High codon adaptation in citrus tristeza virus to its citrus host

Table 2 Relative synonymous codon usage (RSCU) values in the full coding region of CTV and Citrus sinensis

AA^a	Codon	N^b	CTV^c	CS^d	AA	Codon	N	CTV	CS
Phe	UUU	4888	1.26 ^e	1.05	Gln	CAA	1603	1.24	1.06
	UUC	2888	0.74	0.95		CAG	986	0.76	0.94
Leu	UUA	3748	1.57	0.77	His	CAU	1535	1.03	1.08
	UUG	4825	2.02	1.40		CAC	1453	0.97	0.92
	CUU	2149	0.90	1.58	Asn	AAU	2997	1.00	1.07
	CUC	1216	0.51	0.91		AAC	2992	1.00	0.93
	CUA	1053	0.44	0.53	Lys	AAA	3604	0.94	0.86
	CUG	1354	0.57	0.80		AAG	4077	1.06	1.14
Val	GUU	5171	1.52	1.61	Asp	GAU	4988	1.10	1.29
	GUC	2302	0.68	0.67		GAC	4101	0.90	0.71
	GUA	1861	0.55	0.48	Glu	GAA	4188	1.12	0.95
	GUG	4277	1.26	1.24		GAG	3262	0.88	1.05
Ser	UCU	3742	1.50	1.38	Arg	AGA	2080	1.13	1.82
	UCC	2014	0.81	0.77		AGG	2032	1.11	1.82
	UCA	1642	0.66	1.33		CGU	2814	1.53	0.68
	UCG	3125	1.25	0.71		CGC	1599	0.87	0.56
	AGU	2791	1.12	0.87		CGA	1343	0.73	0.58
	AGC	1642	0.66	0.93		CGG	1136	0.62	0.54
Pro	CCU	2261	1.62	1.31	Cys	UGU	2235	1.24	0.98
	CCC	984	0.71	0.87		UGC	1356	0.76	1.02
	CCA	845	0.61	1.25	Tyr	UAU	2500	0.89	1.05
	CCG	1476	1.06	0.57		UAC	3107	1.11	0.95
Thr	ACU	3455	1.74	1.45	Ala	GCU	3824	1.68	1.58
	ACC	1676	0.84	0.83		GCC	1558	0.68	0.86
	ACA	891	0.45	1.18		GCA	1373	0.60	1.11
	ACG	1933	0.97	0.53		GCG	2373	1.04	0.45
Gly	GGU	4337	1.99	1.13	Ile	AUU	2562	1.21	1.37
	GGC	1311	0.60	0.99		AUC	1681	0.79	0.93
	GGA	1329	0.61	1.07		AUA	2135	1.00	0.70
	GGG	1759	0.81	0.81

^aAA is the abbreviation of amino acid.
^bN, the total numbers for each codon used by the 20 CTV isolates.
^cCTV, the mean RSCU values of CTV.
^dCS, the mean RSCU values of Citrus sinensis.
^eThe Preferred codons are under lined. A preferred codon is defined by the codon with the highest RSCU value among all available synonymous codons for a certain amino acid. However a codon with the highest RSCU value but lower than 1.1 cannot be defined as the preferred codon, since this value is statistically insignificantly under 95% confidence interval.

ISSN: 1743-422X