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Table 2 Comparison of repeats in oyster genomes

From: Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

Repeat Class

Pacific oyster (Crassostrea gigas)

Sydney rock oyster (Saccostrea glomerata)

Hong Kong oyster (Magallana hongkongensis) (This study)

Hong Kong oyster (Magallana hongkongensis) ([61]: CNGB Accession: CNP0000529)

No. elements

Total Length (Mb)

Percentage sequence (%)

No. elements

Total Length (Mb)

Percentage sequence (%)

No. elements

Total Length (Mb)

Percentage sequence (%)

No. elements

Total Length (Mb)

Percentage sequence (%)

Retroelement

37,163

28,544,850

5.06

120,895

58.86

7.46

52,102

40.18

5.3

42,786

34.49

5.65

SINE

1223

236,226

0.04

3279

1.11

0.14

1264

0.30

0.04

1105

0.24

0.04

LINE

21,075

13,539,249

2.40

102,086

44.00

5.58

28,141

18.21

2.40

24,710

16.73

2.74

LTR element

14,865

14,769,375

2.62

15,530

13.75

1.74

22,697

21.67

2.86

16,971

17.52

2.87

DNA transposon

267,568

108,351,108

19.18

309,542

118.32

15.01

376,197

151.49

19.99

262,645

129.15

21.17

Rolling-circle

96,923

65,056,555

11.52

158,233

69.40

8.81

138,281

95.49

12.60

105,724

89.47

14.67

Unclassified

24,313

13,835,725

2.45

133,418

61.23

8.81

40,091

23.05

3.04

22,365

14.97

2.45

Other

4829

1,288,331

0.22

10,362

3.48

0.44

5561

1.43

0.19

14,840

3.35

0.55

Small RNA

0

0

0.00

0

0.00

0.00

0

0.00

0.00

0

0.00

0.00

Satellites

991

252,370

0.04

686

0.16

0.02

614

0.19

0.03

634

0.15

0.02

Simple repeats

3795

1,029,211

0.18

9666

3.32

0.42

4902

1.24

0.16

14,150

3.20

0.53

Low complexity

43

6750

0.00

10

0

0.00

45

0.00

0.00

56

0.00

0.00

Total repeats

430,796

217,076,569

38.43

732,450

311.29

40.53

612,232

311.64

41.12

448,360

271.43

44.49