Table 2.
Comparison of codon usage frequencies between P. lactiflora sequences with high and low levels of expression.
| AA | Codon | High RSCU(N) | Low RSCU(N) | AA | Codon | High RSCU(N) | Low RSCU(N) |
|---|---|---|---|---|---|---|---|
| Ala | GCA | 1.245(3868) | 1.296(10,358) | Leu | CUA | 0.637(1889) | 0.510(3679) |
| GCC* | 0.888(2761) | 0.610(4878) | CUC | 1.036(3071) | 0.662(4778) | ||
| GCG | 0.471(1464) | 0.305(2439) | CUG | 0.757(2244) | 0.671(4848) | ||
| GCU* | 1.396(4338) | 1.789(14,297) | CUU* | 1.343(3981) | 1.621(11,707) | ||
| Arg | AGA* | 1.582(2545) | 1.939(8781) | UUA | 0.838(2486) | 0.893(6449) | |
| AGG | 1.478(2378) | 1.552(7025) | UUG | 1.389(4119) | 1.643(11,862) | ||
| CGA | 0.831(1338) | 0.641(2901) | Lys | AAA | 0.911(6111) | 0.925(13,915) | |
| CGC | 0.582(936) | 0.481(2177) | AAG | 1.089(7299) | 1.075(16,161) | ||
| CGG | 0.648(1042) | 0.492(2228) | Met | AUG | 1.000(4764) | 1.000(10,846) | |
| CGU | 0.880(1416) | 0.895(4054) | Pro | CCA* | 1.376(3278) | 1.458(8919) | |
| Asn | AAC | 0.882(3785) | 0.627(6592) | CCC* | 0.779(1855) | 0.590(3608) | |
| AAU | 1.118(4801) | 1.373(14,443) | CCG | 0.606(1444) | 0.383(2340) | ||
| Asp | GAC | 0.742(3791) | 0.529(7071) | CCU | 1.239(2953) | 1.569(9600) | |
| GAU | 1.258(6427) | 1.471(19,638) | Ser | AGC* | 0.807(2057) | 0.573(4176) | |
| Cys | UGC* | 0.949(1812) | 0.748(2950) | AGU | 1.031(2628) | 1.074(7834) | |
| UGU* | 1.051(2005) | 1.252(4937) | UCA* | 1.218(3105) | 1.427(10,405) | ||
| Gln | CAA | 1.086(3875) | 1.099(10,044) | UCC* | 0.961(2450) | 0.670(4885) | |
| CAG | 0.914(3259) | 0.901(8230) | UCG* | 0.620(1580) | 0.431(3144) | ||
| Glu | GAA | 1.038(6811) | 1.112(18,684) | UCU | 1.365(3481) | 1.826(13,318) | |
| GAG | 0.962(6315) | 0.888(14,916) | Thr | ACA* | 1.198(2842) | 1.316(7458) | |
| Gly | GGA* | 1.195(3801) | 1.270(10,495) | ACC | 1.047(2485) | 0.745(4221) | |
| GGC | 0.733(2333) | 0.546(4515) | ACG | 0.491(1166) | 0.365(2069) | ||
| GGG | 0.849(2699) | 0.779(6443) | ACU | 1.263(2997) | 1.574(8922) | ||
| GGU | 1.223(3890) | 1.405(11,615) | Trp | UGG | 1.000(2675) | 1.000(5315) | |
| His | CAC | 0.871(2065) | 0.609(3419) | Tyr | UAC* | 0.917(2611) | 0.702(4462) |
| CAU | 1.129(2679) | 1.391(7818) | UAU* | 1.083(3082) | 1.298(8257) | ||
| Ile | AUA* | 0.765(2676) | 0.730(5857) | Val | GUA* | 0.711(2143) | 0.642(5096) |
| AUC* | 0.939(3286) | 0.632(5066) | GUC | 0.801(2412) | 0.569(4523) | ||
| AUU | 1.296(4532) | 1.638(13,133) | GUG* | 1.106(3331) | 0.930(7389) | ||
| Phe | UUC* | 0.939(4017) | 0.665(6011) | GUU | 1.382(4163) | 1.859(14,764) | |
| UUU* | 1.061(4535) | 1.335(12,077) |
Note: AA: amino acid; N: number of codons; RSCU: Relative Synonymous Codon Usage. Codon usage was compared using a chi-square test to identify optimal codons. * Codons that occur significantly more often (p < 0.01).