Table 2.
Codon usage of fungal genes, of egfp, and of Bcgfp
| Parameter | Value for indicated organism or genea |
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| U. maydis | N. crassa | M. oryzae | G. zeae | C. lagenarium | C. heterostrophus | E. nidulans | A. fumigatus | S. sclerotiorum | B. cinerea | egfp | Bcgfp | |
| GC content (%) | 56.5 | 56.1 | 56.3 | 51.1 | 58.2 | 51.7 | 53.2 | 54.2 | 47.6 | 46.6 | 61.5 | 44.8 |
| Codon usage (%) | ||||||||||||
| Ala | ||||||||||||
| GCG | 19.8 | 19.9 | 19.3 | 11.5 | 16.4 | 15.7 | 20.7 | 21.6 | 8.3 | 12.0 | 0.0 | 0.0 |
| GCA | 19.5 | 14.5 | 18.1 | 19.6 | 11.3 | 27.3 | 19.4 | 17.7 | 27.4 | 29.6 | 0.0 | 37.5 (3) |
| GCT | 26.7 | 24.3 | 19.9 | 35.6 | 24.7 | 29.8 | 28.0 | 26.4 | 38.2 | 34.2 | 0.0 | 25 (2) |
| GCC | 33.9 | 41.4 | 42.8 | 33.4 | 47.7 | 27.3 | 31.8 | 34.3 | 26.0 | 24.1 | 100 (8) | 37.5 (3) |
| Arg | ||||||||||||
| AGG | 9.4 | 19.1 | 18.5 | 10.2 | 13.2 | 11.0 | 10.5 | 9.8 | 10.8 | 10.2 | 0.0 | 0.0 |
| AGA | 8.2 | 12.8 | 9.3 | 14.3 | 12.1 | 13.2 | 10.3 | 12.2 | 27.9 | 27.1 | 0.0 | 33.3 (2) |
| CGG | 6.4 | 13.8 | 13.9 | 9.0 | 10.0 | 11.4 | 16.6 | 18.2 | 4.4 | 6.8 | 0.0 | 0.0 |
| CGA | 17.9 | 11.4 | 12.8 | 23.1 | 10.4 | 18.4 | 16.3 | 15.6 | 19.8 | 21.1 | 0.0 | 0.0 |
| CGT | 22.9 | 14.4 | 14.6 | 19.0 | 17.5 | 18.6 | 18.5 | 18.2 | 23.2 | 20.2 | 100 (6) | 66.7 (4) |
| CGC | 35.2 | 28.5 | 30.9 | 24.3 | 36.7 | 27.5 | 27.8 | 26.1 | 13.8 | 14.6 | 0.0 | 0.0 |
| Asn | ||||||||||||
| AAT | 26.9 | 27.7 | 23.8 | 30.0 | 18.8 | 38.5 | 37.4 | 38.1 | 43.4 | 51.9 | 0.0 | 38.5 (5) |
| AAC | 73.1 | 72.4 | 76.2 | 70.0 | 81.2 | 61.5 | 62.6 | 61.9 | 56.6 | 48.1 | 100 (13) | 61.5 (8) |
| Asp | ||||||||||||
| GAT | 39.5 | 42.4 | 35.6 | 46.9 | 28.7 | 47.4 | 46.7 | 46.5 | 69.2 | 66.5 | 10.0 (2) | 55.5 (10) |
| GAC | 60.5 | 57.6 | 64.4 | 53.1 | 71.3 | 52.6 | 53.3 | 53.5 | 30.8 | 33.5 | 90 (16) | 44.5 (8) |
| Cys | ||||||||||||
| TGT | 31.1 | 30.3 | 27.0 | 39.4 | 22.5 | 40.3 | 36.8 | 37.7 | 46.7 | 53.1 | 0.0 | 0.0 |
| TGC | 68.9 | 69.7 | 73.0 | 60.6 | 77.5 | 59.7 | 63.2 | 62.3 | 53.3 | 46.9 | 100 (2) | 100 (2) |
| Glu | ||||||||||||
| GAG | 62.1 | 65.5 | 70.2 | 63.0 | 75.4 | 54.8 | 58.9 | 61.8 | 46.9 | 45.3 | 93.8 (15) | 62.5 (10) |
| GAA | 37.9 | 34.5 | 29.8 | 37.0 | 24.6 | 45.2 | 41.1 | 38.2 | 53.1 | 54.7 | 6.2 (1) | 37.5 (6) |
