A total of 72 SNPs, including 30 transitions and 42 transversions, were identified between the 93-11 and PA64S chloroplast genomes. The frequencies of major and minor genotypes at each polymorphic site were categorized (Table I  

Table I.
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Minor genotype frequency of each SNP type among three chloroplast genomes

SNP type in 93-11/ PA64S & Nip-G
MF in 93-11
MF in PA64S
MF in Nip-G
%
G/A4.3 (1,583)2.4 (1,384)2.5 (2,961)
C/T5.1 (1,014)3.9 (934)2.7 (1,875)
A/G4.5 (2,207)1.5 (882)2.9 (1,978)
T/C4.5 (1,591)1.8 (529)2.6 (1,375)
A/T3.9 (2,224)2.4 (660)0.7 (848)
T/A2.3 (911)2.4 (1,667)0.9 (2,109)
A/C6.6 (1,219)3.0 (568)2.9 (1,415)
C/A4.2 (1,154)1.4 (709)1.9 (1,442)
G/C000
C/G9.8 (384)01.2 (482)
G/T6.0 (990)3.7 (859)2.5 (1,760)
T/G
5.2 (1,485)
0.5 (610)
2.2 (1,051)
SNP type in 93-11/ PA64S & Nip-G
MF in 93-11
MF in PA64S
MF in Nip-G
%
G/A4.3 (1,583)2.4 (1,384)2.5 (2,961)
C/T5.1 (1,014)3.9 (934)2.7 (1,875)
A/G4.5 (2,207)1.5 (882)2.9 (1,978)
T/C4.5 (1,591)1.8 (529)2.6 (1,375)
A/T3.9 (2,224)2.4 (660)0.7 (848)
T/A2.3 (911)2.4 (1,667)0.9 (2,109)
A/C6.6 (1,219)3.0 (568)2.9 (1,415)
C/A4.2 (1,154)1.4 (709)1.9 (1,442)
G/C000
C/G9.8 (384)01.2 (482)
G/T6.0 (990)3.7 (859)2.5 (1,760)
T/G
5.2 (1,485)
0.5 (610)
2.2 (1,051)

The intersubspecific SNP types and their respective minor genotype frequencies among three varieties, 93-11, PA64S, and Nipponbare-G (Nip-G), are listed. The oblique line in the first column (/) separates the major genotype in 93-11 and PA64S /Nipponbare-G. Minor genotype frequencies (MF) were indicated as percentage of the minor genotype in each SNP type. The statistics was based on the total sites of each SNP type in a given variety. The number in the parenthesis shows the total number of the surveyed sequence traces covering the SNP loci of a given type. MF in 93-11 is about twice as high as that of PA64S or Nipponbare-G chloroplast genome.

Table I.
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Minor genotype frequency of each SNP type among three chloroplast genomes

SNP type in 93-11/ PA64S & Nip-G
MF in 93-11
MF in PA64S
MF in Nip-G
%
G/A4.3 (1,583)2.4 (1,384)2.5 (2,961)
C/T5.1 (1,014)3.9 (934)2.7 (1,875)
A/G4.5 (2,207)1.5 (882)2.9 (1,978)
T/C4.5 (1,591)1.8 (529)2.6 (1,375)
A/T3.9 (2,224)2.4 (660)0.7 (848)
T/A2.3 (911)2.4 (1,667)0.9 (2,109)
A/C6.6 (1,219)3.0 (568)2.9 (1,415)
C/A4.2 (1,154)1.4 (709)1.9 (1,442)
G/C000
C/G9.8 (384)01.2 (482)
G/T6.0 (990)3.7 (859)2.5 (1,760)
T/G
5.2 (1,485)
0.5 (610)
2.2 (1,051)
SNP type in 93-11/ PA64S & Nip-G
MF in 93-11
MF in PA64S
MF in Nip-G
%
G/A4.3 (1,583)2.4 (1,384)2.5 (2,961)
C/T5.1 (1,014)3.9 (934)2.7 (1,875)
A/G4.5 (2,207)1.5 (882)2.9 (1,978)
T/C4.5 (1,591)1.8 (529)2.6 (1,375)
A/T3.9 (2,224)2.4 (660)0.7 (848)
T/A2.3 (911)2.4 (1,667)0.9 (2,109)
A/C6.6 (1,219)3.0 (568)2.9 (1,415)
C/A4.2 (1,154)1.4 (709)1.9 (1,442)
G/C000
C/G9.8 (384)01.2 (482)
G/T6.0 (990)3.7 (859)2.5 (1,760)
T/G
5.2 (1,485)
0.5 (610)
2.2 (1,051)

The intersubspecific SNP types and their respective minor genotype frequencies among three varieties, 93-11, PA64S, and Nipponbare-G (Nip-G), are listed. The oblique line in the first column (/) separates the major genotype in 93-11 and PA64S /Nipponbare-G. Minor genotype frequencies (MF) were indicated as percentage of the minor genotype in each SNP type. The statistics was based on the total sites of each SNP type in a given variety. The number in the parenthesis shows the total number of the surveyed sequence traces covering the SNP loci of a given type. MF in 93-11 is about twice as high as that of PA64S or Nipponbare-G chloroplast genome.

and Supplemental Table I). In general, SNPs in the chloroplast genome occurred at a rate of 5 in 10,000 bases, which is about 8 times lower than that in its nuclear genome (estimated as 0.43%;Yu et al., 2002). Only 6 SNPs were detected in the inverted repeat (IR) regions (about 40 kb). The SNP rate in these regions was 4 times lower than that in the single copy regions. This result is consistent with a previous report that the synonymous substitution rate of IR regions was roughly 5 times lower than that of the single copy regions when the chloroplast genome sequences were compared among different species (Muse, 2000).

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