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Table 3 The comparison of editing between the plastid genomes of S. vulgaris KRA and S. vulgaris KOV and eight angiosperm species. Ambo. – Amborella trichopoda, Spiro. – Spirodela polyrhiza, Aegilops tauschii, Arab.Arabidopsis thaliana, Hevea brasiliensis, Nicot.Nicotiana tabacum, Vigna radiata, Cucumis sativus

From: Variation in plastid genomes in the gynodioecious species Silene vulgaris

 

Genome

position

Edit rate

Genome

position

Edit rate

Ambo.

Spiro.

Aegilops

Arab.

Hevea

Nicot.

Vigna

Cucumis

Gene position

Effect/Notes

KRA

 

KOV

         
 

rps 16 intron

5004

69%

4996

30%

NA

NA

NA

NA

C

NA

NA

NA

 

rps 16 intron

5325

93%

5317

93%

T

C

Edit

T

C

C?

C?

C?

atpAeU914SL

TCA (S) = > TTA (L)

10,003

96%

10,000

96%

Edit

T

T

T

T

T

T

T

 

intergenic

12,532

92%

12,531

93%

NA

NA

NA

NA

NA

NA

NA

NA

 

intergenic

13,336

50%

13,336

72%

NA

NA

NA

NA

NA

NA

NA

NA

rps2eU248SL

TCA (S) = > TTA (L)

14,920

98%

14,920

97%

C

T

T

T

Edit

C

Edit

Edit

rpoC2eU2968HY

CAT (H) = > TAT (Y)

16,608

70%

16,586

85%

C

T

C

T

C

C

C

C

rpoBeU566SL

TCG (S) = > TTG (L)

25,178

52%

25,156

80%

C

T

Edit

T

T

T

Edit

Edit

rpoBeU551SL

TCA (S) = > TTA (L)

25,193

49%

25,171

76%

Edit

T

Edit

Edit

Edit

Edit

Edit

Edit

rpoBeU473SL

TCA (S) = > TTA (L)

25,271

78%

25,249

83%

Edit

Edit

Edit

T

T

Edit

T

T

psbZeU50SL

TCA (S) = > TTA (L)

34,009

0

33,958

6%

C

Edit

C

Edit

C

T

T

C

rps14eU80SL

TCA (S) = > TTA (L)

35,133

98%

35,071

96%

T

T

T

Edit

Edit

Edit

Edit

T

ndhJeU160QX

CAA(Q) = > TAA(Stop)

47,529

13%

47,486

8%

C

C

C

C

C

C

C

C

 

intergenic

47,740

32%

47,697

45%

NA

NA

NA

NA

NA

NA

NA

NA

ndhKeU65SL

TCA (S) = > TTA (L)

48,408

65%

48,365

77%

Edit

T

Edit

T

Edit

T

T

Edit

 

intergenic

49,285

23%

49,243

43%

NA

NA

NA

NA

NA

NA

NA

NA

accDeU1337PL

CCA (P) = > CTA (L)

57,221

95%

57,185

96%

Edit

T

T

C)b

T

T

T

T

psaIeU85HY

CAT (H) = > TAT (Y)

57,642

71%

57,601

82%

Edit

T

T

C

T

C

Edit

Edit

psbLeU2TM

ACG(T) = > ATG (Start)

62,667

96%

62,630

98%

Edit

T

T

T

T

Edit

T

T

petLeU5PL

CCT (P) = > CTT (L)

64,268

86%

64,236

90%

Edit

T

T

Edit

Edit

T

Edit

T

 

intergenic

64,933

83%

64,902

86%

NA

NA

NA

NA

NA

NA

NA

NA

clpPeU559HY

CAT (H) = > TAT (Y)

68,351

97%

68,321

98%

Edit

T

T

Edit

Edit

T

Edit

Edit

petBeU12VV

Silent GTC (V) = > GTT (V)

73,958

32%

73,935

56%

A

C

A

T

C

A

T

G

petBeU418RW

CGG (R) = > TGG (W)

74,364

97%

74,341

93%

Edit

T

T

T

T

T

T

Edit

rpoAeU200SF

TCT (S) = > TTT (F)

77,018

93%

76,983

89%

Edit

Edit

T

Edit

Edit

C

Edit

C

ndhBeU1481PL

CCA (P) = > CTA (L)

