Non-uniqueness of factors constraint on the codon usage in Bombyx mori

BMC Genomics

Table 5 Optimal codons of genes in Bombyx mori

Amino acid	Codon	High		Low		Amino acid	Codon	High		Low
Amino acid	Codon	RSCU	N	RSCU	N	Amino acid	Codon	RSCU	N	RSCU	N
Ala	GCU	0.64	288	1.66	315	Asn	AAU	0.34	130	1.39	549
	GCC *	1.80	818	0.46	88	Asn	AAC *	1.66	631	0.61	239
	GCA	0.29	133	1.65	313	Gln	CAA	0.44	174	1.43	370
	GCG *	1.27	575	0.23	43	Gln	CAG *	1.56	615	0.57	146
Phe	UUU	0.24	91	1.48	396	Ser	UCU	0.71	153	1.49	233
Phe	UUC *	1.76	680	0.52	140		UCC *	1.71	366	0.44	69
Gly	GGU	0.65	240	1.49	291		UCA	0.42	90	1.77	276
	GGC *	1.91	703	0.58	113		UCG *	1.56	335	0.34	53
	GGA	0.75	277	1.55	303		AGU	0.34	72	1.40	219
	GGG *	0.69	254	0.39	76		AGC *	1.26	271	0.55	86
Ile	AUU	0.34	99	1.37	407	Thr	ACU	0.57	146	1.49	275
	AUC *	2.23	652	0.39	115		ACC *	1.68	433	0.43	79
	AUA	0.43	126	1.24	368		ACA	0.43	110	1.85	343
Leu	UUA	0.17	49	2.18	442		ACG *	1.32	339	0.23	43
	UUG	0.61	179	1.30	264	Asp	GAU	0.38	226	1.46	587
	CUU	0.30	88	0.89	181	Asp	GAC *	1.62	958	0.54	217
	CUC *	2.05	602	0.35	71	Glu	GAA	0.57	414	1.59	769
	CUA	0.27	78	0.75	152	Glu	GAG *	1.43	1036	0.41	197
	CUG *	2.60	764	0.53	108	His	CAU	0.38	97	1.44	196
Pro	CCU	0.48	122	1.46	204	His	CAC *	1.62	416	0.56	76
	CCC *	1.65	418	0.35	49	Lys	AAA	0.48	278	1.55	924
	CCA	0.36	91	1.87	261	Lys	AAG *	1.52	870	0.45	269
	CCG *	1.50	380	0.32	45	Arg	CGU	0.63	126	0.76	81
Val	GUU	0.41	144	1.59	363		CGC *	2.49	495	0.21	22
	GUC *	1.32	469	0.48	109		CGA	0.37	74	0.87	93
	GUA	0.36	126	1.26	289		CGG *	1.04	207	0.23	24
	GUG *	1.91	678	0.67	153		AGA	0.61	121	3.05	325
Cys	UGU	0.35	64	1.50	179		AGG	0.86	172	0.89	95
Cys	UGC *	1.65	302	0.50	60	Trp	UGG	1.00	219	1.00	157
Tyr	UAU	0.29	100	1.40	322	TER	UGA	0.94	17	0.61	11
Tyr	UAC *	1.71	595	0.60	138		UAA	1.50	27	1.83	33
Met	AUG	1.00	507	1.00	359		UAG	0.56	10	0.56	10

Note: N is codon frequency, RSCU is relative synonymous codon usage. The codon usage of eleven genes (5% of the total number of genes) from the extremes of the principal were pooled. The codon usage of both pools was compared using a two-way Chi squared contingency test, to identify optimal codons. For the purposes of this test dataset with the lower ENc were putatively assigned as highly expressed. The codon usage and RSCU of both datasets is shown. Those codons that occur significantly more often (p < 0.01) in the highly biased dataset relative to the lower biased dataset are putatively considered optimal, and are indicated with a (*).

ISSN: 1471-2164