Table 1 Genome-wide preferred synonymous codon usage in S. purpuratus
Second Basea
UCAG
First BaseCodonρbP-ValueCodonρP-ValueCodonρP-ValueCodonρP-Value
UUUU (F)0.3817.54E-160UCU (S)0.1913.94E-39UAU (Y)0.3879.07E-165UGU (C)-0.1912.13E-39
UUC (F)-0.3821.43E-160UCC (S)-0.2792.19E-83UAC (Y)-0.3811.12E-159UGC (C)0.2082.18E-46
UUA (L)0.4532.16E-232UCA (S)0.2315.12E-57UAA (X)UGA (X)
UUG (L)0.2741.67E-80UCG (S)−0.0221.27E-01UAG (X)UGG (W)
CCUU (L)0.2082.28E-46CCU (P)0.1577.61E-27CAU (H)0.2422.24E-62CGU (R)−0.0211.46E-01
CUC (L)-0.4612.87E-242CCA (P)0.1855.08E-37CAC (H)-0.2281.10E-55CGC (R)-0.2138.89E-49
CUA (L)0.2531.65E-68CCC (P)-0.3171.19E-108CAA (Q)0.3821.73E-160CGA (R)0.1523.05E-25
CUG (L)−0.3902.64E-167CCG (P)−0.0114.64E-01CAG (Q)-0.3782.78E-157CGG (R)0.0622.56E-05
AAUU (I)0.3423.55E-127ACU (T)0.2773.53E-82AAU (N)0.4542.42E-233AGU (S)0.2041.68E-44
AUC (I)-0.5361.00E-223ACC (T)-0.4206.96E-197AAC (N)-0.4525.70E-232AGC (S)−0.2301.61E-56
AUA (I)0.3856.16E-163ACA (T)0.2842.66E-86AAA (K)0.4662.95E-248AGA (R)0.3024.55E-98
AUG (M)ACG (T)−0.0397.81E-03AAG (K)-0.4671.36E-248AGG (R)−0.1791.90E-34
GGUU (V)0.3464.56E-130GCU (A)0.1321.55E-19GAU (D)0.3383.48E-124GGU (G)0.0523.99E-04
GUC (V)-0.3944.42E-171GCC (A)-0.4419.31E-219GAC (D)-0.3372.06E-123GGC (G)-0.2492.88E-66
GUA (V)0.3091.48E-102GCA (A)0.3111.99E-104GAA (E)0.4166.46E-193GGA (G)0.1501.44E-24
GUG (V)−0.0951.17E-10GCG (A)0.0452.14E-03GAG (E)-0.4162.82E-193GGG (G)0.0721.03E-06
  • a Bold identifies the synonymous codon in a codon family with the strongest significant negative correlation.

  • b Spearman’s correlation coefficient between frequency of a synonymous codon usage to the overall codon bias of the gene.