. 2012 Jul 23;29(12):3755–3766. doi: 10.1093/molbev/mss184

Table 1.

Optimal Codons and tRNA Genes in T. castaneum.

AA	Optimal	Anticodon	tRNA^b	tRNA^c	Male	Female	Whole
	Codon^a	5′-3′	number	decoding OC	RT^d	RT^e	body^f
Ala	GCU	AGC	14		−0.014^g	−0.028	0.005^g
	GCC	GGC	0	AGC	0.16	0.176	0.184
	GCA	UGC	2		−0.15	−0.17	−0.155
	GCG	CGC	3	CGC/UGC	0.061	0.078	0.017^g
Pro	CCU	AGG	7		0.004^g	−0.001^g	0.011^g
	CCC	GGG	0	AGG	0.185	0.186	0.17
	CCA	UGG	13		−0.075	−0.078	−0.059
	CCG	CGG	1		0.001^g	0.015^g	−0.004^g
Val	GUU	AAC	7		−0.031	−0.049	−0.038
	GUC	GAC	0	AAC	0.077	0.09	0.106
	GUA	UAC	5		−0.069	−0.057	−0.058
	GUG	CAC	3	CAC /UAC	0.112	0.104	0.081
Thr	ACU	AGU	5		0.031	0.004^g	0.025
	ACC	GGU	0	AGU	0.097	0.111	0.142
	ACA	UGU	3		−0.119	−0.12	−0.123
	ACG	CGU	2	CGU/UGU	0.079	0.088	0.039
Gly	GGU	ACC	0		0.022^g	0.008^g	0.03
	GGC	GCC	8	GCC	0.069	0.095	0.067
	GGA	UCC	15		−0.203	−0.196	−0.145
	GGG	CCC	1	CCC/UCC	0.205	0.196	0.157
Ile	AUU	AAU	7		−0.059	−0.089	−0.087
	AUC	GAU	0	AAU	0.137	0.148	0.171
	AUA	UAU	2		−0.065	−0.043	−0.078
Arg	CGU	ACG	5		0.008^g	0.016^g	0.0002^g
	CGC	GCG	0	ACG	0.075	0.068	0.052
	CGA	UCG	4		−0.154	−0.15	−0.13
	CGG	CCG	0		−0.029	−0.012^g	−0.038
	AGA	UCU	3		0.012^g	−0.006^g	0.031
	AGG	CCU	3	CCU/UCU	0.225	0.23	0.209
Leu	CUU	AAG	5		−0.111	−0.123	−0.081
	CUC	GAG	0	AAG	0.05	0.076	0.084
	CUA	UAG	2		−0.019^g	−0.013^g	0.0003^g
	CUG	CAG	2	UAG/CAG	0.055	0.059	0.06
	UUA	UAA	2		−0.096	−0.07	−0.121
	UUG	CAA	4	CAA/UAA	0.237	0.182	0.188
Ser	AGU	ACU	0	GCU	0.108	0.071	0.075
	AGC	GCU	3	GCU	0.045	0.056	0.06
	UCU	AGA	4		−0.071	−0.06	−0.053
	UCC	GGA	0		−0.001^g	0.015^g	0.037
	UCA	UGA	2		−0.039	−0.041	−0.048
	UCG	CGA	2	CGA/UGA	0.09	0.103	0.073
Asp	GAU	AUC	0		−0.023^g	−0.028	−0.043
	GAC	GUC	10
Cys	UGU	ACA	0		0.009^g	−0.014^g	−0.011^g
	UGC	GCA	3
Asn	AAU	AUU	0		−0.1	−0.112	−0.135
	AAC	GUU	5	GUU
His	CAU	AUG	0		−0.054	−0.043	−0.052
	CAC	GUG	7	GUG
Tyr	UAU	AUA	0		−0.107	−0.094	−0.124
	UAC	GUA	13	GUA
Phe	UUU	AAA	1		−0.122	−0.143	−0.17
	UUC	GAA	5	GAA/AAA
Gln	CAA	UUG	5		−0.075	−0.101	−0.064
	CAG	CUG	3	CUG/UUG
Glu	GAA	UUC	8		−0.137	−0.156	−0.108
	GAG	CUC	5	CUC/UUC
Lys	AAA	UUU	6		−0.161	−0.194	−0.158
	AAG	CUU	5	CUU/UUU

^aOptimal codons (underlined) identified by positive correlation between codon frequency and gene expression levels in tissues from male and female reproductive tracts.

^btRNA gene copy number.

^cPredicted decoding tRNA for optimal codons assigned according to classical wobble rules (first anticodon–third codon positions): G-C/U; C-G; I-U/C>A; U-A/G. Spearman’s correlation between codon frequency and expression levels in ^dmale reproductive tract, ^efemale reproductive tract, and ^fwhole body. ^gNonsignificant after Bonferroni sequential correction.