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Table 3 Number of diagnostic SNPs of the Bayer’s Clade encountered from the in silico mining

From: Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR

Bayer's Clade

atpB-coding region

rbcL-atpB spacer

rps16 spacer

trnL-F region

rps4-trnT spacer

matK-5'trnK spacer

psbM-trnDGUC spacer

trnG intron

Total

D

D'

D

D'

D

D'

D

D'

D

D'

D

D'

D

D'

D

D'

D

D'

A

0

0

0

0

1

0

1

2

0

0

4

2

3

1

3

0

12

5

B

0

0

2

0

0

0

0

0

1

0

0

0

0

0

0

0

3

0

C

0

0

1

0

1

0

0

2

0

0

0

0

0

0

2

0

4

2

D

1

0

3

0

0

0

0

0

0

0

0

0

0

0

0

0

4

0

E/G

0

0

1

0

0

0

0

1

3

0

1

0

0

0

0

0

5

1

F

2

0

1

1

1

0

0

0

1

0

0

0

3

0

0

1

8

2

H

0

0

0

0

0

0

0

0

0

0

0

0

1

0

1

0

2

0

I

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

J

0

0

0

1

0

0

0

0

0

0

0

0

1

0

0

0

1

1

K

2

0

0

0

2

3

0

0

0

0

1

0

0

0

3

0

8

3

L

2

0

2

0

0

0

0

0

0

0

0

0

0

0

0

0

4

0

L1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

L2

3

0

0

0

1

0

0

0

0

0

0

0

0

0

0

0

4

0

L3

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

0

1

0

M

1

0

0

0

0

0

0

0

1

0

0

1

0

0

0

0

2

1

N

0

0

0

0

0

0

0

0

0

0

0

1

1

0

0

0

1

1

O

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

P

0

0

0

0

0

0

0

0

0

0

1

0

0

1

1

0

2

1

Q

0

2

1

1

0

0

0

0

1

0

1

0

0

0

4

0

7

3

R

0

0

0

0

0

0

0

0

0

0

0

0

1

0

0

0

1

0

S

0

0

1

0

0

0

0

0

0

0

0

0

0

0

0

0

1

0

T

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

U

0

0

0

0

1

0

0

0

0

0

1

0

1

0

1

0

4

0

V

0

0

0

0

0

0

0

0

1

0

1

0

2

0

2

1

6

1

W

0

0

0

0

0

0

0

0

0

0

1

0

0

0

0

0

1

0

X

0

0

1

0

0

0

0

0

0

0

0

0

0

0

1

1

2

1

Y

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

Z

0

0

0

0

1

0

0

0

0

0

0

0

1

0

1

0

3

0

AA

0

0

0

0

0

0

0

0

0

0

0

0

1

0

1

0

2

0

BB

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

0

1

0

CC

0

0

0

0

0

0

0

0

0

0

1

3

0

0

0

0

1

3

DD

0

0

0

0

1

1

1

0

0

0

0

0

0

0

0

0

2

1

EE

0

0

0

0

1

0

1

0

0

0

0

0

1

0

0

0

3

0

FF1

0

0

0

0

0

0

1

0

0

0

0

0

0

0

0

0

1

0

FF2

0

0

0

0

0

0

3

0

1

0

1

0

1

0

1

1

7

1

GG1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

0

1

GG2

0

0

0

0

0

0

0

0

2

0

0

0

0

0

0

0

2

0

GG3

0

0

0

0

1

0

0

0

0

0

0

0

0

0

1

0

2

0

GG4

0

0

0

0

0

0

1

0

0

0

0

0

0

0

0

0

1

0

GG5

1

2

0

0

1

0

0

0

0

0

0

0

0

0

0

0

2

2

GG6

0

0

0

0

0

0

0

0

0

0

0

0

2

0

0

0

2

0

HH

1

0

1

0

0

0

0

0

0

0

0

0

2

0

1

0

5

0

II

0

0

0

0

1

1

1

1

0

0

0

0

0

0

0

0

2

2

JJ

0

0

0

0

0

0

1

0

0

0

0

0

0

1

0

0

1

1

KK

0

0

0

0

0

0

0

0

0

0

0

0

0

0

3

0

3

0

LL

0

0

0

0

1

0

0

0

1

0

0

0

1

0

1

0

4

0

MM

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

NN

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

OO

1

0

1

1

0

1

1

0

1

1

1

2

1

0

0

0

6

5

PP

3

0

2

3

2

0

2

0

0

0

1

0

3

0

1

0

14

3

QQ

0

0

2

0

2

1

0

0

0

0

1

0

0

0

0

0

5

1

RR

1

1

1

0

1

1

2

0

0

0

3

0

2

1

2

1

12

4

SS

0

0

0

0

0

0

0

0

0

0

1

0

0

0

0

0

1

0

TT

1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

0

Total

19

5

20

7

19

8

15

6

13

1

20

9

28

4

32

6

166

46

  1. D: marker totally diagnostic of the Clade; D’: markers shared by all accession of the Clade and very few accessions outside the Clade