Table 2.

Optimal codon table in Citrus sinensis.

Amino acid	Codon	ΔRSCU	Frequency per thousand bases
		From EST	From CDS
Ala	GCU	0.59	29.3
	GCA	0.75	20.6
	GCC	−0.81	15.9
	GCG	−0.52	8.3
Arg	AGA	0.81	14.9
	AGG	0.26	14.9
	CGU	−0.02	5.5
	CGA	0.09	4.8
	CGG	−0.32	4.4
	CGC	−0.8	4.6
Gly	GGU	0.46	19.7
	GGA	0.37	18.7
	GGG	−0.12	14
	GGC	−0.71	17.2
His	CAU	0.76	12.4
	CAC	−0.76	10.6
Val	GUU	0.59	27.6
	GUA	0.38	8.3
	GUC	−0.66	11.5
	GUG	−0.31	21.2
Lys	AAA	0.17	25.7
	AAG	−0.17	34
Phe	UUU	0.63	23.3
	UUC	−0.63	21
Pro	CCU	0.78	16.8
	CCC	−0.53	11.2
	CCG	−0.86	7.3
	CCA	0.61	16
Thr	ACU	0.69	18.5
	ACA	0.67	15.1
Asn	AAU	0.67	24.8
	AAC	−0.67	21.7
Asp	GAU	0.56	33.8
	GAC	−0.56	18.6
Cys	UGU	0.52	8.5
	UGC	−0.52	8.8
Gln	CAA	0.13	18.7
	CAG	−0.13	16.5
Glu	GAA	0.32	28.6
	GAG	−0.32	31.3
Ile	AUU	0.49	24.2
	AUA	0.32	12.6
	AUC	−0.81	16.4
Leu	UUA	0.48	12.3
	UUG	0.25	22.4
	CUU	0.47	25.2
	CUA	0.16	8.4
	CUC	−1.24	14.6
	CUG	−0.11	13
Met	AUG	0	0
Tyr	UAU	0.72	15.4
	UAC	−0.72	13.9
Ser	UCU	0.7	17.7
	UCA	0.52	17
	AGU	0.6	11.2
	UCC	−0.81	9.8
	UCG	−0.73	9.1
	AGC	−0.27	12
Thr	ACC	−0.71	10.6
	ACG	−0.66	6.9

Notes: ΔRSCU: Relative synonymous codon usage in predicted genes with high and low gene expression levels based on the EST sequence in Citrus sinensis. Optimal codons (red box) were identified based on differences in relative synonymous codon usage. Frequency per thousand bases: use frequency per thousand bases in identified high-confidence coding sequences from full-length cDNA in Citrus sinensis. Optimal codons (green box) were identified based on different frequencies per thousand bases (P < 0.05).