Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data

Table 3

Comparison of codon usage frequencies between highly and lowly expressed sequences of Alexandrium tamarense CCMP 1598 genes. AA: amino acid; N: number of codons High: putatively highly expressed gene (10% of total genes with most negative value along axis 2 in Figure 3); Low: putatively low expressed gene (10% of total genes with most positive value along axis 2 in Figure 3). The codons displayed in bold are significantly more frequent between the highly expressed genes and the lowly expressed genes according to χ ² test. Significant relationships are marked by: ^∗𝑃<.05; ^∗∗𝑃<.01; ^∗∗∗𝑃<.001.

AA	Codon	High		Low		AA	Codon	High		Low
		N	RSCU	N	RSCU			N	RSCU	N	RSCU
Ala	GCU	996	0.67	843	0.61	Ile	AUU***	583	0.78	286	0.51
	GCC	2167	1.45	1957	1.40		AUC	1596	2.14	1113	1.98
	GCA*	1282	0.86	1068	0.77		AUA	61	0.08	287	0.51
	GCG	1528	1.02	1702	1.22	Thr	ACU***	463	0.69	297	0.49
Gly	GGU***	778	0.65	470	0.44		ACC	935	1.40	775	1.29
	GGC	2795	2.34	2435	2.27		ACA**	468	0.70	341	0.57
	GGA	477	0.40	527	0.49		ACG	809	1.21	989	1.65
	GGG	734	0.61	861	0.80	Asn	AAU	328	0.43	329	0.50
Val	GUU***	536	0.56	366	0.41		AAC	1197	1.57	975	1.50
	GUC	1403	1.47	1251	1.42	Lys	AAA	309	0.18	346	0.24
	GUA	156	0.16	165	0.19		AAG	3066	1.82	2542	1.76
	GUG	1732	1.81	1752	1.98	Tyr	UAU	259	0.39	179	0.37
Phe	UUU*	517	0.50	366	0.43		UAC	1076	1.61	785	1.63
	UUC	1545	1.50	1335	1.57	Cys	UGU	195	0.34	138	0.28
Leu	UUA	37	0.05	59	0.07		UGC	941	1.66	842	1.72
	UUG***	885	1.12	696	0.86	Asp	GAU**	815	0.57	682	0.49
	CUU***	632	0.80	471	0.59		GAC	2058	1.43	2103	1.51
	CUC***	1607	2.03	1396	1.74	Glu	GAA	517	0.28	602	0.31
	CUA	58	0.07	135	0.17		GAG	3158	1.72	3322	1.69
	CUG	1530	1.93	2064	2.57	His	CAU	324	0.54	253	0.46
Pro	CCU	502	0.73	509	0.71		CAC	879	1.46	846	1.54
	CCC**	929	1.35	812	1.14	Gln	CAA	273	0.26	340	0.30
	CCA	556	0.80	566	0.79		CAG	1856	1.74	1921	1.70
	CCG	774	1.12	970	1.36	Arg	CGU***	609	1.36	64	0.12
Ser	UCU	339	0.62	305	0.56		CGC***	1335	2.97	470	0.91
	UCC***	1018	1.86	602	1.10		CGA	104	0.23	361	0.70
	UCA**	320	0.58	240	0.44		CGG	425	0.95	642	1.25
	UCG**	642	1.17	544	0.99		AGA	30	0.07	437	0.85
	AGU	224	0.41	261	0.48		AGG	190	0.42	1115	2.17
	AGC	745	1.36	1327	2.43