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TABLE 7. Nucleotide diversity (π) within and between group I and II alleles of the P. falciparum Msp-1 genes

   

Synonymous

Nonsynonymous

Block

Length, codons

Group I

Group II

Group I + group II

Group I

Group II

Group 1 + group II

1

55

0.019

0.021

0.017

0.017

0.010

0.013

2

55

0.106

0.185

0.150

0.449

0.497

0.553

3

202

0.038

0.006

0.042

0.018

0.000

0.023

4

31

0.031

0.000

0.020

0.307

0.000

0.215

5

35

0.000

0.000

0.070

0.000

0.000

0.026

6

227

0.000

0.000

0.282

0.004

0.001

0.300

7

73

0.000

0.000

0.361

0.003

0.000

0.072

8

95

0.000

0.000

0.338

0.000

0.003

0.711

9

107

0.000

0.023

0.409

0.005

0.043

0.126

10

126

0.008

0.000

0.448

0.011

0.000

0.394

11

35

0.000

0.000

0.128

0.000

0.000

0.068

12

79

0.000

0.000

0.000

0.000

0.000

0.000

13

84

0.000

0.042

0.040

0.005

0.007

0.052

14

60

0.000

0.018

0.212

0.002

0.005

0.371

15

89

0.000

0.000

0.216

0.001

0.003

0.089

16

217

0.002

0.032

0.277

0.027

0.027

0.185

17

99

0.002

0.019

0.007

0.010

0.027

0.016

Blocks are as defined by Tanabe et al. (1987). Some block lengths vary between group I and II alleles; thevalue given is the average length of group I and II alleles.

for generating polymorphism (in block 4 there is considerable nonsynonymous polymorphism among group I alleles). Table 7 gives the nucleotide diversity (π) for synonymous and nonsynonymous substitutions for each of the 17 blocks, both within and between groups (see Fig. 3). The most extensive amino acid polymorphism between the two allele groups occurs in block 8, which has been assumed to have no simple repeats, but that we will show below to be composed of tandem and proximal repeats (see Fig. 4).

The dimorphism observed among group I and II alleles within block 2 has been shown to result by processes analogous to those within the Csp central repeat region (Frontali and Pizzi, 1991; Frontali, 1994). The occurrence of repetitive DNA within other blocks has not been described to date. However, we have identified repeats within several of the most polymorphic Msp-1 blocks; in particular, blocks 4, 8, and 14, which heretofore were assumed to be NR. We focus on the repeats detected within block 8, identified by Tanabe et al. (1987) as showing the lowest amino acid similarity between groups (10%; π = 0.711 in Table 7). We have identified three group-specific repeats within this block, two in group I alleles (R1a and R1b), and one in group II alleles (R2a). R2a is a 9-bp repeat



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