72
0.56
0.73
0.71
0.58
0.51
0.51
0.58
UUG
1.33
1.45
1.35
1.28
0.93
0.79
0.73
0.92
LYS
AAA
0.96
0.93
0.91
1.04
0.98
1
1
1
AAG
1.04
1.07
1.09
0.96
1.02
1
1
1
PHE
UUC
1.02
1.03
1.04
1
1.03
1.05
1.01
1.02
UUU
0.98
0.97
0.96
1
0.97
0.95
0.99
0.98
PRO
CCA
0.91
0.86
0.88
0.97
1.27
1.2
1.16
1.31
CCC
1.05
1.05
1.1
0.98
1.08
1.09
1.13
1.05
CCG
0.58
0.68
0.5
0.68
0.54
0.61
0.54
0.48
CCU
1.46
1.41
1.52
1.38
1.12
1.1
1.17
1.16
SER
AGC
0.56
0.58
0.55
0.57
1.37
1.38
1.36
1.37
AGU
0.61
0.61
0.64
0.57
0.92
0.87
0.93
0.92
UCA
1.3
1.41
1.35
1.19
1.16
1.15
1.05
1.2
UCC
1.17
1.09
1.17
1.19
1.13
1.15
1.17
1.1
UCG
0.48
0.42
0.53
0.42
0.39
0.43
0.38
0.34
UCU
1.87
1.89
1.76
2.05
1.03
1.03
1.11
1.06
TER
UAA
1.7
0.9
1.96
1.52
0.69
0.71
0.72
0.69
UAG
0.57
0.7
0.12
1.46
0.54
0.47
0.43
0.54
UGA
0.73
1.4
0.92
0.02
1.77
1.82
1.85
1.77
THR
ACA
1.22
1.26
1.2
1.23
1.33
1.3
1.26
1.38
ACC
1.28
1.34
1.3
1.24
1.19
1.18
1.25
1.18
ACG
0.37
0.24
0.39
0.34
0.52
0.56
0.47
0.44
ACU
1.14
1.17
1.11
1.18
0.97
0.95
1.02
1
TYR
UAC
0.89
0.95
0.87
0.92
1.03
1.05
1.02
1.02
UAU
1.11
1.05
1.13
1.08
0.97
0.95
0.98
0.98
VAL
GUA
0.63
0.73
0.65
0.58
0.62
0.59
0.57
0.62
GUC
1.15
1.18
1.16
1.12
0.95
1.06
1.01
0.93
GUG
1.19
1.17
1.16
1.24
1.55
1.46
1.52
1.55
GUU
1.03
0.92
1.03
1.06
0.88
0.89
0.9
0.9
Note: AA means, amino acids; green marked the value of RSCU <0.6 (underrepresented); orange marked the value of RSCU >1; red marked the value of RSCU >1.6 (overrepresented); the most preferred codons and dispreferred codons used in coding each amino acid are marked in bold and italic, respectively. Most preferred or dispreferred codons in both of virus and host are underline.