91,996

89%

91,961

80%

Edit

Edit

Edit

Edit

Edit

Edit

Edit

Edit

ndhBeU836SL

TCA (S) = > TTA (L)

92,641

90%

92,606

88%

T

Edit

Edit

Edit

C

Edit

Edit

C

ndhBeU830SL

TCA (S) = > TTA (L)

92,647

88%

92,612

84%

Edit

Edit

Edit

Edit

Edit

Edit

Edit

Edit

ndhBeU746SF

TCT (S) = > TTT (F)

93,399

74%

93,364

80%

T

T

T

Edit

Edit

Edit

Edit

C

ndhBeU737PL

CCA (P) = > CTA (L)

93,408

87%

93,373

81%

Edit

Edit

Edit

T

T

Edit

Edit

Edit

ndhBeU586HY

CAT (H) = > TAT (Y)

93,559

60%

93,524

56%

Edit

Edit

Edit

Edit

Edit

Edit

Edit

Edit

ndhBeU542TM

ACG (T) = > ATG (M)

93,603

30%

93,568

45%

Edit

Edit

T

T

Edit

T

Edit

Edit

ndhBeU467PL

CCA (P) = > CTA (L)

93,678

73%

93,643

79%

Edit

Edit

Edit

Edit

Edit

Edit

T

Edit

ndhBeU149SL

TCA (S) = > TTA (L)

93,996

58%

93,961

69%

Edit

Edit

Edit

Edit

Edit

Edit

Edit

Edit

ndhDeU1298SL

TCA (S) = > TTA (L)

113,839

96%

113,810

96%

T

T

T

T

T

C

T

T

ndhDeU887PL

CCC (P) = > CTC (L)

114,250

84%

114,221

87%

T

T

T

Edit

Edit

T

T

Edit

ndhDeU383HY

CAT (H) = > TAT (Y)

114,754

78%

114,722

87%

Edit

T

T

Edit

T

Edit

Edit

Edit

ndhDeU2TM

ACG(T) = > ATG (Start)

115,135

13%

115,103

16%

Edit

Edit

T

Edit

T

Edit

Edit

Edit

ndhGeU50TI

ACA (T) = > ATA (I)

116,860

78%

116,828

86%

C

T

T

Edit

T

C)c

C)d

Edit

ndhAeU1073SF

TCC (S) = > TTC (F)

117,937

83%

117,905

75%

Edit

Edit

Edit

T

T

Edit

Edit

T

ndhAeU961PS

CCT (P) = > TCT (S)

118,049

74%

118,017

83%

Edit

Edit

T

T

Edit

Edit

T

T

ndhAeU566SL

TCA (S) = > TTA (L)

118,444

6%

118,412

21%

Edit

Edit

Edit

T

Edit

T

T

Edit

ndhAeU341SL

TCA (S) = > TTA (L)

119,692

89%

119,660

73%

T

T

T

Edit

C

Edit

Edit

Edit

ndhHeU303II

Silent ATC (I) = > ATT (I)

120,913

29%

120,881

7%

C

C

T

C

C

C

C

C

 

Editing below threshold)a

           

psaIeU82LF

CTT (L) = > TTT (F)

57,639

5%

57,598

4%

C

C

C

C

C

C

C

C

 

intergenic

57,712

9%

57,671

15%

NA

NA

NA

NA

NA

NA

NA

NA

 

intergenic

57,717

7%

57,676

12%

NA

NA

NA

NA

NA

NA

NA

NA

 

intergenic

57,740

4%

57,699

9%

NA

NA

NA

NA

NA

NA

NA

NA

 

intergenic

57,745

5%

57,704

9%

NA

NA

NA

NA

NA

NA

NA

NA

 

intergenic

57,892

4%

57,854

8%

NA

NA

NA

NA

NA

NA

NA

NA

 

intergenic

57,897

2%

57,859

13%

NA

NA

NA

NA

NA

NA

NA

NA

  1. C? information about editing not available
  2. a) Editing rate did not achieve the threshold in most plants (using GSNAP or ChloroSeq),
  3. but editing events observed across all 12 individuals of S. vulgaris KO and KRA
  4. )b GCA triplet in Arabidopsis encoding alanine
  5. )c TCG triplet in Nicotiana, encoding serine
  6. )d TCA triplet in Vigna, encoding serine