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Table 1 Theoretical background used for the explanation of de novo methylation (DNM), demethylation (DM), preservation of non-methylated sites (NMSP) and preservation of methylated sites (MSP) events based on known properties of HpaII and MspI isoschizomers

From: A relative quantitative Methylation-Sensitive Amplified Polymorphism (MSAP) method for the analysis of abiotic stress

 

Non-stressed (NS) lines

Stressed (S) lines

Background (restriction site)

Events and their quantification

Events affecting CG/CHG sequence methylation status change

Digest/MSAP profile

NS (5′-3′/3′-5′)

S (5′-3′/3′-5′)

NS - > S

4-digit code/events

EcoRI/HpaII

EcoRI/MspI

EcoRI/HpaII

EcoRI/MspI

0000

0

0

0

0

mCmCGG

GGCmCm

mCmCGG

GGCmCm

MM/MM-> MM/MM

MSPex × 2; MSPin × 2

 

MM/MM- > M−/−M

MSPex × 2; DMin × 2

DM-CG × 2

mCCGG

GGCCm

mCCGG

GGCCm

M−/−M- > M−/−M

MSPex × 2; NMSPin × 2

 

M−/−M- > MM/MM

MSPex × 2; DNMin × 2

DNM-CG × 2

0001

0

0

0

1

mCmCGG

GGCmCm

CmCGG

GGCC

MM/MM- > −M/−−

DMex × 2; DMin; MSPin

DM-CHG × 2; DM-CG

MM/MM- > −M/M-

DMex × 2; MSPin × 2

DM-CHG × 2;

mCCGG

GGCCm

CmCGG

GGCmC

M−/−M- > −M/−−

DMex × 2; DNMin; NMSPin

DM-CHG × 2; DNM-CG

M−/−M- > −M/M-

DMex × 2; DNMin × 2

DM-CHG × 2; DNM-CG × 2

0010

0

0

1

0

mCmCGG

GGCmCm

mCCGG

GGCC

MM/MM - > M−/−−

DMex; DMin × 2; MSPex

DM-CHG; DM-CG × 2

mCCGG

GGCCm

M−/−M- > M−/−−

DMex; NMSPin × 2; MSPex

DM-CHG

0011

0

0

1

1

mCmCGG

GGCmCm

CCGG

GGCC

MM/MM- > −−/−−

DMex × 2; DMin × 2

DM-CHG × 2; DM-CG × 2

mCCGG

GGCCm

M−/−M- > −−/−−

DMex × 2; NMSPin × 2

DM-CHG × 2

0100

0

1

0

0

CmCGG

GGCC

mCmCGG

GGCmCm

-M/−− − > MM/MM

DNMex × 2; DNMin; MSPin

DNM-CHG × 2; DNM-CG

-M/−− − > M−/−M

DNMex × 2; DMin; NMSPin

DNM-CHG × 2; DM-CG

CmCGG

GGCmC

mCCGG

GGCCm

-M/M- - > MM/MM

DNMex × 2; MSPin × 2

DNM-CHG × 2

-M/M- - > M−/−M

DNMex × 2; DMin × 2

DNM-CHG × 2; DM-CG × 2

0101

0

1

0

1

CmCGG

GGCC

CmCGG

GGCC

-M/−− − > −M/−−

NMSPex × 2; MSPin; NMSPin

 

-M/−− − > −M/M-

NMSPex × 2; MSPin; DNMin

DNM-CG

CmCGG

GGCmC

CmCGG

GGCmC

-M/M- - > −M/−−

NMSPex × 2; MSPin; DMin

DM-CG

-M/M- - > −M/M-

NMSPex × 2; MSPin × 2

 

0110

0

1

1

0

CmCGG

GGCC

mCCGG

GGCC

-M/−− − > M−/−−

DNMex; DMin; NMSPex; NMSPin

DNM-CHG; DM-CG

CmCGG

GGCmC

-M/M- - > M−/−−

DNMex; DMin × 2; NMSPex

DNM-CHG; DM-CG × 2

0111

0

1

1

1

CmCGG

GGCC

CCGG

GGCC

-M/−− − > −−/−−

NMPex × 2; DMin; NMSPin

DM-CG

CmCGG

GGCmC

-M/M- - > −−/−−

NMSPex × 2; DMin × 2

DM-CG × 2

1000

1

0

0

0

mCCGG

GGCC

mCmCGG

GGCmCm

M−/−− − > MM/MM

MSPex; DNMex; DNMin × 2

DNM-CHG; DNM-CG × 2

mCCGG

GGCCm

M−/−− − > M−/−M

MSPex; DNMex; NMSP × 2

DNM-CHG

1001

1

0

0

1

mCCGG

GGCC

CmCGG

GGCC

M−/−− − > −M/−−

DMex; DNMin; NMSPex; NMSPin

DM-CHG; DNM-CG

CmCGG

GGCmC

M−/−− − > −M/M-

DMex; DNMin; NMSPex; DNMin

DM-CHG; DNM-CG × 2

1010

1

0

1

0

mCCGG

GGCC

mCCGG

GGCC

M−/−− − > M−/−−

MSPex; NMSPin × 2; NMSPex

 

1011

1

0

1

1

mCCGG

GGCC

CCGG

GGCC

M−/−− − > −−/−−

DMex; NMSPin × 2; NMSPex

DM-CHG

1100

1

1

0

0

CCGG

GGCC

mCmCGG

GGCmCm

−−/−− − > MM/MM

DNMex × 2; DNMin × 2

DNM-CHG × 2; DNM-CG × 2

mCCGG

GGCCm

−−/−− − > M−/−M

DNMex × 2; NMSPin × 2

DNM-CHG × 2

1101

1

1

0

1

CCGG

GGCC

CmCGG

GGCC

−−/−− − > −M/−−

NMSPex × 2; DNMin; NMSPin

DNM-CG

CmCGG

GGCmC

−−/−− − > −M/M-

NMSPex × 2; DNMin × 2

DNM-CG × 2

1110

1

1

1

0

CCGG

GGCC

mCCGG

GGCC

−−/−− − > M−/−−

NMSPin × 2; NMSPex; DNMex;

DNM-CHG

1111

1

1

1

1

CCGG

GGCC

CCGG

GGCC

−−/−− − > −−/−−

NMSPex × 2; NMSPin × 2

 
  1. NS states for non-stressed (control) whereas S for Al stressed data. Putative MSAP banding patterns, as well as their respective 4-bit binary codes, are given in the left part of the table. Restriction sites of the NS and S, as well as genetic representation of the sites, are depicted in the middle followed by two columns illustrating events explaining the given code and those related to CHG and CG methylation types. ‘M’ and ‘m’ state for the methylated cytosine whereas ‘-’ for the non-methylated one; ‘in’ - internal, ‘ex’ - external cytosine. The numbers abbreviations in the last two columns reflect the number of events of the given type