Table 2.

Comparison of codon usage and relative synonymous codon usage (RSCU) between the high and low expressed genes in begomoviruses

Amino acid	Codon	High	Low	ΔRSCU
Ala	GCA	1.107	0.885	0.222**
	GCC	0.734	1.401	−0.667
	GCG	0.438	0.977	−0.539
	GCT	1.722	0.737	0.985***
Cys	TGC	0.060	1.556	−1.495
	TGT	1.940	0.444	1.495***
Asp	GAC	0.387	1.043	−0.657
	GAT	1.613	0.957	0.657***
Glu	GAA	0.859	1.087	−0.228
	GAG	1.141	0.913	0.228**
Phe	TTC	0.748	1.106	−0.358
	TTT	1.252	0.894	0.358***
Gly	GGA	0.647	1.485	−0.838
	GGC	0.849	0.782	0.067
	GGG	0.696	1.042	−0.347
	GGT	1.809	0.691	1.118***
His	CAC	0.376	1.075	−0.698
	CAT	1.624	0.925	0.698***
Ile	ATA	0.907	0.692	0.215**
	ATC	0.804	1.286	−0.481
	ATT	1.288	1.022	0.266
Lys	AAA	0.451	1.034	−0.583
	AAG	1.549	0.966	0.583***
Leu	CTA	0.186	1.330	−1.145
	CTC	0.594	0.923	−0.329
	CTG	0.755	1.045	−0.291
	CTT	0.829	1.412	−0.583
	TTA	1.113	0.937	0.177*
	TTG	2.524	0.353	2.171***
Asn	AAC	0.866	0.835	0.031
	AAT	1.134	1.165	−0.031
Pro	CCA	1.096	1.383	−0.287
	CCC	1.773	0.697	1.077***
	CCG	0.162	0.886	−0.723
	CCT	0.968	1.035	−0.067
Gln	CAA	0.780	1.277	−0.497
	CAG	1.220	0.723	0.497***
Arg	AGA	1.199	1.192	0.007
	AGG	1.438	1.611	−0.174
	CGA	0.570	1.336	−0.767
	CGC	0.526	0.537	−0.011
	CGG	0.461	0.511	−0.050
	CGT	1.807	0.812	0.994***
Ser	AGC	1.142	0.748	0.394***
	AGT	1.042	0.830	0.212**
	TCA	0.592	1.477	−0.886
	TCC	0.917	0.985	−0.068
	TCG	0.867	1.094	−0.228
	TCT	1.442	0.866	0.575***
Thr	ACA	0.661	1.237	−0.576
	ACC	0.602	0.728	−0.127
	ACG	0.558	1.546	−0.988
	ACT	2.179	0.489	1.690***
Val	GTA	0.448	1.208	−0.760
	GTC	0.998	0.849	0.149*
	GTG	1.034	0.784	0.250**
	GTT	1.520	1.159	0.361
Tyr	TAC	0.540	0.938	−0.399
	TAT	1.460	1.062	0.399

^***Major codons, defined by a higher RSCU value in highly expressed genes, are indicated as (ΔRSCU≥0.30)

^**Major codons, defined by a higher RSCU value in highly expressed genes, are indicated as (ΔRSCU≥0.20)

^*Major codons, defined by a higher RSCU value in highly expressed genes, are indicated as (ΔRSCU≥0.08)