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Rice

Table 1 Identification and classification of repetitive elements in all Oryza species using RepeatMasker, in conjunction with individual species-specific repeat databases

From: Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents

Repeat class

Classs

Repeat type

Percent repetitive content of the genome (percent of total repetitive)

Os

On

Or

Og

Op

Oo

Oa

Ob

Ogr

Om

Oal

Ori

Oc

Class I TEs

 

Ty1-copia

3.34 (5.65)

3 (4.51)

3.09 (5.02)

3.55 (6.65)

4.16 (6.31)

4.27 (5.54)

7.14 (8.33)

3.98 (8.84)

4.28 (5.21)

4.43 (6.17)

5.55 (7.99)

5.14 (6.94)

5.73 (11.65)

 

Ty3-gypsy

11.54 (19.51)

14.28 (21.45)

13.34 (21.65)

9.1 (17.04)

17.56 (26.63)

17.95 (23.28)

32.3 (37.69)

2.84 (6.31)

13.68 (16.64)

18.98 (26.45)

12.78 (18.39)

14.06 (18.98)

3.86 (7.85)

 

CRRs

2.73 (4.61)

3.23 (4.85)

3.27 (5.31)

2.01 (3.77)

2.75 (4.18)

2.03 (2.63)

2.39 (2.79)

0.48 (1.07)

2.51 (3.05)

1.88 (2.62)

1.66 (2.39)

2.44 (3.29)

1.05 (2.13)

 

TRIM

0.04 (0.08)

0.05 (0.08)

0.05 (0.09)

0.05 (0.1)

0.05 (0.08)

0.04 (0.05)

0.02 (0.02)

0.06 (0.14)

0.05 (0.06)

0.04 (0.05)

0.04 (0.06)

0.02 (0.02)

0.04 (0.08)

 

Solo LTRs

0.05 (0.08)

0.04 (0.05)

0.04 (0.06)

0.05 (0.1)

0.04 (0.06)

0.06 (0.08)

0.03 (0.04)

0.18 (0.4)

0.42 (0.51)

0.06 (0.08)

0.04 (0.06)

0.18 (0.24)

0.05 (0.09)

 

Unique(LTR_STRUC)

8.99 (15.19)

10.14 (15.23)

10.27 (16.67)

7.75 (14.51)

8.86 (13.44)

18.94 (24.57)

7.74 (9.03)

4.41 (9.79)

5.75 (6.99)

13.57 (18.91)

8.94 (12.87)

6.63 (8.96)

3.38 (6.87)

 

LINEs

0.32 (0.55)

0.34 (0.51)

0.37 (0.6)

0.36 (0.67)

0.29 (0.45)

0.26 (0.34)

0.43 (0.5)

0.17 (0.38)

0.16 (0.2)

0.26 (0.36)

0.38 (0.54)

0.19 (0.25)

0.21 (0.42)

 

SINEs

0.05 (0.09)

0.05 (0.08)

0.05 (0.09)

0.07 (0.13)

0.04 (0.06)

0.03 (0.04)

0.01 (0.01)

0.06 (0.14)

0.01 (0.01)

0.03 (0.04)

0.03 (0.04)

0.02 (0.02)

0.01 (0.03)

 

Evirus/ERTBV

0.21 (0.36)

0.05 (0.07)

0.09 (0.14)

0.03 (0.06)

0.09 (0.14)

0.19 (0.25)

0.14 (0.17)

0.01 (0.02)

0.16 (0.19)

0.13 (0.18)

0.13 (0.18)

0.2 (0.28)

0.09 (0.17)

 

Unknown

0.56 (0.95)

0.41 (0.62)

0.44 (0.72)

0.45 (0.84)

0.45 (0.69)

0.73 (0.95)

0.51 (0.59)

0.22 (0.49)

0.85 (1.03)

0.52 (0.72)

0.64 (0.92)

0.43 (0.58)

0.88 (1.79)

 

Total

27.85 (47.08)

31.59 (47.45)

31.01 (50.34)

23.42 (43.87)

34.31 (52.02)

44.49 (57.71)

50.73 (59.18)

12.42 (27.59)

27.87 (33.91)

39.88 (55.58)

30.18 (43.44)

29.3 (39.57)

15.29 (31.09)

Class II TEs

(Non MITEs)

CACTA/EnSpm

2.67 (4.51)

2.26 (3.4)

2.36 (3.83)

2 (3.75)

3.48 (5.27)

3.6 (4.67)

2.62 (3.05)

0.92 (2.05)

0.43 (0.53)

3.54 (4.93)

1.76 (2.53)

2.47 (3.33)

0.99 (2.01)

Mutator (MULEs)

2.65 (4.49)

2.73 (4.1)

2.88 (4.68)

2.97 (5.56)

2.74 (4.15)

2.28 (2.96)

1.62 (1.89)

1.82 (4.04)

1.23 (1.49)