| Gln | ||||||||||||
| CAG | 64.4 | 60.6 | 64.0 | 57.2 | 69.8 | 53.5 | 62.5 | 64.2 | 28.2 | 32.3 | 100 (8) | 12.5 (1) |
| CAA | 35.6 | 39.4 | 36.0 | 42.8 | 30.2 | 46.5 | 37.5 | 35.8 | 71.8 | 67.7 | 0.0 | 87.5 (7) |
| Gly | ||||||||||||
| GGG | 6.2 | 15.2 | 12.7 | 8.3 | 7.3 | 10.9 | 15.2 | 14.9 | 6.0 | 10.1 | 13.6 (3) | 0.0 |
| GGA | 18.0 | 18.9 | 18.0 | 26.3 | 16.7 | 24.3 | 21.1 | 20.7 | 34.3 | 33.4 | 0.0 | 40.9 (9) |
| GGT | 31.6 | 25.5 | 23.4 | 33.5 | 26.6 | 28.7 | 28.0 | 27.0 | 43.7 | 35.7 | 0.0 | 36.4 (8) |
| GGC | 44.1 | 40.4 | 45.8 | 31.9 | 49.3 | 36.2 | 35.7 | 37.4 | 16.1 | 20.9 | 86.4 (19) | 22.7 (5) |
| His | ||||||||||||
| CAT | 37.9 | 39.0 | 31.8 | 47.9 | 24.9 | 45.7 | 45.2 | 46.9 | 50.2 | 58.2 | 0.0 | 44.4 (4) |
| CAC | 62.1 | 61.0 | 68.2 | 52.1 | 75.1 | 54.3 | 54.8 | 53.1 | 49.8 | 41.8 | 100 (9) | 55.6 (5) |
| Ile | ||||||||||||
| ATA | 4.1 | 9.2 | 13.0 | 11.0 | 6.0 | 15.2 | 11.0 | 9.2 | 10.4 | 15.6 | 0.0 | 0.0 |
| ATT | 26.2 | 31.4 | 30.5 | 36.2 | 30.7 | 38.3 | 36.6 | 34.5 | 38.3 | 44.8 | 0.0 | 33.3 (4) |
| ATC | 69.8 | 59.4 | 56.4 | 52.8 | 63.3 | 46.5 | 52.3 | 56.3 | 51.3 | 39.6 | 100 (12) | 66.7 (8) |
| Leu | ||||||||||||
| TTG | 15.5 | 18.0 | 15.3 | 17.7 | 13.8 | 17.7 | 15.2 | 17.2 | 23.5 | 23.2 | 0.0 | 33.3 (7) |
| TTA | 1.6 | 3.3 | 3.7 | 3.0 | 1.4 | 5.8 | 5.7 | 4.5 | 11.4 | 11.4 | 0.0 | 0.0 |
| CTG | 22.7 | 22.0 | 28.9 | 18.2 | 28.3 | 19.5 | 22.5 | 28.1 | 7.7 | 10.7 | 85.7 (18) | 0.0 |
| CTA | 5.2 | 7.2 | 6.4 | 8.8 | 4.3 | 11.2 | 9.1 | 7.2 | 6.5 | 9.5 | 0.0 | 0.0 |
| CTT | 16.0 | 17.2 | 15.2 | 24.9 | 14.7 | 20.8 | 21.3 | 17.0 | 25.4 | 24.4 | 0.0 | 28.6 (6) |
| CTC | 39.0 | 32.3 | 30.3 | 27.3 | 37.5 | 25.0 | 26.2 | 26.0 | 25.5 | 20.7 | 14.3 (3) | 38.1 (8) |
| Lys | ||||||||||||
| AAG | 72.7 | 77.6 | 75.3 | 75.9 | 85.5 | 64.6 | 66.9 | 70.7 | 62.7 | 54.3 | 95.0 (19) | 70 (14) |
| AAA | 27.3 | 22.5 | 24.7 | 24.1 | 14.5 | 35.4 | 33.1 | 29.3 | 37.3 | 45.7 | 5.0 (1) | 30 (6) |
| Phe | ||||||||||||
| TTT | 40.9 | 34.8 | 38.4 | 41.9 | 27.3 | 41.1 | 34.9 | 33.5 | 30.8 | 41.8 | 0.0 | 33.3 (4) |
| TTC | 59.1 | 65.2 | 61.6 | 58.1 | 72.7 | 58.9 | 65.1 | 66.5 | 69.2 | 58.2 | 100 (12) | 66.7 (8) |
| Pro | ||||||||||||
