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Table 3 The variability and discrimination rates of cp genomes, specific and universal barcodes

From: An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin

No

Markers

Aligned length

Polymorphic sites

Parsimony informative sites (PICs)

Mean K2P distance

Discrimination rates by tree-based method

Numbers

%

Numbers

%

 

Complete cp genomes

136,352

4664

3.42%

2175

1.60%

0.00824

100%

 

Specific barcodes

1

trnH(GUG)-psbA

506

65

12.85%

30

5.93%

0.03880

100%

2

trnE(UUC)-trnT(GGU)

1155

118

10.22%

58

5.02%

0.02759

35.29%

3

psbZ-trnG(GCC)

1189

138

11.61%

55

4.63%

0.03028

64.71%

4

trnF(GAA)-ndhJ

977

157

16.07%

108

11.05%

0.04316

70.59%

5

petA-psbL

1580

129

8.16%

69

4.37%

0.03071

64.71%

6

ccsA-ndhD

300

46

15.33%

24

8.00%

0.04475

41.18%

7

ndhF-trnL(UAG)

1923

222

11.54%

93

4.84%

0.03428

47.06%

 

Combination (1–2-3)

2850

321

11.26%

143

5.02%

0.03034

100%

 

Universal barcodes

1

psbK-psbI

424

25

5.90%

17

4.01%

0.02121

41.18%

2

atpF-atpH

625

46

7.36%

15

2.40%

0.01793

47.06%

 

Combination (1–2)

1049

71

6.77%

32

3.05%

0.01929

47.06%

  1. Discrimination rates (%) = [the number of species with bootstrap values more than 50% / the total number of species] × 100%