Background
Methods
Parasite collection and DNA extraction
Polymerase chain reaction (PCR) amplification and sequencing
Quantitative real-time PCR (qPCR)
Statistical analyses
Results
Polymorphism of the surf 4.1 gene and its product in the western Kenyan P. falciparum population
Selection on the surf 4.1 gene in the western Kenyan P. falciparum population
Region (position) | Number of sites (base) | Indels | k |
Nd
|
N
|
Sd
|
S
| π |
d
N
|
d
S
|
d
N/d
S
|
p
|
---|---|---|---|---|---|---|---|---|---|---|---|---|
(SE) | (SE) | (SE) | (SE) | (SE) | (SE) | (SE) | (SE) | (d
N > d
S) | ||||
Extracellular | 2286 | 9 | 104.64 | 87.22 | 1791.60 | 17.43 | 488.40 | 0.048 | 0.051 | 0.037 | 1.38 | 0.004 |
(4–2289) | (5.50) | (6.03) | (8.40) | (2.25) | (8.40) | (0.003) | (0.003) | (0.005) | ||||
Nter | 147 | 0 | 0.24 | 0.24 | 118.30 | 0.00 | 28.70 | 0.002 | 0.002 | 0.000 | ∞ | ns* |
(4–150) | (0.19) | (0.17) | (2.01) | (0.00) | (2.10) | (0.001) | (0.002) | (0.000) | ||||
CRD | 435 | 0 | 2.99 | 1.52 | 351.61 | 1.47 | 80.39 | 0.007 | 0.004 | 0.019 | 0.21 | ns* |
(151–585) | (1.11) | (0.70) | (3.68) | (0.79) | (3.64) | (0.003) | (0.002) | (0.011) | ||||
Var1 | 918 | 3 | 20.23 | 17.86 | 721.42 | 2.37 | 196.58 | 0.023 | 0.026 | 0.012 | 2.17 | ns* |
(586–1506) | (2.15) | (2.16) | (5.52) | (0.64) | (5.57) | (0.002) | (0.003) | (0.003) | ||||
Var2 | 783 | 6 | 81.19 | 67.60 | 600.28 | 13.59 | 182.72 | 0.115 | 0.126 | 0.080 | 1.58 | 0.0003 |
(1507–2289) | (4.73) | (4.62) | (4.74) | (1.97) | (4.57) | (0.007) | (0.009) | (0.011) |
Region | Nucleotide position | Number of sites (base) | η | S | Two variants | More than two variants | π | θ | Tajima’s D
| Fu and Li’s | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Singleton | Not singleton |
D*
|
F*
| |||||||||
Extracellular | 4–2289 | 2286 | 439 | 410 | 115 | 266 | 29 | 0.046 | 0.048 | −0.19 | −0.29 | −0.30 |
Nter | 4–150 | 147 | 2 | 2 | 1 | 1 | 0 | 0.002 | 0.004 | −1.20 | −0.66 | −0.93 |
CRD | 151–585 | 435 | 11 | 10 | 3 | 6 | 1 | 0.007 | 0.006 | 0.39 | −0.61 | −0.36 |
Var1 | 586–1506 | 918 | 109 | 107 | 44 | 61 | 2 | 0.022 | 0.031 | −1.17 | −0.93 | −1.18 |
Var2 | 1507–2289 | 783 | 317 | 291 | 67 | 198 | 26 | 0.104 | 0.100 | 0.17 | −0.02 | 0.05 |
Frequency of the frameshift mutation that would result no SURFIN4.1 expression on the iRBC surface varies between western Kenyan and Thai parasite populations
Frameshift (nucleotide positionsa) | Number (%) of parasite line/cloneb
| ||||||
---|---|---|---|---|---|---|---|
2498–2503 | 3894–3903 | 4529–4536 | Western Kenya | Thai | |||
Pattern 1 | Yes | Yes | No | 8 | (35) | 17 | (47) |
Pattern 2 | Yes | No | No | 14 | (61) | 5 | (14) |
Pattern 3 | No | Yes | No | 0 | (0) | 1 | (3) |
Pattern 4 | No | No | No | 1 | (4) | 13 | (36) |
Total | 23 | (100) | 36 | (100) | |||
3D7c
| Yes | Yes | No | ||||
FCR3c
| No | No | Yes | ||||
ITd
| No | No | No | ||||
PrCDCd
| No | No | No |