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Table 1 Genome and cytosine coverage in biological replicates of the control line and the LR2 epiline (fourth selfing) using plant-RRBS, and comparison to WGBS

From: Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions

Line with biological replicatesa

Restriction endonuclease combination

Genome coverage (%)b

Cytosine coverage (%)c

Efficiencyd

Number of analyzed cytosine sites

CG

CHG

CHH

(millions)e

Plant-RRBS

       

 Control-1

MspI-DpnII

39.6

42.8

1.1

15.3

13.1

48.1

 Control-2

MspI-DpnII

42.3

44.9

1.1

15.6

13.6

51.1

 Control-3

MspI-DpnII

30.8

32.8

1.1

11.6

10.0

37.0

 Control-4

MspI-DpnII

35.0

37.1

1.1

13.0

11.3

42.0

 Control-5

MspI-DpnII

21.3

22.9

1.1

8.3

7.1

25.5

 LR2–1

MspI-DpnII

46.0

48.7

1.1

16.7

14.7

55.6

 LR2–2

MspI-DpnII

45.7

48.5

1.1

16.7

14.7

55.3

 LR2–3

MspI-DpnII

27.6

28.8

1.0

9.4

8.6

33.5

 LR2–4

MspI-DpnII

45.1

48.4

1.1

17.0

14.7

54.7

 LR2–5

MspI-DpnII

41.2

43.9

1.1

15.1

13.2

50.0

 Control-6

MspI-ApeKI

29.9

34.1

1.1

13.1

11.1

36.6

 Control-7

MspI-ApeKI

26.2

30.0

1.1

11.7

10.0

31.9

 Control-8

MspI-ApeKI

25.3

28.7

1.1

11.0

9.5

30.7

 Control-9

MspI-ApeKI

21.2

24.5

1.2

9.6

8.3

25.9

 Control-10

MspI-ApeKI

27.8

32.4

1.2

13.0

10.8

34.1

 LR2–6

MspI-ApeKI

23.0

26.0

1.1

9.8

8.8

27.9

 LR2–7

MspI-ApeKI

21.8

24.9

1.1

9.5

8.5

26.5

 LR2–8

MspI-ApeKI

22.3

25.4

1.1

9.6

8.7

27.1

 LR2–9

MspI-ApeKI

23.2

26.6

1.1

10.2

9.0

28.3

 LR2–10

MspI-ApeKI

24.0

27.1

1.1

10.0

9.0

29.3

WGBS

       

 Control −11

-

84.3

52.4

0.6

14.4

15.4

63.9

 LR2–11

-

83.7

52.6

0.6

14.5

15.6

63.9

  1. Leaf material from five individual plants per line and per restriction endonuclease combination was used
  2. The bisulfite conversion efficiency rate per biological replicate was higher than approximately 99%
  3. a Name scheme: line–individual plant number (1–11) from selfing generation 4
  4. b Genome coverage: coverage as number of genome nucleotide positions covered by at least one read *100% / 427,026,737 nucleotides in the reference genome [38]
  5. c Cytosine coverage: proportion of analyzed (sufficiently covered) cytosine positions in the genome = sum of analyzed cytosines in CG, CHG and CHH context covered by at least ten informative nucleotides (means C or T) * 100% /178,637,468 cytosines in the reference genome for both strands [38]
  6. d Ratio of cytosine coverage per genome coverage
  7. e Millions of positions of a certain cytosine context (CG, CHG and CHH) in the reference genome for both strands that are sufficiently covered by at least ten informative nucleotides (means C or T) and therefore methylation level of cytosine sites was analyzed [38]