Table 2.
Relative synonymous codon usage (RSCU) as determined from concatenated EST sequences of female- and male-specific genes in Zea mays and Triticum aestivum and male-specific and flower-specific sequences in Brassica napus.
| Amino acid | Codon | RSCUa | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Zea mays | Triticum aestivum | Brassica napus | ||||||||||
| Female | Male | Difference (female minus male) b | Codon(s) previously identified as Preferredc | Female | Male | Difference (female minus male) | Codon(s) previously identified as Preferredc | Male | Flower | Difference (male minus flower)d | ||
| Phe | UUU | 0.65 | 0.86 | -0.21 | 0.60 | 0.82 | -0.22 | 0.83 | 0.90 | -0.07 | ||
| UUC | 1.35 | 1.14 | +0.21 | * | 1.40 | 1.18 | +0.22 | * | 1.17 | 1.10 | +0.07 | |
| Leu | UUA | 0.26 | 0.43 | -0.17 | 0.27 | 0.42 | -0.15 | 0.49 | 0.61 | -0.12 | ||
| UUG | 0.87 | 1.07 | -0.20 | * | 0.79 | 0.98 | -0.19 | 1.26 | 1.27 | -0.01 | ||
| CUU | 1.13 | 1.30 | -0.17 | 0.98 | 1.28 | -0.30 | 1.44 | 1.46 | -0.02 | |||
| CUC | 1.61 | 1.23 | +0.38 | * | 1.82 | 1.39 | +0.43 | * | 1.46 | 1.29 | +0.17 | |
| CUA | 0.47 | 0.56 | -0.09 | 0.39 | 0.49 | -0.10 | 0.52 | 0.60 | -0.08 | |||
| CUG | 1.66 | 1.40 | +0.26 | * | 1.77 | 1.44 | +0.33 | 0.82 | 0.76 | +0.06 | ||
| Ile | AUU | 0.92 | 1.11 | -0.19 | 0.84 | 1.07 | -0.23 | 1.06 | 1.05 | +0.01 | ||
| AUC | 1.57 | 1.22 | +0.35 | * | 1.65 | 1.27 | +0.38 | * | 1.39 | 1.26 | +0.13 | |
| AUA | 0.51 | 0.67 | -0.16 | 0.52 | 0.65 | -0.13 | 0.55 | 0.69 | -0.14 | |||
| Val | GUU | 0.96 | 1.25 | -0.29 | 0.89 | 1.19 | -0.30 | 1.43 | 1.46 | -0.03 | ||
| GUC | 1.26 | 1.07 | +0.19 | * | 1.30 | 1.10 | +0.20 | * | 0.95 | 0.89 | +0.06 | |
| GUA | 0.35 | 0.46 | -0.11 | 0.33 | 0.43 | -0.10 | 0.39 | 0.47 | -0.08 | |||
| GUG | 1.44 | 1.22 | +0.22 | * | 1.49 | 1.28 | +0.21 | * | 1.22 | 1.17 | +0.05 | |
| Ser | UCU | 0.98 | 1.20 | -0.22 | 0.88 | 1.18 | -0.30 | 1.52 | 1.54 | -0.02 | ||
| UCC | 1.23 | 1.02 | +0.21 | * | 1.37 | 1.13 | +0.24 | * | 1 | 0.88 | +0.12 | |
| UCA | 0.93 | 1.26 | -0.33 | 0.88 | 1.13 | -0.25 | 1 | 1.11 | -0.11 | |||
| UCG | 0.75 | 0.61 | +0.14 | * | 0.90 | 0.63 | +0.27 | 0.75 | 0.68 | +0.07 | ||
| AGU | 0.61 | 0.82 | -0.21 | 0.57 | 0.77 | -0.2 | 0.77 | 0.84 | -0.07 | |||
| AGC | 1.51 | 1.09 | +0.42 | * | 1.40 | 1.16 | +0.24 | * | 0.96 | 0.95 | +0.01 | |
| Pro | CCU | 1.07 | 1.27 | -0.20 | 0.93 | 1.18 | -0.25 | 1.55 | 1.49 | +0.06 | ||
| CCC | 0.99 | 0.73 | +0.26 | * | 1.07 | 0.84 | +0.23 | * | 0.63 | 0.57 | +0.06 | |
| CCA | 1.04 | 1.35 | -0.31 | 0.92 | 1.21 | -0.29 | 1.08 | 1.19 | -0.11 | |||
| CCG | 0.90 | 0.65 | +0.25 | * | 1.08 | 0.78 | +0.30 | * | 0.73 | 0.76 | -0.03 | |
| Thr | ACU | 0.92 | 1.13 | -0.21 | 0.80 | 1.06 | -0.26 | 1.26 | 1.25 | +0.01 | ||
| ACC | 1.41 | 1.05 | +0.36 | * | 1.51 | 1.17 | +0.34 | * | 1.07 | 0.96 | +0.11 | |
| ACA | 0.91 | 1.21 | -0.30 | 0.83 | 1.15 | -0.32 | 0.93 | 1.09 | -0.16 | |||
| ACG | 0.77 | 0.60 | +0.17 | * | 0.86 | 0.62 | +0.24 | * | 0.74 | 0.71 | +0.03 | |
| Ala | GCU | 1.13 | 1.34 | -0.21 | 0.87 | 1.19 | -0.32 | 1.74 | 1.69 | +0.05 | ||
| GCC | 1.23 | 0.99 | +0.24 | * | 1.44 | 1.12 | +0.32 | * | 0.76 | 0.72 | +0.04 | |
| GCA | 0.88 | 1.07 | -0.19 | 0.74 | 1 | -0.26 | 0.81 | 0.96 | -0.15 | |||
