Table 2.
The length, identity, nucleotide diversity, neutrality test, and selection pressure on each gene among the overall sugarcane yellow leaf virus (SCYLV) population and each phylogroup.
| ORF (protein) | Group | Length | Identity (%) | π | Tajima's D | dN/dS | ||
|---|---|---|---|---|---|---|---|---|
| aa | nt | aa | nt | |||||
| ORF0 (P0) | all (n = 47) | 255–256 | 765–768 | 88.61 | 91.72 | 0.10735 | 1.48728 (ns) | 0.4018 |
| G1 (n = 22) | 256 | 768 | 97.37 | 98.43 | 0.02458 | − 0.66815 (ns) | 0.3564 | |
| G2 (n = 10) | 256 | 768 | 98.87 | 99.25 | 0.01195 | − 0.04311 (ns) | 0.2966 | |
| G3 (n = 15) | 255–256 | 765–768 | 91.15 | 98.06 | 0.02837 | − 0.33086 (ns) | 0.1467 | |
| ORF1 (P1) | all (n = 47) | 633–650 | 1899–1950 | 91.26 | 92.96 | 0.09007 | 1.17081 (ns) | 0.2774 |
| G1 (n = 22) | 633–650 | 1899–1950 | 97.67 | 98.16 | 0.02388 | − 0.75623 (ns) | 0.2237 | |
| G2 (n = 10) | 650 | 1950 | 99.25 | 98.97 | 0.01589 | 0.63196 (ns) | 0.1048 | |
| G3 (n = 15) | 642–650 | 1926–1950 | 96.48 | 97.67 | 0.02627 | − 0.15383 (ns) | 0.1962 | |
| ORF1/2 (RdRP) | all (n = 47) | 1053–1070 | 3159–3210 | 91.45 | 94.17 | 0.07324 | 0.96401 (ns) | 0.3757 |
| G1 (n = 22) | 1053–1070 | 3159–3210 | 95.02 | 98.35 | 0.02163 | − 0.67551 (ns) | 0.3594 | |
| G2 (n = 10) | 1070 | 3210 | 97.64 | 98.69 | 0.01948 | 0.77878 (ns) | 0.0884 | |
| G3 (n = 15) | 1062–1070 | 3186–3210 | 95.02 | 98.14 | 0.02109 | − 0.29946 (ns) | 0.2980 | |
| ORF3 (CP) | all (n = 47) | 196 | 588 | 98.77 | 98.43 | 0.02242 | − 0.14750 (ns) | 0.2523 |
| G1 (n = 22) | 196 | 588 | 99.72 | 99.71 | 0.0054 | − 1.63275 (ns) | 0.2138 | |
| G2 (n = 10) | 196 | 588 | 99.85 | 99.63 | 0.00606 | − 0.34066 (ns) | 0.1165 | |
| G3 (n = 15) | 196 | 588 | 99.29 | 99.53 | 0.0078 | − 0.95978 (ns) | 0.1567 | |
| ORF4 (MP) | all (n = 47) | 150 | 450 | 98.85 | 99.03 | 0.01463 | − 0.65870 (ns) | 0.2244 |
| G1 (n = 22) | 150 | 450 | 99.61 | 99.74 | 0.00441 | − 1.71042 (ns) | 0.3124 | |
| G2 (n = 10) | 150 | 450 | 99.76 | 99.89 | 0.00209 | − 1.00300 (ns) | 1.3254 | |
| G3 (n = 15) | 150 | 450 | 99.11 | 99.58 | 0.00668 | − 0.85026 (ns) | 0.6926 | |
| ORF3/5 (RTD) | all (n = 47) | 675–676 | 2025–2028 | 94.29 | 94.30 | 0.07779 | 0.76678 (ns) | 0.2235 |
| G1 (n = 22) | 676 | 2028 | 98.05 | 98.17 | 0.02737 | − 0.48646 (ns) | 0.1782 | |
| G2 (n = 10) | 676 | 2028 | 99.20 | 98.95 | 0.0174 | − 0.31252 (ns) | 0.1381 | |
| G3 (n = 15) | 674–675 | 2022–2025 | 97.79 | 98.0 | 0.02983 | − 0.40820 (ns) | 0.1736 | |
aa, amino acid; nt, nucleotide; π, nucleotide diversity; ns, not significant (P > 0.05); nonsynonymous/synonymous ratio (dN/dS) < 1 (negative or purifying selection), dN/dS = 1 (neutral evolution), and dN/dS > 1 (positive selection).