| CCG | 22.7 | 22.6 | 26.1 | 11.0 | 25.0 | 17.3 | 24.3 | 22.3 | 9.1 | 11.4 | 0.0 | 0.0 |
| CCA | 20.3 | 19.2 | 21.1 | 26.3 | 10.9 | 30.9 | 20.9 | 19.5 | 42.3 | 39.1 | 0.0 | 60 (6) |
| CCT | 27.1 | 23.4 | 21.0 | 33.1 | 21.7 | 27.5 | 27.8 | 28.0 | 34.6 | 31.6 | 0.0 | 40 (4) |
| CCC | 29.9 | 34.8 | 31.8 | 29.6 | 42.4 | 24.3 | 26.9 | 30.1 | 14.0 | 17.9 | 100 (10) | 0.0 |
| Ser | ||||||||||||
| AGT | 7.7 | 10.6 | 8.3 | 11.6 | 6.7 | 13.4 | 11.1 | 11.5 | 13.7 | 16.3 | 0.0 | 10 (1) |
| AGC | 21.3 | 21.3 | 24.9 | 19.4 | 23.8 | 19.0 | 19.4 | 19.2 | 12.8 | 12.9 | 70.0 (7) | 10 (1) |
| TCG | 30.6 | 17.7 | 22.7 | 11.7 | 20.3 | 15.8 | 16.9 | 18.2 | 9.9 | 12.0 | 0.0 | 0.0 |
| TCA | 9.9 | 11.3 | 12.5 | 16.5 | 7.3 | 16.8 | 13.5 | 12.1 | 14.7 | 19.4 | 0.0 | 20 (2) |
| TCT | 13.1 | 14.6 | 13.6 | 24.1 | 15.8 | 18.9 | 18.5 | 16.5 | 22.5 | 22.8 | 0.0 | 30 (3) |
| TCC | 17.4 | 24.4 | 18.0 | 16.7 | 26.1 | 16.2 | 20.5 | 22.4 | 26.4 | 16.6 | 30.0 (3) | 30 (3) |
| Thr | ||||||||||||
| ACG | 27.0 | 22.5 | 25.0 | 13.9 | 26.5 | 20.2 | 20.6 | 20.7 | 9.0 | 12.4 | 0.0 | 0.0 |
| ACA | 18.0 | 17.9 | 19.6 | 24.6 | 12.6 | 27.5 | 21.9 | 20.0 | 19.6 | 28.8 | 0.0 | 31.3 (5) |
| ACT | 17.4 | 18.6 | 17.4 | 28.9 | 16.8 | 25.3 | 24.2 | 23.2 | 33.9 | 31.6 | 6.3 (1) | 37.5 (6) |
| ACC | 37.5 | 41.1 | 38.0 | 32.5 | 44.1 | 27.0 | 33.3 | 36.0 | 37.5 | 27.1 | 93.8 (15) | 31.3 (5) |
| Tyr | ||||||||||||
| TAT | 25.9 | 32.7 | 27.6 | 33.6 | 18.6 | 38.4 | 37.6 | 38.2 | 45.7 | 49.3 | 9.9 (1) | 45.5 (5) |
| TAC | 74.1 | 67.3 | 72.4 | 66.4 | 81.4 | 61.6 | 62.4 | 61.8 | 54.3 | 50.7 | 90.1 (10) | 54.5 (6) |
| Val | ||||||||||||
| GTG | 27.6 | 26.0 | 25.8 | 17.3 | 20.4 | 22.3 | 23.4 | 27.1 | 11.2 | 15.6 | 72.2 (13) | 0.0 |
| GTA | 10.2 | 9.1 | 8.9 | 10.5 | 6.1 | 16.0 | 9.5 | 8.7 | 12.0 | 16.2 | 5.6 (1) | 5.6 (1) |
| GTT | 18.1 | 23.2 | 21.8 | 32.4 | 21.0 | 25.9 | 28.4 | 23.3 | 38.4 | 36.7 | 0.0 | 38.9 (7) |
| GTC | 44.1 | 41.7 | 43.5 | 39.7 | 52.5 | 35.8 | 38.7 | 40.8 | 38.3 | 31.5 | 22.2 (4) | 55.6 (10) |
a
Numbers in parentheses indicate codon frequencies in eGFP-encoding genes. Bold numbers indicate codons mainly used in egfp but underrepresented in B. cinerea and S. sclerotiorum compared to other fungi. GC content and codon frequencies of fungal coding sequences were taken from http://www.kazusa.or.jp/codon/.