2.52 (3.51)

2.08 (3)

2.96 (4)

1.3 (2.65)

hAT

1.19 (2)

1.07 (1.6)

1.09 (1.76)

1.06 (1.99)

1.05 (1.6)

0.89 (1.15)

0.76 (0.89)

0.96 (2.13)

0.91 (1.1)

0.99 (1.38)

0.81 (1.16)

0.81 (1.09)

0.57 (1.15)

Tc1

0.1 (0.17)

0.1 (0.15)

0.1 (0.16)

0.12 (0.22)

0.05 (0.08)

0.05 (0.07)

0.02 (0.03)

0.03 (0.06)

0.03 (0.04)

0.06 (0.09)

0.06 (0.08)

0.04 (0.06)

0.03 (0.07)

Helitron

1.68 (2.84)

1.44 (2.17)

1.58 (2.57)

1.68 (3.15)

1.25 (1.89)

0.9 (1.17)

0.29 (0.34)

0.5 (1.11)

0.4 (0.49)

0.97 (1.35)

0.88 (1.27)

0.39 (0.53)

0.4 (0.81)

Othersa

0.48 (0.82)

0.42 (0.64)

0.45 (0.73)

0.43 (0.8)

0.44 (0.67)

0.38 (0.49)

0.28 (0.33)

0.4 (0.88)

0.4 (0.49)

0.26 (0.36)

0.32 (0.46)

0.35 (0.48)

0.19 (0.39)

Unknown

0.21 (0.35)

0.21 (0.32)

0.23 (0.38)

0.23 (0.44)

0.2 (0.3)

0.15 (0.19)

0.08 (0.1)

0.26 (0.57)

0.08 (0.1)

0.14 (0.2)

0.14 (0.2)

0.14 (0.19)

0.14 (0.29)

MITEs

Tourist

1.4 (2.37)

1.44 (2.16)

1.5 (2.44)

1.63 (3.04)

0.74 (1.12)

0.6 (0.78)

0.26 (0.3)

1.94 (4.32)

0.38 (0.47)

0.6 (0.83)

0.55 (0.79)

0.44 (0.6)

0.43 (0.88)

Stowaway

0.96 (1.63)

0.92 (1.38)

1.02 (1.66)

1.12 (2.09)

0.68 (1.04)

0.56 (0.73)

0.24 (0.28)

0.82 (1.81)

0.32 (0.39)

0.53 (0.74)

0.52 (0.74)

0.35 (0.48)

0.34 (0.69)

Explorer

0.08 (0.14)

0.08 (0.11)

0.08 (0.14)

0.08 (0.16)

0.04 (0.06)

0.03 (0.03)

0.01 (0.01)

1.11 (2.46)

0.02 (0.02)

0.03 (0.04)

0.03 (0.05)

0.07 (0.09)

0.04 (0.07)

Others

0.15 (0.25)

0.13 (0.2)

0.16 (0.26)

0.18 (0.33)

1.48 (2.24)

0.11 (0.14)

0.06 (0.07)

0.14 (0.31)

0.05 (0.06)

0.1 (0.14)

0.09 (0.13)

0.13 (0.17)

0.07 (0.14)

Total

11.58 (19.57)

10.8 (16.22)

11.47 (18.61)

11.5 (21.53)

12.15 (18.42)

9.56 (12.4)

6.26 (7.3)

8.89 (19.74)

4.25 (5.18)

9.75 (13.59)

7.24 (10.41)

8.16 (11.02)

4.51 (9.16)

Others

 

RECON novel

9.58 (16.2)

14.15 (21.25)

8.66 (14.06)

8.43 (15.8)

9.25 (14.02)

13.64 (17.7)

22.07 (25.74)

17.2 (38.2)

45.95 (55.91)

12.65 (17.63)

17.65 (25.4)

28.5 (38.48)

24.43 (49.65)

 

Unclassified

0.17 (0.29)

0.15 (0.23)

0.15 (0.24)

0.18 (0.34)

0.12 (0.18)

0.13 (0.17)

0.08 (0.09)

0.06 (0.14)

0.04 (0.05)

0.14 (0.2)

7.32 (10.54)

0.13 (0.17)

0.06 (0.13)

Repetitiveb

  

45.65

56.82

51.39

43.41

52.37

65.14

75.92

37.74

73.82

60.32

58.95

61.86

43.74

  1. Os O. sativa, On O. nivara, Or O. rufipogon, Og O. glaberrima, Op O. punctata, Oo O. officinalis, Oa O. australiensis, Ob O. brachyantha, Ogr O. granulata, Om O. minuta, Oal O. alta, Ori O. ridleyi, Oc O. coarctata
  2. aOthers include Osmar/Mariner (MLE), Basho, PILE, POLE, and Micropon
  3. bThese values also include the following categories: other centromeric, telomeric, simple repeats, and low-complexity repeats
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