Introduction
Materials and methods
Study site
Sample collection
Genomic DNA extraction and amplification
Data analysis
Results
Polymorphism of Pvs25
Haplotypes | Number (%) | EGF-1 | EGF-2 | EGF-3 | |||
---|---|---|---|---|---|---|---|
27 | 87 | 97 | 100 | 130 | 131 | ||
Sal-I | – | D | Q | E | T | I | Q |
pv01* | Q | T | |||||
H1 | 82 (25.3) | T | |||||
H2 | 1 (0.3) | N | T | ||||
H3 | 46 (14.2) | Q | T | ||||
H4 | 2 (0.6) | S | T | ||||
H5 | 176 (54.3) | T | K | ||||
H6 | 10 (3.1) | Q | T | K | |||
H7 | 6 (1.9) | L | Q | T | K | ||
H8 | 1 (0.3) | N | Q | T | K | ||
Total | 324 (100) | – | – | – | – | – | – |
Polymorphism of Pvs28
Haplotypes | Number (%) | EGF-1 | EGF-2 | EGF-3 | GSGGE/D repeats | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
52 | 53 | 65 | 81 | 95 | 98 | 105 | 116 | 125 | 131 | 140 | |||
Sal-I | – | M | A | T | A | G | L | E | L | D | S | T | 6 |
WT | 8 (2.9) | 6–7 | |||||||||||
H1 | 5 (1.8) | L | 5–7 | ||||||||||
H2 | 2 (0.7) | V | 6–8 | ||||||||||
H3 | 3 (1.1) | N | 6 | ||||||||||
H4 | 7 (2.6) | K | 5–6 | ||||||||||
H5 | 15 (5.5) | V | 6 | ||||||||||
H6 | 1 (0.3) | N | 6 | ||||||||||
H7 | 13 (4.8) | S | 5–7 | ||||||||||
H8 | 1 (0.3) | L | V | 6 | |||||||||
H9 | 79 (29.0) | L | S | 5–7 | |||||||||
H10 | 10 (3.7) | V | V | 6 | |||||||||
H11 | 16 (5.9) | V | S | 6–7 | |||||||||
H12 | 1 (0.3) | N | K | 6 | |||||||||
H13 | 13 (4.8) | I | V | 6 | |||||||||
H14 | 51 (18.8) | K | V | 5–7 | |||||||||
H15 | 1 (0.3) | L | I | V | 6 | ||||||||
H16 | 1 (0.3) | L | V | S | 6 | ||||||||
H17 | 11 (4.0) | L | K | S | 4–6 | ||||||||
H18 | 6 (2.2) | L | S | S | 6 | ||||||||
H19 | 1 (0.3) | L | N | S | 6 | ||||||||
H20 | 7 (2.6) | V | T | V | 6–7 | ||||||||
H21 | 2 (0.7) | I | V | S | 6 | ||||||||
H22 | 18 (6.6) | L | K | V | S | 5–6 | |||||||
Total | 272 (100) | – | – | – | – | – | – | – | – | – | – | – | – |
Gene polymorphisms of pvs25 and pvs28
Sites | No. of isolates | S | H | Hd ± SD | K | π ± SD | Tajima’s D (P value) | dN |
---|---|---|---|---|---|---|---|---|
Dandong | 7 | 1 | 2 | 0.571 ± 0.119 | 0.571 | 0.00097 ± 0.00020 | 1.34164 (P > 0.10) | 0.57143 |
Suining | 10 | 1 | 2 | 0.467 ± 0.132 | 0.467 | 0.00079 ± 0.00022 | 0.81980 (P > 0.10) | 0.46667 |
Hainan | 24 | 2 | 3 | 0.507 ± 0.093 | 0.623 | 0.00106 ± 0.00023 | 0.35972 (P > 0.10) | 0.62319 |
Nyingchi | 24 | 3 | 4 | 0.699 ± 0.048 | 1.054 | 0.00179 ± 0.00015 | 0.78580 (P > 0.10) | 1.05434 |
Tengchong | 205 | 4 | 7 | 0.489 ± 0.039 | 0.724 | 0.00123 ± 0.00011 | 0.12056 (P > 0.10) | 0.72434 |
Yingjiang | 54 | 3 | 4 | 0.473 ± 0.071 | 0.521 | 0.00089 ± 0.00016 | − 0.42264 (P > 0.10) | 0.52131 |
Total | 324 | 5 | 8 | 0.621 ± 0.021 | 0.859 | 0.00146 ± 0.00007 | 0.16474 (P > 0.10) | 0.00186 |
Sites | No. of isolates | S | H | Hd ± SD | K | π ± SD | Tajima’s D (P value) | dN | dS |
---|---|---|---|---|---|---|---|---|---|
Nyingchi | 5 | 4 | 3 | 0.800 ± 0.164 | 2.400 | 0.00417 ± 0.00101 | 1.64070 (P > 0.10) | 2.40000 | 0.00000 |
Tengchong | 206 | 10 | 21 | 0.841 ± 0.008 | 1.671 | 0.00966 ± 0.00031 | 0.86672 (P > 0.10) | 2.97016 | 0.91120 |
Yingjiang | 45 | 7 | 5 | 0.470 ± 0.081 | 1.513 | 0.00263 ± 0.00051 | − 0.48164 (P > 0.10) | 1.46869 | 0.04444 |
Total | 256 | 11 | 22 | 0.485 ± 0.087 | 1.679 | 0.00305 ± 0.00061 | − 0.52637 (P > 0.10) | 2.73584 | 0.72924 |