| GCG | 0.77 | 0.60 | +0.17 | * | 0.96 | 0.68 | +0.28 | 0.68 | 0.64 | +0.04 | ||
| Tyr | UAU | 0.65 | 0.88 | -0.23 | 0.63 | 0.82 | -0.19 | 0.78 | 0.83 | -0.05 | ||
| UAC | 1.35 | 1.12 | +0.23 | * | 1.37 | 1.18 | +0.19 | * | 1.22 | 1.17 | +0.05 | |
| His | CAU | 0.85 | 1.08 | -0.23 | 0.77 | 0.99 | -0.22 | 0.99 | 1.07 | -0.08 | ||
| CAC | 1.15 | 0.92 | +0.23 | * | 1.23 | 1.01 | +0.22 | * | 1.01 | 0.93 | +0.08 | |
| Gln | CAA | 0.63 | 0.77 | -0.14 | 0.57 | 0.73 | -0.16 | 0.89 | 0.98 | -0.09 | ||
| CAG | 1.37 | 1.23 | +0.14 | * | 1.43 | 1.27 | +0.16 | * | 1.11 | 1.02 | +0.09 | |
| Asn | AAU | 0.68 | 0.97 | -0.29 | 0.71 | 0.92 | -0.21 | 0.76 | 0.79 | -0.03 | ||
| AAC | 1.32 | 1.03 | +0.29 | * | 1.29 | 1.08 | +0.21 | * | 1.24 | 1.21 | +0.03 | |
| Lys | AAA | 0.50 | 0.70 | -0.20 | 0.49 | 0.64 | -0.15 | 0.72 | 0.88 | -0.16 | ||
| AAG | 1.50 | 1.30 | +0.20 | * | 1.51 | 1.36 | +0.15 | * | 1.28 | 1.12 | +0.16 | |
| Asp | GAU | 0.87 | 1.09 | -0.22 | 0.82 | 1.04 | -0.22 | 1.18 | 1.21 | -0.03 | ||
| GAC | 1.13 | 0.91 | +0.22 | * | 1.18 | 0.96 | +0.22 | * | 0.82 | 0.79 | +0.03 | |
| Glu | GAA | 0.63 | 0.83 | -0.20 | 0.60 | 0.75 | -0.15 | 0.81 | 0.90 | -0.09 | ||
| GAG | 1.37 | 1.17 | +0.20 | * | 1.40 | 1.25 | +0.15 | * | 1.19 | 1.10 | +0.09 | |
| Cys | UGU | 0.58 | 0.77 | -0.19 | 0.51 | 0.73 | -0.22 | 0.98 | 1.01 | -0.03 | ||
| UGC | 1.42 | 1.23 | +0.19 | * | 1.49 | 1.27 | +0.22 | * | 1.02 | 0.99 | +0.03 | |
| Arg | CGU | 0.66 | 0.77 | -0.11 | 0.60 | 0.72 | -0.12 | 1.08 | 0.98 | +0.10 | ||
| CGC | 1.29 | 1.06 | +0.23 | * | 1.57 | 1.21 | +0.36 | * | 0.68 | 0.54 | +0.14 | |
| CGA | 0.41 | 0.55 | -0.14 | 0.34 | 0.46 | -0.12 | 0.54 | 0.58 | -0.04 | |||
| CGG | 0.89 | 0.77 | +0.12 | 1.06 | 0.91 | +0.15 | 0.45 | 0.51 | -0.06 | |||
| AGA | 0.90 | 1.17 | -0.27 | 0.84 | 1.13 | -0.29 | 1.71 | 1.92 | -0.21 | |||
| AGG | 1.84 | 1.68 | +0.16 | * | 1.58 | 1.56 | +0.02 | * | 1.54 | 1.48 | +0.06 | |
| Gly | GGU | 0.86 | 1.03 | -0.17 | 0.74 | 0.97 | -0.23 | 1.27 | 1.22 | +0.05 | ||
| GGC | 1.41 | 1.13 | +0.28 | * | 1.65 | 1.30 | +0.35 | * | 0.66 | 0.64 | +0.02 | |
| GGA | 0.86 | 1.02 | -0.16 | 0.71 | 0.92 | -0.21 | 1.34 | 1.41 | -0.07 | |||
| GGG | 0.88 | 0.83 | -0.05 | 0.90 | 0.82 | +0.08 | 0.72 | 0.73 | -0.01 | |||
Positive differences in RSCU greater than 0.1 in the tissue comparisons (highlighting codon preferences in female tissues) are in bold. Start and termination codons and the single codon for tryptophan have been excluded. Preferred codon data is not available for B napus.
a The total number of codons used to estimate RSCU: Zea mays 116 919 (sperm) and 94 794 (egg), Triticum aestivum 453 286 (anther) and 199 397 (ovary) and Brassica napus 232 516 (microspore) and 400 964 (flower). RSCU indicates the difference from a 1:1 ratio for all available codons within synonymous codon groups.
b +, higher RSCU in female-specific genes; -, higher RSCU in male-specific genes.
c Previously described as preferred codons in Z. mays and T. aestivum as indicated by their frequencies in high-versus low-biased genes by Kawabe and Miyashita (2003) [42]. Asterisk (*) indicates a preferred codon. No values available for B. napus.
d +, higher RSCU in male-specific genes; -, higher RSCU in flower-specific genes.