Repeats

Transposons were annotated by the wuBLAST version of RepeatMasker against the dicots section of mipsREdat (REdat_v8.6_Eudico, 91 Mb, 10,561 entries).

This transposon library is connected to a repeat classification scheme (mips_REcat) and contains a collection of transposons from public sources (1,974 entries) as well as de novo detected LTR-retrotransposons (8,587 entries) from At, Gm, Lj, Solanum esculentum, and Mt using LTR-STRUC (McCarthy and McDonald, 2003).

Transposon Classification

#

# perc

bp (Mb)

perc of TE bp

% of genome

Mobile Element (-)

206,112

100

80.1

100

30.5

Class I: Retroelement (RXX)

177,271

86

69.5

86.7

26.5

LTR Retrotransposon (RLX)

163,826

79.5

63.4

79.1

24.2

Ty1/copia (RLC)

14,510

7

10.8

13.5

4.1

Ty3/gypsy (RLG)

11,849

5.8

14.9

18.6

5.7

unclassified LTR (RLX)

137,467

66.7

37.7

47.1

14.4

non-LTR Retrotransposon (RXX)

13,210

6.4

6

7.5

2.3

LINE (RIX)

11,511

5.6

5.8

7.3

2.2

SINE (RSX)

1,699

0.8

0.2

0.2

0.1

unclassified retrotroelement (RXX)

235

0.1

0

0

0

Class II: DNA Transposon (DXX)

26,487

12.9

8.4

11.2

3.4

DNA Transposon Superfamily (DTX)

16,456

8

6.2

7.8

2.4

CACTA superfamily (DTC)

549

0.3

0.4

0.5

0.1

hAT superfamily (DTA)

1,551

0.8

0.6

0.7

0.2

Mutator superfamily (DTM)

10,753

5.2

3.9

4.9

1.5

Tc1/Mariner superfamily (DTT)

158

0.1

0.1

0.1

0

PIF/Harbinger (DTH)

3,445

1.7

1.3

1.6

0.5

MITE (DXX)

3,012

1.5

0.5

0.6

0.2

Helitron (DHH)

1,548

0.8

0.6

0.8

0.2

Unclassified DNA transposon (DXX)

5,471

2.7

1.6

2

0.6

Unclassified Element (XXX)

2,354

1.1

1.7

2.1

0.6

#

# perc

bp (Mb)

perc of TE bp

% of genome

Mobile Element

84,253

100

19.9

100

18.3

Class I: Retroelement (RXX)

75,777

89.9

18.3

92.3

16.9

LTR Retrotransposon (RLX)

67,602

80.2

14.6

73.4

13.5

Ty1/copia (RLC)

7,892

9.4

2.6

13.2

2.4

Ty3/gypsy (RLG)

4,833

5.7

1.5

7.6

1.4

unclassified LTR (RLX)

54,877

65.1

10.4

52.5

9.6

non-LTR Retrotransposon (RXX)

8,064

9.6

3.7

18.8

3.5

LINE (RIX)

7,213

8.6

3.7

18.4

3.4

SINE (RSX)

851

1

0.1

0.5

0.1

unclassified retrotroelement (RXX)

111

0.1

0

0.1

0

Class II: DNA Transposon (DXX)

8,042

10.1

1.4

7.7

1.4

DNA Transposon Superfamily (DTX)

5,683

6.7

1.1

5.3

1

CACTA superfamily (DTC)

239

0.3

0

0.3

0.1

hAT superfamily (DTA)

676

0.8

0.1

0.7

0.1

Mutator superfamily (DTM)

3,539

4.2

0.7

3.4

0.6

Tc1/Mariner superfamily (DTT)

53

0.1

0

0.1

0

PIF/Harbinger (DTH)

1,176

1.4

0.2

0.9

0.2

MITE (DXX)

952

1.1

0.1

0.7

0.1

Helitron (DHH)

434

0.5

0.2

0.9

0.2

unclassified DNA transposon (DXX)

1,407

1.7

0.2

0.9

0.2

 
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