Table 1 PepMV strains used in the study and changes in the genomes
From: Strain-dependent mutational effects for Pepino mosaic virus in a natural host
Strain | Isolate | Gene | Location in particular genea | Codon substitution | Amino acid change | Effectb | t-test P |
|---|---|---|---|---|---|---|---|
CH2 | P22 | RdRp | 926 (309) | GTC-GAC | V-D | Beneficial | <0.0001 |
CH2 | P22 | RdRp | 1647 (549) | GAC-CAC | D-H | Neutral | 0.0686 |
CH2 | P22 | RdRp | 4192 (1398) | CAA-AAA | Q-K | Neutral | 0.1904 |
CH2 | P22 | TGB1 | 118 (40) | AGG-TGG | R-W | Neutral | 0.3804 |
CH2 | P22 | TGB1 | 235 (79) | GAC – CAC | D-H | Neutral | 0.0920 |
CH2 | P22 | TGB1 | 272 (91) | CCU-CAU | P-H | Neutral | 0.8217 |
CH2 | P22 | TGB1 | 431 (144) | GCA-GAA | A-E | Lethal | <0.0001 |
CH2 | P22 | TGB1 | 467 (156) | GCA-GAA | A-E | Lethal | <0.0001 |
CH2 | P22 | TGB2 | 130 (44) | AGA – GGA | R-G | Neutral | 0.0203 |
CH2 | P22 | TGB2 | 193 (65) | CAA-AAA | Q-K | Beneficial | <0.0001 |
CH2 | P22 | TGB2 | 310 (104) | CAT-TAT | H-Y | Beneficial | 0.0106 |
CH2 | P22 | TGB2 | 313 (105) | CAT-TAT | H-Y | Beneficial | 0.0004 |
CH2 | P22 | TGB3 | 50 (17) | ATA-AGA | I-R | Neutral | 0.0858 |
CH2 | P22 | TGB3 | 68 (23) | TTA-TCA | L-S | Neutral | 0.2530 |
CH2 | P22 | TGB3 | 175 (59) | TGT - CGT | C-R | Neutral | 0.0237 |
CH2 | P22 | TGB3 | 199 (67) | AAA- GAA | K-E | Neutral | 0.9274 |
CH2 | P22 | TGB3 | 397 (133) | CAG-AAG | Q-K | Beneficial | 0.0006 |
CH2 | P22 | CP | 5 (2) | GAA-GCA | E-A | Deleterious | 0.0026 |
CH2 | P22 | CP | 22 (8) | TCT-GCT | S-A | Neutral | 0.0113 |
CH2 | P22 | CP | 26 (9) | AAC-AGC | N-S | Lethal | <0.0001 |
CH2 | P22 | CP | 127 (43) | GTC-ATC | V-I | Neutral | 0.0420 |
CH2 | P22 | CP | 233 (78) | GCC-GAC | A-D | Lethal | <0.0001 |
CH2 | P22 | CP | 418 (140) | GAC-CAC | D-H | Neutral | 0.0827 |
CH2 | P22 | CP | 463 (155) | GAA-AAA | E-K | Neutral | 0.0183 |
CH2 | P22 | CP | 497 (166) | GAT-GGT | D-G | Beneficial | 0.0029 |
EU | P11 | RdRp | 4192 (1398) | GAG-AAG | E-K | Neutral | 0.0607 |
EU | P11 | TGB2 | 130 (44) | CGT-GGT | R-G | Neutral | 0.0292 |
EU | P11 | TGB3 | 68 (23) | TTA-TCA | L-S | Neutral | 0.1023 |
EU | P11 | CP | 463 (155) | GAA-AAA | E-K | Deleterious | 0.0171 |
EU | P11 | CP | 497 (166) | GAT-GGT | D-G | Neutral | 0.6633 |
EU | P11 | CP | (155/166) | GAA-AAA GAT-GGT | E-K D-G | Beneficial | 0.0030 |