Table 1. The difference (Δ) in mean RSCU for the 5% most highly vs. lowly expressed genes in Gryllus bimaculatus, Oncopeltus fasciatus, and Parhyale hawaiensis.

		Gryllus		Oncopeltus		Parhyale
GC3/AT3 optimal codons		AT3		AT3		GC3
No. optimal codons		17		16		13
Amino acid	Codon	∆RSCU	Pa	∆RSCU	Pa	∆RSCU	Pa
Ala	GCT	+0.279	***	+0.370	***	+0.048
Ala	GCC	−0.060		−0.081	*	+0.028	**
Ala	GCA	−0.055		−0.120	**	+0.012
Ala	GCG	−0.123	***	−0.101	**	−0.079
Arg	CGT	+0.277	**	+0.098	**	+0.060
Arg	CGC	+0.013		−0.101	**	−0.001
Arg	CGA	+0.081		−0.019		−0.051
Arg	CGG	+0.029		−0.047		−0.163
Arg	AGA	−0.259	**	+0.050		+0.122
Arg	AGG	−0.019		+0.117		+0.064
Asn	AAT	+0.074	**	+0.126	***	−0.054	**
Asn	AAC	−0.060	*	−0.110	***	+0.078	***
Asp	GAT	+0.132	***	+0.129	***	+0.078
Asp	GAC	−0.091	**	−0.113	***	−0.031
Cys	TGT	+0.170	**	+0.216	***	−0.167	**
Cys	TGC	−0.033		+0.003		−0.013
Gln	CAA	−0.070	*	+0.063		−0.064	**
Gln	CAG	+0.097	**	−0.013		+0.078	**
Glu	GAA	+0.063	*	+0.107	***	−0.005
Glu	GAG	−0.021		−0.091	**	+0.030
Gly	GGT	+0.180	***	+0.317	***	+0.021
Gly	GGC	−0.018		−0.183	***	+0.017
Gly	GGA	+0.011		−0.026		+0.096	*
Gly	GGG	−0.133	**	−0.074	*	−0.127	***
His	CAT	+0.129	**	+0.102	**	+0.013
His	CAC	−0.034		−0.029		−0.035
Ile	ATT	+0.311	***	+0.167	***	−0.027
Ile	ATC	−0.135	**	−0.033		+0.136	***
Ile	ATA	−0.125	**	−0.100	**	−0.112	**
Leu	TTA	−0.034		+0.073	*	−0.226	***
Leu	TTG	+0.300	***	+0.017		+0.053
Leu	CTT	+0.068		+0.346	***	+0.004
Leu	CTC	−0.217	***	−0.147	**	+0.146	***
Leu	CTA	−0.075		−0.112	**	−0.064	**
Leu	CTG	−0.021		−0.177	***	+0.087
Lys	AAA	−0.032		+0.019		−0.100	***
Lys	AAG	+0.059		−0.002		+0.110	***
Phe	TTT	+0.062b		+0.118	***	−0.075	**
Phe	TTC	−0.015		−0.078	**	+0.091	***
Pro	CCT	+0.158c	*	+0.194	**	+0.164
Pro	CCC	−0.190	***	−0.052		+0.063	**
Pro	CCA	+0.139c	**	−0.009		−0.108	*
Pro	CCG	−0.038		−0.124	***	−0.129	**
Ser	TCT	+0.297	***	+0.359	***	+0.015
Ser	TCC	−0.200	***	−0.142	**	−0.023
Ser	TCA	−0.024		+0.123	*	+0.038	**
Ser	TCG	−0.007		−0.127	***	+0.089	**
Ser	AGT	+0.024		−0.081		−0.079	**
Ser	AGC	−0.090		−0.131	**	−0.040
Thr	ACT	+0.163	**	+0.244	***	+0.033
Thr	ACC	−0.104	**	−0.122	**	+0.114	**
Thr	ACA	+0.040		−0.033		−0.091
Thr	ACG	−0.114	**	−0.080	**	−0.052
Tyr	TAT	+0.081b		+0.176	***	−0.106
Tyr	TAC	+0.061		−0.140	***	+0.086b
Val	GTT	+0.243	***	+0.261	***	−0.031
Val	GTC	−0.141	***	−0.100	**	+0.081	*
Val	GTA	−0.126	**	−0.108	*	−0.121	**
Val	GTG	+0.037		−0.041		+0.069	**

The codon identified as the primary optimal codon for each amino acid is in boldface. RSCU, relative synonymous codon usage.

^aAsterisks indicate P value using t-tests where **P < 0.05, ***P < 0.001. Codons with *0.05 > P < 0.1 are also indicated and considered putative optimal codons. The means and standard errors for highly and for lowly expressed CDS are provided in Table S2. Species are abbreviated using their genus name.

^bThe codons TTT and TAT for G. bimaculatus and TAC for P. hawaiensis are identified as candidate optimal codons with P values at or slightly above 0.1.

^cFor the amino acid Pro in G. bimaculatus, CCA was selected as the optimal codon due to the fact that it had a lower P value than CCT, although both exhibit signals of being optimal codons.