Table 2.

The Difference in Relative Synonymous Codon Usage (▵RSCU) in Highly Versus Lowly Expressed Genes in Neurospora tetrasperma and N. discreta

		N. tetrasperma				N. discreta
		Mean RSCU		▵RSCU	P Value	Mean RSCU		▵RSCU	P Value
Codon	Amino Acid	High Exp	Low Exp			High Exp	Low Exp
GCC	Ala	2.2219	1.7797	+0.4422	**	2.1579	1.7937	+0.3642	**
GCT	Ala	1.0598	0.8731	+0.1867	**	1.1142	0.8552	+0.2589	**
GCA	Ala	0.1956	0.4777	−0.2821	**	0.2250	0.4806	−0.2556	**
GCG	Ala	0.5228	0.8695	−0.3467	**	0.5029	0.8704	−0.3675	**
CGC	Arg	2.8901	2.0840	+0.8061	**	2.7968	2.0820	+0.7148	**
CGT	Arg	1.3149	0.8111	+0.5038	**	1.3491	0.8175	+0.5316	**
AGA	Arg	0.4472	0.6415	−0.1943	**	0.4670	0.6282	−0.1612	**
CGA	Arg	0.2029	0.5418	−0.3390	**	0.2552	0.5433	−0.2881	**
CGG	Arg	0.4235	0.7713	−0.3478	**	0.4070	0.7761	−0.3691	**
AGG	Arg	0.6866	1.1374	−0.4508	**	0.6823	1.1442	−0.4619	**
AAC	Asn	1.7438	1.5007	+0.2431	**	1.7106	1.4822	+0.2284	**
AAT	Asn	0.2504	0.4893	−0.2388	**	0.2837	0.5047	−0.2211	**
GACa	Asp	1.2528	1.1994	+0.0534		1.2209	1.1920	+0.0289
GAT	Asp	0.7297	0.7949	−0.0651	*	0.7563	0.8036	−0.0473
TGC	Cys	1.4708	1.3093	+0.1615	*	1.4880	1.3006	+0.1874	**
TGT	Cys	0.2152	0.4578	−0.2426	**	0.2157	0.4583	−0.2426	**
CAG	Gln	1.6003	1.2852	+0.3151	**	1.5706	1.2830	+0.2876	**
CAA	Gln	0.3881	0.7019	−0.3138	**	0.4180	0.7097	−0.2917	**
GAG	Glu	1.6666	1.3836	+0.2830	**	1.6307	1.3854	+0.2452	**
GAA	Glu	0.3305	0.6150	−0.2845	**	0.3636	0.6117	−0.2480	**
GGT	Gly	1.4238	0.9472	+0.4766	**	1.4477	0.9362	+0.5115	**
GGC	Gly	2.0348	1.8612	+0.1736	**	1.9888	1.8626	+0.1262	**
GGA	Gly	0.3594	0.6709	−0.3115	**	0.3850	0.6634	−0.2784	**
GGG	Gly	0.1820	0.5178	−0.3358	**	0.1785	0.5349	−0.3564	**
CAC	His	1.5375	1.2801	+0.2574	**	1.5154	1.2620	+0.2534	**
CAT	His	0.4014	0.6610	−0.2595	**	0.4219	0.6799	−0.2579	**
ATC	Ile	2.0657	1.8729	+0.1928	**	2.0337	1.8630	+0.1708	**
ATT	Ile	0.8619	0.9150	−0.0531		0.8770	0.9196	−0.0426
ATA	Ile	0.0549	0.2078	−0.1529	**	0.0637	0.2153	−0.1516	**
CTC	Leu	2.9099	2.0755	+0.8344	**	2.8151	2.0548	+0.7603	**
CTT	Leu	1.1064	0.9779	+0.1285	*	1.1957	0.9677	+0.2280	**
TTA	Leu	0.0391	0.1267	−0.0876	**	0.0474	0.1303	−0.0829	**
CTA	Leu	0.1668	0.3896	−0.2228	**	0.1693	0.3999	−0.2306	**
TTG	Leu	0.7561	1.0437	−0.2876	**	0.7508	1.0453	−0.2944	**
CTG	Leu	1.0216	1.3779	−0.3563	**	1.0046	1.4020	−0.3974	**
AAG	Lys	1.8633	1.6207	+0.2427	**	1.8431	1.6130	+0.2302	**
AAA	Lys	0.1338	0.3765	−0.2427	**	0.1569	0.3841	−0.2273	**
TTC	Phe	1.5947	1.3220	+0.2727	**	1.5631	1.3051	+0.2580	**
TTT	Phe	0.3908	0.6737	−0.2829	**	0.4283	0.6905	−0.2622	**
CCC	Pro	2.3242	1.6341	+0.6901	**	2.2490	1.6394	+0.6097	**
CCTa	Pro	0.9147	0.8604	+0.0543		0.9765	0.8508	+0.1256	*
CCA	Pro	0.2523	0.5846	−0.3322	**	0.2679	0.5970	−0.3291	**
CCG	Pro	0.4855	0.9180	−0.4325	**	0.4838	0.9099	−0.4260	**
TCC	Ser	2.1815	1.5580	+0.6235	**	2.0904	1.5761	+0.5143	**
TCT	Ser	0.9250	0.7278	+0.1972	**	0.9664	0.7151	+0.2513	**
AGC	Ser	1.3687	1.4512	−0.0825		1.3735	1.4404	−0.0668
TCG	Ser	1.0090	1.1733	−0.1642	*	0.9901	1.1778	−0.1877	*
AGT	Ser	0.2827	0.5621	−0.2794	**	0.3103	0.5628	−0.2525	**
TCA	Ser	0.2156	0.5276	−0.3120	**	0.2523	0.5278	−0.2756	**
ACC	Thr	2.3811	1.7518	+0.6293	**	2.3053	1.7700	+0.5353	**
ACT	Thr	0.7616	0.6536	+0.1079	*	0.7898	0.6393	+0.1504	**
ACA	Thr	0.3168	0.6412	−0.3243	**	0.3561	0.6244	−0.2683	**
ACG	Thr	0.5405	0.9533	−0.4128	**	0.5431	0.9662	−0.4231	**
TAC	Tyr	1.5653	1.3606	+0.2047	**	1.5366	1.3610	+0.1756	**
TAT	Tyr	0.4027	0.5991	−0.1964	**	0.4179	0.6056	−0.1877	**
GTC	Val	2.2600	1.7407	+0.5193	**	2.2085	1.7176	+0.4909	**
GTT	Val	0.9744	0.8771	+0.0973	*	1.0108	0.8908	+0.1199	**
GTA	Val	0.1475	0.3198	−0.1723	**	0.1673	0.3160	−0.1488	**
GTG	Val	0.6124	1.0538	−0.4414	**	0.6021	1.0696	−0.4676	**

Note.—Pair-wise t-tests were conducted for each codon across all highly expressed versus all lowly expressed genes. P values are shown and have been adjusted for Bonferroni correction (*indicates 0.05< P > 0.00001; **indicates P ≤ 0.00001). Codons in bold have been assigned as optional codons (N = 26). Underlined codons are the primary optimal codon per synonymous codon family that is largest positive ▵RSCU. The standard errors for mean RSCU values are provided in supplementary table 1 (Supplementary Material online).

^aThis codon was designated as a putative optimal codon for this amino acid as RSCU has a greater value in the highly expressed genes, even though comparison is not statistically significant.